To highlight described properties click the boxes . Move the molecules anytime with the mouse. If you do try to view this with InternetExplorer, be very patient. It takes a lot of time to sort this page out. Gram-negative bacteria are characterized by the construction of their cell wall: the cytoplasmic or inner membrane engulfes the cytoplasm, a murein layer lends mechanical stability and shape. A second, outer membrane surrounds the cell with few contacts to the inner membrane. In between is the periplasm; in this compartment there are some metabolic activities which would disturb the metabolism within the cell proper - e.g. reactions dealing with toxic substances. The exchange of substances between cytoplasm and periplasm is regulated by highly specific transport systems. The exchange between periplasm and environment occurs via porins, which may be unspecific or specific for groups of substances. The expression of porins is regulated (the total protein content of the outer membrane is constant). In Escherichia coli grown in media with low osmotic pressure predominates the nonspecific porin (outer membrane protein) OmpF, at higher osmolarity more OmpC is inserted into the membrane. Lack of phosphate induces PhoE, group specific porins are e.g. LamB (sugar) and Tsx (nucleosides). OmpF-Pore from Escherichia coli reset General properties: The construction principle of porins is the same irrespective of their type: a chain of 300 - 420 amino acids folds to an antiparallel beta-barrel of 16 or 18 strands (exemplified here by the unspecific porin OmpF) . The wall of the pore has a thickness of one amino acid only. On the side of the barrel facing the periplasm the beta strands are connected by short loops or turns . On the other side the loops directed to the environment are larger and variable. The loop connecting beta strands 5 and 6 is of special importance: it is folded into the barrel and constricts the cross section . At the narrowest point there are some ionizable amino acids . The filter properties of the pore are defined at this point. This principle is found in other nonspecific porins too, although there is no sequence homology. In the frames below the starting view is from the periplasm through the pores to the outside. Use the mouse to see the details! Porin from Rhodobacter capsulatus reset Porin from Rhodpseudomonas blastica reset PhoE from Escherichia coli reset OmpF porin in the membrane of Escherichia coli if it is messed up: reset Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
The expression of porins is regulated (the total protein content of the outer membrane is constant). In Escherichia coli grown in media with low osmotic pressure predominates the nonspecific porin (outer membrane protein) OmpF, at higher osmolarity more OmpC is inserted into the membrane. Lack of phosphate induces PhoE, group specific porins are e.g. LamB (sugar) and Tsx (nucleosides). OmpF-Pore from Escherichia coli reset General properties: The construction principle of porins is the same irrespective of their type: a chain of 300 - 420 amino acids folds to an antiparallel beta-barrel of 16 or 18 strands (exemplified here by the unspecific porin OmpF) . The wall of the pore has a thickness of one amino acid only. On the side of the barrel facing the periplasm the beta strands are connected by short loops or turns . On the other side the loops directed to the environment are larger and variable. The loop connecting beta strands 5 and 6 is of special importance: it is folded into the barrel and constricts the cross section . At the narrowest point there are some ionizable amino acids . The filter properties of the pore are defined at this point. This principle is found in other nonspecific porins too, although there is no sequence homology. In the frames below the starting view is from the periplasm through the pores to the outside. Use the mouse to see the details! Porin from Rhodobacter capsulatus reset Porin from Rhodpseudomonas blastica reset PhoE from Escherichia coli reset OmpF porin in the membrane of Escherichia coli if it is messed up: reset Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
OmpF-Pore from Escherichia coli reset General properties: The construction principle of porins is the same irrespective of their type: a chain of 300 - 420 amino acids folds to an antiparallel beta-barrel of 16 or 18 strands (exemplified here by the unspecific porin OmpF) . The wall of the pore has a thickness of one amino acid only. On the side of the barrel facing the periplasm the beta strands are connected by short loops or turns . On the other side the loops directed to the environment are larger and variable. The loop connecting beta strands 5 and 6 is of special importance: it is folded into the barrel and constricts the cross section . At the narrowest point there are some ionizable amino acids . The filter properties of the pore are defined at this point. This principle is found in other nonspecific porins too, although there is no sequence homology. In the frames below the starting view is from the periplasm through the pores to the outside. Use the mouse to see the details! Porin from Rhodobacter capsulatus reset Porin from Rhodpseudomonas blastica reset PhoE from Escherichia coli reset OmpF porin in the membrane of Escherichia coli if it is messed up: reset Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
General properties: The construction principle of porins is the same irrespective of their type: a chain of 300 - 420 amino acids folds to an antiparallel beta-barrel of 16 or 18 strands (exemplified here by the unspecific porin OmpF) . The wall of the pore has a thickness of one amino acid only. On the side of the barrel facing the periplasm the beta strands are connected by short loops or turns . On the other side the loops directed to the environment are larger and variable. The loop connecting beta strands 5 and 6 is of special importance: it is folded into the barrel and constricts the cross section . At the narrowest point there are some ionizable amino acids . The filter properties of the pore are defined at this point. This principle is found in other nonspecific porins too, although there is no sequence homology. In the frames below the starting view is from the periplasm through the pores to the outside. Use the mouse to see the details! Porin from Rhodobacter capsulatus reset Porin from Rhodpseudomonas blastica reset PhoE from Escherichia coli reset OmpF porin in the membrane of Escherichia coli if it is messed up: reset Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
OmpF porin in the membrane of Escherichia coli if it is messed up: reset Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Quarternary structure: Porins are inserted in the outer membrane as trimers. Amino and carboxy termini of the single molecules face the threefold symmetry axis of the complex. As found in other transmembrane proteins there are two belts of aromatic amino acids pointed to the surfaces of the membrane (amino acids at the outer face of the outer membrane are marked green, those facing the periplasmic side are in blue). Between the belts the surface of the barrels is composed mainly from hydrophobic amino acids. The belts are placed in a distance of ~ 25 Å corresponding to the thickness of the outer membrane. The loops at the outer face narrow down the entrance opening of the pores. One loop is positioned in a way to line the opening of a neighboring pore . This 'domain swapping' stabilizes the quarternary structure. Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Function: Porins are tubes with a diameter of about 1 nm which are filled with water. Nonspecific porins allow the diffusion of ions and molecules up to a molecular weight of 600. The diffusion speed depends on both the difference of concentration in the periplasm and outside and the molecular weight of the solute. The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
The passing of ions may be regulated electrically. If (in vitro) a voltage of + or - 100mV is applied, the channel is closed for ions (voltage gating). This phenomenon is also found in another class of beta-barrel pores, the toxins. From mutation experiments it was concluded that there is no movement of the loop constricting the inside of the channel. Probably the applied voltage changes the electrostatic properties of the interior wall. A physiological function of voltage gating is not obvious. Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Sugar selective porins The enzymatic degradation of starch results in maltodextrines (alpha-1-4-connected polyglucose molecules). The entry system into the periplasm for maltodextrines up to seven residues in length is the maltoporin. Previously this protein was recognized as the receptor for phage lambda and therefore termed LamB. It is induced together with other proteins neccessary for maltose metabolism, among them a system for transport through the cytoplasmic membrane. Besides maltoporines LamB allows the passage of some monosaccharides (in some cases with a larger diffusion speed) and disaccharides (trehalose; lactose and sucrose pass much slower). LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
LamB pore from Escherichia coli reset The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
The barrel of sugar selective porins is composed of 18 antiparallel beta strands . In LamB three loops extend into the barrel . From the spacefilling view it is obvious that this channel is tighter at the narrowest spot than the general porins (the opening is 7 Å x 10 Å). This shows in the ion conductivity: LamB has a conductivity of 0.15 nS vs. 0.8 nS in OmpF. The sugar (here maltotriose) fills up the opening completely. What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
What is the reason for the sugar selectivity of these pores? The X-ray structure determination of the protein crystal with bound sugar gives a snapshot of the diffusion process in the moment when the maltodextrin (here trimeric glucose) is stuck at the narrow point. So we can read the interchange of sugar and protein in the recognition moment. In the inner Wall of the channel there is a helical belt of aromatic amino acids, a "greasy slide" . Opposite to this there is a tyrosine in the constricting loop . This restricts the way in a manner, that only sugar with a flat geometry (like maltodextrin composed of glucose) may pass the channel. The 'uppermost' tryptophan of the slide is part of a loop of a neighboring pore. There are apolar van der Waals contacts between the sugar and the greasy slide . Besides the slide there are a couple of amino acids detecting the sugar via hydrogen bonds (if you lost your orientation now, use the mouse to turn the molecule). In a total view you may see: the greasy slide (blue), the hydrophilic narrow spot (yellow), the amino acids involved in phage binding (green) and the sugar in one of the pores (red). Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Saccharose: example of rotational movement between glucose and fructoseSaccharose in LamB: contacts with amino acidskeep the sugar in a fixed position,rotations along single bonds are not possible The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
The disaccharide saccharose is more bulky in structure than maltose. The space between the slide and Tyr118 is too narrow to let saccharose pass, in addition one asparagine and arginine each obstruct the way more than in the case with maltose. So the diffusion speed of saccharose is only 2.5% of that of maltose. However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
However, in enteric bacteria there is a saccharose specific transport system too. A plasmid codes a regulon containing a PTS situated in the cytoplasmic membrane and a porin (ScrY) in the outer membrane. This porin exhibits only 20% amino acid homology to maltoporin, but there is an identical topology in the structure of the beta-barrel. ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
ScrY-Pore (Plasmid pUR400) reset The functional difference is caused by the arrangement of the narrow spot. The aromatic amino acids of the slide are positioned as in LamB, with the last one facing the periplasm missing. Instead of the limiting tyrosine and asparagine (LamB) there are differently positioned asparagine and phenylalanine. The hydrophilic amino acids are spaced somewhat further apart, so there is an opening of 8,5 Å x 11 Å. The ion conductivity of this channel is 1.4 nS. As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
As in LamB there is a loop in ScrY that hooks on the rim of a neighboring pore lending one aromatic amino acid to the slide and tightening the contacts in the trimer. On the periplasmic face another connecting device is found: each monomer contains two phenylalanines parallel to each other (stacking of pi-electrons of the aromatic rings). These stacks are adjacent in the trimer giving strong hydrophobic contacts around the trifold axis . Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Relationships Structural relationships of proteins may be found in special databanks, e.g. CAMPASS (Cambridge University). For each protein family there are alignment data (primary structure) together with structural data (secondary structure). Additionally atomic coordinates are given with spatial superpositioning of the protein chains. The porin family in CAMPASS contains OmpF, the porin from Rhodobacter capsulatus (both 16-stranded) and maltoporin (LamB, 18-stranded). Here please find an excerpt of the data bank: porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b 2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb 2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb 2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb 2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb 2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb 2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb 2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb 2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
porins 1mal-0 maltoporin (escherichia coli) 3.10:21.70 0 1 1 421 (DDBASE: 2omf-0 matrix porin outer membrane protein f (escherichia coli) 2.40:16.70 0 1 1 340 (DDBASE: 2por-0 porin (crystal form b) ((rhodobacter $capsulatus) (strain 37b4) (formerly) 1.80: 9.99 0 1 1 301 (DDBASE: Percentage identity matrix 2por-0 2omf-0 1mal-0 2por-0 100.0 16.0 10.2 2omf-0 16.0 100.0 7.6 1mal-0 10.2 7.6 100.0 2por-0 2omf-0 1mal-0 high highest percentage identity low lowest percentage identity Alignment based on similarities in structural features (COMPARER alignment) 2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b
2por-0( 1 ) evklsgdarmgvmy----------nGd----dw--nfssrs 2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b
2omf-0( 1 ) aeiynkdgnkvdlyGkaVgLhyfSkg-------nGenSyggn--gdmtya 1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b
1mal-0( 1 ) vdfhGyarsgiGwTGsggeqqçFqTtgAqskYRLgNEçet bbbbbbbbbbbb b
bbbbbbbbbbbb b
2por-0( 26 ) rvlftmsgttd---sgl-efgasfk---ahes--vgaetg---edgtvfl 2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb
2omf-0( 42 ) rlGfkgetqin---sdltgygqweyNfqgnnsegadaqtgnktrlafagl 1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb
1mal-0( 41 ) yaelklGqevwkegdksfyfdtNvAysvaqqn----dweatdpafrEaNv bbbbbbbbb bbbbbbb bbbb
bbbbbbbbb bbbbbbb bbbb
2por-0( 64 ) sga-------fgkiemgdAlGASEalFgdLyeVGYtdLddrgGNdIpYLT 2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb
2omf-0( 89 ) kyad------vgsfdygrnyGVVydAlg-yTdmLpef-----GgdtAysd 1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb
1mal-0( 87 ) qGknliewlpgStiWagkrfYq-----rh--dVhMId------FyYWdIs bb bbbbb
bb bbbbb
2por-0( 107 ) GderlTaedNpVlLytysa-----gafsvAasmSdgkvge---------- 2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb
2omf-0( 127 ) DFFVGrVg--gVaTyrNsnffglvdglnfAvQyLgknerd---------- 1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb
1mal-0( 124 ) ---------gpgaglenidvg----fgklslAaTrsseaGGSSsfasnni bbbbbb bbbbbb
bbbbbb bbbbbb
2por-0( 142 ) ts-eddaqEmAvAaaytf----gnytvglGyEkIdSp--dta-lma---- 2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb
2omf-0( 165 ) tarrSNGdgvggSisyey----egfGiVGAyGaAdRTnlQeaqpLGn--g 1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb
1mal-0( 161 ) ydYtneTaNdVfDvRlaqmeinpgGtlelGvDyGrAnlr-dnyrLvdgAS bbbbbbbbbb bbbbbbbbbbb
bbbbbbbbbb bbbbbbbbbbb
2por-0( 180 ) -dMeQlElAaiakfgatnvkaYyAdge-----lDrdfAravfdlt---pv 2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb
2omf-0( 209 ) kkAeQwAtGlkydanniylAaNygetrnATpItnkft------------- 1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb
1mal-0( 210 ) kdgwLfTaEhtqsvlkgfnkfVvQyAtdSMTsqGkGlSqGSgVafDnekf bbbbbbbbbbbb bbbbbbbbbbb
bbbbbbbbbbbb bbbbbbbbbbb
2por-0( 221 ) aaaAtavdHkAyglSvdstf----gattvggYvQvldId-tIddvt-yyG 2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb
2omf-0( 246 ) -ntsGFAnkTqdvLlVaQyqfdfglrpSiAyTkSkAkdVegigdVdlvnY 1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb
1mal-0( 260 ) AyninNnghMlRiLdhGAismgdnwDmMyVgMyQdinwd-ndnGtk-WwT bbbbbbbbbbb bbbbbbbbbbbb bb bbb
bbbbbbbbbbb bbbbbbbbbbbb bb bbb
2por-0( 265 ) lgasydlg--ggasivggiAdndlp-----nSdmVaDlgvkfkf 2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb
2omf-0( 295 ) fEvGatyyfnknmstyvDyIiNqIdsdnkLgvGsddTVAvGivyqf 1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb
1mal-0( 308 ) vgiRpMykwtpimStVmEiGyDnVeSqrtgdkNnQyKiTlAqQwQagdsI bbbbbbbb bbbbbbbbbb bbbbbbbb
bbbbbbbb bbbbbbbbbb bbbbbbbb
2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x
2por-0( ) 2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww
2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd 2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww
2omf-0( ) 1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd
1mal-0( 358 ) wsRpAiRvFaTyAkwdEkWGyDytgnAdnnanfGkAVpadfnggsfgrgd
2por-0( ) 2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww
2omf-0( ) 1mal-0( 408 ) sdewTfgaqmEiww
1mal-0( 408 ) sdewTfgaqmEiww
Keysolvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x
solvent inaccessible UPPER CASE Xsolvent accesible lower case xalpha helix red xbeta strand blue x3 - 10 helix maroon xhydrogen bond to main chain amide bold xhydrogen bond to mainchain carbonyl underline xdisulphide bond cedilla çpositive phi italic x
Mind the low amino acid homology, which is 16% only for the two 16-stranded pores. Nevertheless the Calpha atoms of the beta-barrel structures may be superimposed with small deviations only (the frame to the left shows the backbone structures of the proteins, e.i. lines connecting the Calpha atoms). Even the 18-stranded pore has homology in the part where the subunits contact each other (switch LamB on in the table below). onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
onporeoff OmpF R. caps. pore LamB Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
Literature: R Benz & K Bauer, Permeation of hydrophilic molecules through the outer membrane of gram-negative bacteria, Eur. J. Biochem. 176 (1988) 1-19 T Schirmer, General and specific porins from bacterial outer membranes, J. Struct. Biol. 121 (1998) 101-109 G Bainbridge et al, Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels, FEBS Lett. 431 (1998) 305-308 R Dutzler et al, Crystal structures of various maltooligosaccharides bound to maltoporin reveal specific sugar translocation pathway, Structure 4 (1996) 127-134 D Forst et al, Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose, Nature Structural Biology 5 (1998) 37-46 R Sowdhamini et al, CAMPASS: A database of structurally aligned protein superfamilies, Structure 6 (1998) 1087-1094 6-99 © Rolf Bergmann
6-99 © Rolf Bergmann
