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Transmembrane protein - Revision history
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WikiBot
https://www.wikidoc.org/index.php?title=Transmembrane_protein&diff=549273&oldid=prev
Brian Blank at 19:28, 12 June 2009
2009-06-12T19:28:58Z
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Brian Blank
https://www.wikidoc.org/index.php?title=Transmembrane_protein&diff=549271&oldid=prev
Brian Blank at 19:27, 12 June 2009
2009-06-12T19:27:42Z
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==Overview==<br />
<br />
A '''transmembrane protein''' is a [[protein]] that spans the entire [[biological membrane]]. Transmembrane proteins aggregate and precipitate in water. They require [[detergent]]s or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.<br />
<br />
==Types==<br />
There are two basic types of transmembrane proteins:<br />
#Alpha-helical. These proteins are present in all types of [[biological membranes]] including [[outer membrane]]s. This is the major category of transmembrane proteins.<br />
#Beta-barrels. These proteins are found only in [[outer membrane]]s of [[Gram-negative bacteria]], [[cell wall]] of [[Gram-positive bacteria]], and [[outer membrane]]s of [[mitochondria]] and [[chloroplasts]]. All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their common evolutionary origin and similar folding mechanism.<br />
<br />
==Thermodynamic stability and folding==<br />
===Stability of α-helical transmembrane proteins===<br />
[[Transmembrane helix|Transmembrane α-helical]] proteins are unusually stable judging from thermal [[Denaturation (biochemistry)|denaturation]] studies, because they do not unfold completely within the membranes (the complete unfolding would require breaking down too many α-helical H-bonds in the nonpolar media). On the other hand, these proteins easily ''misfold'', due to non-native aggregation in membranes, transition to the molten globule states, formation of non-native [[disulfide bonds]], or unfolding of peripheral regions and nonregular loops that are locally less stable. <br />
<br />
It is also important to properly define the ''unfolded state''. The ''unfolded state'' of membrane proteins in [[detergent]] [[micelles]] is different from that in the thermal [[Denaturation (biochemistry)|denaturation]] experiments. This state represents a combination of folded hydrophobic α-helices and partially unfolded segments covered by the detergent. For example, the "unfolded" [[bacteriorhodopsin]] in [[SDS]] micelles has four transmembrane α-helices folded, while the rest of the protein is situated at the micelle-water interface and can adopt different types of non-native [[amphiphilic]] structures. Free energy differences between such detergent-denatured and native states are similar to stabilities of water-soluble proteins (< 10 kcal/mol).<br />
<br />
===Folding of α-helical transmembrane proteins===<br />
Refolding of α-helical transmembrane proteins ''in vitro'' is technically difficult. There are relatively few examples of the successful refolding experiments, as for [[bacteriorhodopsin]]. ''In vivo'' all such proteins are normally folded co-translationally within the large transmembrane [[translocon]]. The translocon channel provides a highly heterogeneous environment for the nascent transmembane α-helices. A relatively polar amphiphilic α-helix can adopt a transmembrane orientation in the translocon (although it would be at the membrane surface or unfolded ''in vitro''), because its polar residues can face the central water-filled channel of the translocon. Such mechanism is necessary for incorporation of polar α-helices into structures of transmembrane proteins. The amphiphilic helices remain attached to the translocon until the protein is completely synthesized and folded. If the protein remains unfolded and attached to the translocon for too long, it is degraded by specific "quality control" cellular systems.<br />
<br />
===Stability and folding of β-barrel transmembrane proteins===<br />
Stability of β-barrel transmembrane proteins is similar to stability of water-soluble proteins, based on chemical denaturation studies. Their folding ''in vivo'' is facilitated by water-soluble [[chaperones]], such as protein Skp [http://faculty.virginia.edu/tamm/pages/BBA_Folding_Review.pdf].<br />
<br />
==3D structures==<br />
===Light absorption-driven transporters===<br />
*[[Bacteriorhodopsin]]-like proteins including [[rhodopsin]] (see also [[opsin]])[http://opm.phar.umich.edu/families.php?superfamily=6]<br />
*Bacterial [[photosynthetic reaction centre]]s and [[photosystem]]s I and II [http://opm.phar.umich.edu/families.php?superfamily=2]<br />
*Light harvesting complexes from [[bacteria]] and [[chloroplasts]] [http://opm.phar.umich.edu/families.php?superfamily=1]<br />
<br />
===Oxidoreduction-driven transporters===<br />
*Transmembrane cytochrome b-like proteins [http://opm.phar.umich.edu/families.php?superfamily=3]: [[coenzyme Q - cytochrome c reductase]] (cytochrome bc1 ); [[cytochrome b6f complex]]; formate dehydrogenase, respiratory [[nitrate reductase]]; [[succinate - coenzyme Q reductase]] (fumarate reductase); and [[succinate dehydrogenase]]. See [[electron transport chain]].<br />
*[[Cytochrome c oxidase]]s [http://opm.phar.umich.edu/families.php?superfamily=4] from [[bacteria]] and [[mitochondria]]<br />
<br />
===Electrochemical potential-driven transporters===<br />
*Proton or sodium translocating F-type and V-type [[ATPase]]s [http://opm.phar.umich.edu/families.php?superfamily=5]<br />
<br />
===P-P-bond hydrolysis-driven transporters===<br />
*P-type [[calcium ATPase]] (five different conformations) [http://opm.phar.umich.edu/families.php?superfamily=22]<br />
*Calcium ATPase regulators [[phospholamban]] and sarcolipin[http://opm.phar.umich.edu/families.php?superfamily=70]<br />
*[[ABC transporter]]s: [http://opm.phar.umich.edu/families.php?superfamily=17 BtuCD], [http://opm.phar.umich.edu/families.php?superfamily=18 multidrug transporter], and [http://opm.phar.umich.edu/families.php?superfamily=198 molybdate uptake transporter]<br />
*General [[secretory pathway]] (Sec) [[translocon]] (preprotein translocase SecY) [http://opm.phar.umich.edu/families.php?superfamily=19]<br />
<br />
===Porters (uniporters, [[symporters]], [[antiporters]])===<br />
*[[Mitochondrial]] [[carrier protein]]s [http://opm.phar.umich.edu/families.php?superfamily=21]<br />
*Major Facilitator Superfamily (Glycerol-3-hosphate transporter, Lactose [[permease]], and Multidrug transporter EmrD) [http://opm.phar.umich.edu/families.php?superfamily=15]<br />
*Resistance-nodulation-cell division (multidrug [[efflux]] transporter AcrB, see [[multidrug resistance]])[http://opm.phar.umich.edu/families.php?superfamily=16]<br />
*Dicarboxylate/amino acid:cation symporter (proton glutamate symporter) [http://opm.phar.umich.edu/families.php?superfamily=20]<br />
*Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA) [http://opm.phar.umich.edu/families.php?superfamily=66]<br />
*[[Neurotransmitter]] sodium symporter [http://opm.phar.umich.edu/families.php?superfamily=67]<br />
*Ammonia transporters [http://opm.phar.umich.edu/families.php?superfamily=13] <br />
*Drug/Metabolite Transporter (small multidrug resistance transporter EmrE - the structures are retracted as erroneous) [http://opm.phar.umich.edu/families.php?superfamily=77]<br />
<br />
===Alpha-helical channels including [[ion channels]]===<br />
*[[Voltage-gated ion channel]] like, including [[potassium channel]]s KcsA and KvAP, and [[inward-rectifier potassium ion channel]] Kirbac [http://opm.phar.umich.edu/families.php?superfamily=8]<br />
*Large-conductance mechanosensitive channel, MscL [http://opm.phar.umich.edu/families.php?superfamily=12]<br />
*[[Mechanosensitive ion channel|Small-conductance mechanosensitive ion channel (MscS)]] [http://opm.phar.umich.edu/families.php?superfamily=11]<br />
*[[Magnesium transporters|CorA metal ion transporters]] [http://opm.phar.umich.edu/families.php?superfamily=72]<br />
*[[Ligand-gated ion channel]] of [[neurotransmitter]] receptors ([[acetylcholine receptor]]) [http://opm.phar.umich.edu/families.php?superfamily=14]<br />
*[[Aquaporin]]s [http://opm.phar.umich.edu/families.php?superfamily=7]<br />
*[[Chloride channel]]s [http://opm.phar.umich.edu/families.php?superfamily=10]<br />
*Outer membrane auxiliary proteins (polysaccharide transporter) [http://opm.phar.umich.edu/families.php?superfamily=188] - α-helical transmembrane proteins from the outer bacterial membrane<br />
<br />
===Enzymes===<br />
*[[Methane monooxygenase]] [http://opm.phar.umich.edu/families.php?superfamily=23]<br />
*Rhomboid protease [http://opm.phar.umich.edu/families.php?superfamily=186]<br />
*[[Disulfide bond]] formation protein (DsbA-DsbB complex) [http://opm.phar.umich.edu/protein.php?pdbid=2hi7]<br />
<br />
===Proteins with alpha-helical transmembrane anchors===<br />
*[[T cell receptor]] transmembrane dimerization domain [http://opm.phar.umich.edu/families.php?superfamily=187]<br />
*Cytochrome c [[nitrite reductase]] complex [http://opm.phar.umich.edu/protein.php?pdbid=2j7a]<br />
*Steryl-sulfate sulfohydrolase [http://opm.phar.umich.edu/families.php?superfamily=24]<br />
*Stannin [http://opm.phar.umich.edu/families.php?superfamily=180]<br />
*[[Glycophorin]] A dimer [http://opm.phar.umich.edu/families.php?superfamily=25]<br />
*Inovirus (filamentous phage) major coat protein [http://opm.phar.umich.edu/families.php?superfamily=73]<br />
*[[Pilin]] [http://opm.phar.umich.edu/families.php?superfamily=74]<br />
*[[Pulmonary surfactant]]-associated protein [http://opm.phar.umich.edu/families.php?superfamily=75]<br />
*[[Monoamine oxidase]]s A and B [http://opm.phar.umich.edu/families.php?family=176], <br />
*[[Cytochrome P450 oxidase]]s [http://opm.phar.umich.edu/families.php?superfamily=41], <br />
*[[Mineralocorticoid|Corticosteroid 11β-dehydrogenases]] [http://opm.phar.umich.edu/families.php?superfamily=127].<br />
*Signal Peptide Peptidase [http://opm.phar.umich.edu/families.php?superfamily=178]<br />
*Membrane protease specific for a stomatin homolog [http://opm.phar.umich.edu/protein.php?pdbid=2deo]<br />
<br />
===β-Barrels composed by a single polypeptide chain ===<br />
*Beta barrels from eight beta-strands and with "shear number" of ten (''n=8, S=10'') [http://opm.phar.umich.edu/families.php?superfamily=26]. They include:<br />
**OmpA-like transmembrane domain (OmpA), <br />
**Virulence-related outer membrane protein family (OmpX), <br />
**Outer membrane protein W family (OmpW), <br />
**Antimicrobial peptide resistance and lipid A acylation protein family (PagP)<br />
**Lipid A deacylase PagL, and<br />
**Opacity family porins (NspA)<br />
* Autotransporter domain (''n=12,S=14') [http://opm.phar.umich.edu/families.php?superfamily=28]<br />
* FadL outer membrane protein transport family, including [[Fatty acid]] transporter FadL (''n=14,S=14'') [http://opm.phar.umich.edu/families.php?superfamily=30]<br />
* General bacterial porin family, known as trimeric [[porin (protein)|porins]] (''n=16,S=20'') [http://opm.phar.umich.edu/families.php?superfamily=31]<br />
* Maltoporin, or sugar [[porin (protein)|porins]] (''n=18,S=22'') [http://opm.phar.umich.edu/families.php?superfamily=32]<br />
* Nucleoside-specific porin (''n=12,S=16'') [http://opm.phar.umich.edu/families.php?superfamily=71]<br />
* Outer membrane phospholipase A1(''n=12,S=16'') [http://opm.phar.umich.edu/families.php?superfamily=29]<br />
*TonB dependent receptors and their plug domain. They are ligand-gated outer membrane channels (''n=22,S=24''), including cobalamin transporter BtuB, Fe(III)-pyochelin receptor FptA, receptor FepA, ferric hydroxamate uptake receptor FhuA, transporter FecA, and pyoverdine receptor FpvA [http://opm.phar.umich.edu/families.php?superfamily=33]<br />
*Outer membrane protein OpcA family (''n=10,S=12'') that includes outer membrane [[protease]] OmpT and [[adhesin]]/invasin OpcA protein [http://opm.phar.umich.edu/families.php?superfamily=27]<br />
*Outer membrane protein G porin family (''n=14,S=16'') [http://opm.phar.umich.edu/families.php?superfamily=181]<br />
<br />
Note: ''n'' and ''S'' are, respectively, the number of beta-strands and the "shear number" [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=8126726&query_hl=3&itool=pubmed_docsum] of the beta-barrel<br />
<br />
===β-barrels composed by several polypeptide chains===<br />
*Trimeric autotransporter (''n=12,S=12'') [http://opm.phar.umich.edu/families.php?superfamily=179]<br />
* Outer membrane efflux proteins, also known as trimeric outer membrane factors (n=12,S=18) including TolC and multidrug resistance proteins [http://opm.phar.umich.edu/families.php?superfamily=34]<br />
* MspA porin (octamer, ''n=S=16'') and α-hemolysin (heptamer ''n=S=14'') [http://opm.phar.umich.edu/families.php?superfamily=35]. These proteins are secreted. <br />
<br />
See also [[Gramicidin]] A [http://opm.phar.umich.edu/protein.php?pdbid=1grm], a peptide that forms a dimeric transmembrane β-helix. It is also secreted by [[Gram-positive]] bacteria.<br />
<br />
==References==<br />
*Booth, P.J., Templer, R.H., Meijberg, W., Allen, S.J., Curran, A.R., and Lorch, M. 2001. In vitro studies of membrane protein folding. ''Crit. Rev. Biochem. Mol. Biol.'' 36: 501-603.<br />
*Bowie J.U. 2001. Stabilizing membrane proteins. ''Curr. Op. Struct. Biol.'' 11: 397-402.<br />
*Bowie J.U. 2005. Solving the membrane protein folding problem. ''Nature'' 438: 581-589.<br />
*DeGrado W.F., Gratkowski H. and Lear J.D. 2003. How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. ''Protein Sci.'' 12: 647-665.<br />
*Lee, A.G. 2003 Lipid-protein interactions in biological membranes: a structural perspective. ''Biochim. Biophys. Acta'' 1612: 1-40.<br />
*Lee, A.G. 2004. How lipids affect the activities of integral membrane proteins. ''Biochim. Biophys. Acta'' 1666: 62-87. <br />
*le Maire, M., Champeil, P., and Moller, J.V. 2000. Interaction of membrane proteins and lipids with solubilizing detergents. ''Biochim. Biophys. Acta'' 1508: 86-111.<br />
*Popot J-L. and Engelman D.M. 2000. Helical membrane protein folding, stability, and evolution. ''Annu. Rev. Biochem.'' 69: 881-922.<br />
*''Protein-lipid interactions'' (Ed. L.K. Tamm) Wiley, 2005.<br />
*Tamm, L.K., Hong, H., and Liang, B.Y. 2004. Folding and assembly of beta-barrel membrane proteins. ''Biochim. Biophys. Acta'' 1666: 250-263.<br />
<br />
==Additional examples==<br />
*Some [[cell adhesion]] proteins<br />
*[[Transmembrane receptor|Some receptor proteins]]<br />
*[[Insulin receptor]]<br />
*[[Integrin]]<br />
*[[Cadherin]]<br />
<br />
==External links==<br />
*[http://www.tcdb.org/ TCDB] - [[Transporter Classification database|Transporter classification database]] from Milton H. Saier, Jr. laboratory<br />
*[http://www.membranetransport.org/ TransportDB] Genomics-oriented database of transporters from TIGR<br />
*[http://www.mpdb.ul.ie/ Membrane PDB] Database of 3D structures of integral membrane proteins and hydrophobic peptides with an emphasis on crystallization conditions<br />
*[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html Membrane proteins of known 3D structure] from Stephen White laboratory<br />
*[http://pdbtm.enzim.hu/ PDBTM] ''All'' 3D models of transmembrane peptides and proteins currently in the PDB including theoretical models. Approximate positions of membrane boundary planes were calculated for each PDB entry.<br />
*[http://opm.phar.umich.edu/ Orientations of proteins in membranes database] - [[Orientations of Proteins in Membranes database|Calculated spatial positions of transmembrane, integral monotopic, and peripheral proteins in membranes]]<br />
<br />
==See also==<br />
* [[cell membrane]]<br />
* [[transmembrane receptor]]s<br />
* [[membrane topology]]<br />
* [[transmembrane helix]]<br />
* [[membrane protein]]<br />
* [[integral membrane protein]]<br />
* [[peripheral membrane protein]]<br />
<br />
[[Category:Integral membrane proteins]]<br />
[[Category:Cell-surface receptors]]<br />
[[Category:Transmembrane receptors]]<br />
[[Transporter Classification database]]<br />
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[[fr:Protéine transmembranaire]]<br />
[[it:Proteina transmembrana o integrale]]<br />
[[pl:Białko transbłonowe]]<br />
[[pt:Proteína transmembranar]]<br />
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{{WS}}</div>
Brian Blank