메뉴 건너뛰기




Volumn 10, Issue 8, 2011, Pages 3324-3331

An introduction to membrane proteins

Author keywords

bioinformatics; membrane proteins; protein biogenesis; protein evolution; protein structure; translocon insertion

Indexed keywords

AMINO ACID; MEMBRANE PROTEIN;

EID: 79961226780     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200145a     Document Type: Article
Times cited : (58)

References (59)
  • 2
    • 70350038016 scopus 로고    scopus 로고
    • Mapping the human membrane proteome: A majority of the human membrane proteins can be classified according to function and evolutionary origin
    • Almen, M.; Nordstrom, K.; Fredriksson, R.; Schioth, H. Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin BMC Biol. 2009, 7, 50
    • (2009) BMC Biol. , vol.7 , pp. 50
    • Almen, M.1    Nordstrom, K.2    Fredriksson, R.3    Schioth, H.4
  • 3
    • 33745698481 scopus 로고    scopus 로고
    • A limited universe of membrane protein families and folds
    • Oberai, A.; Ihm, Y.; Kim, S.; Bowie, J. A limited universe of membrane protein families and folds Protein Sci. 2006, 15, 1723-1734
    • (2006) Protein Sci. , vol.15 , pp. 1723-1734
    • Oberai, A.1    Ihm, Y.2    Kim, S.3    Bowie, J.4
  • 4
    • 57749117163 scopus 로고    scopus 로고
    • Mitochondrial beta-barrel proteins, an exclusive club
    • author reply 1159.60
    • Imai, K.; Gromiha, M.; Horton, P. Mitochondrial beta-barrel proteins, an exclusive club ? Cell 2008, 135, 1158-1159; author reply 1159.60.
    • (2008) Cell , vol.135 , pp. 1158-1159
    • Imai, K.1    Gromiha, M.2    Horton, P.3
  • 5
    • 25444484398 scopus 로고    scopus 로고
    • TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
    • Garrow, A.; Agnew, A.; Westhead, D. TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins BMC Bioinform. 2005, 6, 56
    • (2005) BMC Bioinform. , vol.6 , pp. 56
    • Garrow, A.1    Agnew, A.2    Westhead, D.3
  • 6
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: Prediction versus reality
    • Elofsson, A.; von Heijne, G. Membrane protein structure: prediction versus reality Annu. Rev. Biochem. 2007, 76, 125-140
    • (2007) Annu. Rev. Biochem. , vol.76 , pp. 125-140
    • Elofsson, A.1    Von Heijne, G.2
  • 7
    • 24044436844 scopus 로고    scopus 로고
    • Experimentally constrained topology models for 51,208 bacterial inner membrane proteins
    • DOI 10.1016/j.jmb.2005.07.053, PII S0022283605008545
    • Granseth, E.; Daley, D.; Rapp, M.; Melen, K.; von Heijne, G. Experimentally constrained topology models for 51,208 bacterial inner membrane proteins J. Mol. Biol. 2005, 352, 489-494 (Pubitemid 41225461)
    • (2005) Journal of Molecular Biology , vol.352 , Issue.3 , pp. 489-494
    • Granseth, E.1    Daley, D.O.2    Rapp, M.3    Melen, K.4    Von Heijne, G.5
  • 8
    • 0026729232 scopus 로고
    • Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure
    • Wiener, M.; White, S. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure Biophys. J. 1992, 61, 434-447
    • (1992) Biophys. J. , vol.61 , pp. 434-447
    • Wiener, M.1    White, S.2
  • 10
    • 0027401021 scopus 로고
    • Ether polar lipids of methanogenic bacteria: Structures, comparative aspects, and biosyntheses
    • Koga, Y.; Nishihara, M.; Morii, H.; Akagawa-Matsushita, M. Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses Microbiol. Rev. 1993, 57, 164-182 (Pubitemid 23078441)
    • (1993) Microbiological Reviews , vol.57 , Issue.1 , pp. 164-182
    • Koga, Y.1    Nishihara, M.2    Morii, H.3    Akagawa-Matsushita, M.4
  • 11
    • 33845343261 scopus 로고    scopus 로고
    • Membrane-protein topology
    • DOI 10.1038/nrm2063, PII NRM2063
    • von Heijne, G. Membrane-protein topology Nat. Rev. Mol. Cell. Biol. 2006, 7, 909-918 (Pubitemid 44871417)
    • (2006) Nature Reviews Molecular Cell Biology , vol.7 , Issue.12 , pp. 909-918
    • Von Heijne, G.1
  • 12
    • 0030983047 scopus 로고    scopus 로고
    • Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
    • Wallin, E.; Tsukihara, T.; Yoshikawa, S.; von Heijne, G.; Elofsson, A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria Protein Sci. 1997, 6, 808-815 (Pubitemid 27154807)
    • (1997) Protein Science , vol.6 , Issue.4 , pp. 808-815
    • Wallin, E.1    Tsukihara, T.2    Yoshikawa, S.3    Von Heijne, G.4    Elofsson, A.5
  • 15
    • 0038122825 scopus 로고    scopus 로고
    • In silico prediction of the peroxisomal proteome in fungi, plants and animals
    • DOI 10.1016/S0022-2836(03)00553-9
    • Emanuelsson, O.; Elofsson, A.; von Heijne, G.; Cristobal, S. In silico prediction of the peroxisomal proteome in fungi, plants and animals J. Mol. Biol. 2003, 330, 443-456 (Pubitemid 36773715)
    • (2003) Journal of Molecular Biology , vol.330 , Issue.2 , pp. 443-456
    • Emanuelsson, O.1    Elofsson, A.2    Von Heijne, G.3    Cristobal, S.4
  • 16
    • 33750381048 scopus 로고    scopus 로고
    • The bacterial twin-arginine translocation pathway
    • DOI 10.1146/annurev.micro.60.080805.142212
    • Lee, P.; Tullman-Ercek, D.; Georgiou, G. The bacterial twin-arginine translocation pathway Annu. Rev. Microbiol. 2006, 60, 373-395 (Pubitemid 44627954)
    • (2006) Annual Review of Microbiology , vol.60 , pp. 373-395
    • Lee, P.A.1    Tullman-Ercek, D.2    Georgiou, G.3
  • 18
    • 33748602095 scopus 로고    scopus 로고
    • Molecular mechanisms of aquaporin biogenesis by the endoplasmic reticulum Sec61 translocon
    • DOI 10.1016/j.bbamem.2006.04.021, PII S0005273606001738, Auquporins
    • Pitonzo, D.; Skach, W. Molecular mechanisms of aquaporin biogenesis by the endoplasmic reticulum Sec61 translocon Biochim. Biophys. Acta 2006, 1758, 976-988 (Pubitemid 44376752)
    • (2006) Biochimica et Biophysica Acta - Biomembranes , vol.1758 , Issue.8 , pp. 976-988
    • Pitonzo, D.1    Skach, W.R.2
  • 19
    • 33746361201 scopus 로고    scopus 로고
    • Structural Classification and Prediction of Reentrant Regions in α-Helical Transmembrane Proteins: Application to Complete Genomes
    • DOI 10.1016/j.jmb.2006.06.037, PII S0022283606007583
    • Viklund, H.; Granseth, E.; Elofsson, A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes J. Mol. Biol. 2006, 361, 591-603 (Pubitemid 44118335)
    • (2006) Journal of Molecular Biology , vol.361 , Issue.3 , pp. 591-603
    • Viklund, H.1    Granseth, E.2    Elofsson, A.3
  • 20
    • 0034663513 scopus 로고    scopus 로고
    • Turning an opinion inside-out: Rees and Eisenberg's commentary (proteins 2000;38:121-122) on 'Are membrane proteins 'inside-out' proteins?' (Proteins 1999;36:135-143)
    • DOI 10.1002/1097-0134(20000815)40:3<463::AID-PROT120>3.0.CO;2-D
    • Stevens, T.; Arkin, I. Turning an opinion inside-out: Rees and Eisenberg's commentary (Proteins 2000;38:121-122) on "Are membrane proteins 'inside-out' proteins?" (Proteins 1999;36:135-143) Proteins 2000, 40, 463-464 (Pubitemid 30624454)
    • (2000) Proteins: Structure, Function and Genetics , vol.40 , Issue.3 , pp. 463-464
    • Stevens, T.J.1    Arkin, I.T.2
  • 21
    • 33747184794 scopus 로고    scopus 로고
    • Prediction of transmembrane helix orientation in polytopic membrane proteins
    • Adamian, L.; Liang, J. Prediction of transmembrane helix orientation in polytopic membrane proteins BMC Struct. Biol. 2006, 6, 13
    • (2006) BMC Struct. Biol. , vol.6 , pp. 13
    • Adamian, L.1    Liang, J.2
  • 23
    • 0029002720 scopus 로고
    • The hydrophobic effect in protein folding
    • Lins, L.; Brasseur, R. The hydrophobic effect in protein folding FASEB J. 1995, 9, 535-540
    • (1995) FASEB J. , vol.9 , pp. 535-540
    • Lins, L.1    Brasseur, R.2
  • 24
    • 79551683006 scopus 로고    scopus 로고
    • Membrane protein folding: How important are hydrogen bonds?
    • Bowie, J. Membrane protein folding: how important are hydrogen bonds? Curr. Opin. Struct. Biol. 2010, 11, 42-49
    • (2010) Curr. Opin. Struct. Biol. , vol.11 , pp. 42-49
    • Bowie, J.1
  • 27
    • 70349436810 scopus 로고    scopus 로고
    • Protein contents in biological membranes can explain abnormal solvation of charged and polar residues
    • Johansson, A.; Lindahl, E. Protein contents in biological membranes can explain abnormal solvation of charged and polar residues Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15684-15689
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 15684-15689
    • Johansson, A.1    Lindahl, E.2
  • 28
    • 0007949690 scopus 로고    scopus 로고
    • Interhelical hydrogen bonding drives strong interactions in membrane proteins
    • DOI 10.1038/72430
    • Zhou, F.; Cocco, M.; Russ, W.; Brunger, A.; Engelman, D. Interhelical hydrogen bonding drives strong interactions in membrane proteins Nat. Struct. Biol. 2000, 7, 154-160 (Pubitemid 30082514)
    • (2000) Nature Structural Biology , vol.7 , Issue.2 , pp. 154-160
    • Zhou, F.X.1    Cocco, M.J.2    Russ, W.P.3    Brunger, A.T.4    Engelman, D.M.5
  • 30
    • 0036568229 scopus 로고    scopus 로고
    • Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers
    • DOI 10.1002/prot.10071
    • Adamian, L.; Liang, J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers Proteins 2002, 47, 209-218 (Pubitemid 34266091)
    • (2002) Proteins: Structure, Function and Genetics , vol.47 , Issue.2 , pp. 209-218
    • Adamian, L.1    Liang, J.2
  • 31
    • 44049094995 scopus 로고    scopus 로고
    • Hydrogenbonding and packing features of membrane proteins: Functional implications
    • Hildebrand, P.; Gunther, S.; Goede, A.; Forrest, L.; Frommel, C.; Preissner, R. Hydrogenbonding and packing features of membrane proteins: functional implications Biophys. J. 2008, 94, 1945-1953
    • (2008) Biophys. J. , vol.94 , pp. 1945-1953
    • Hildebrand, P.1    Gunther, S.2    Goede, A.3    Forrest, L.4    Frommel, C.5    Preissner, R.6
  • 32
    • 10044249042 scopus 로고    scopus 로고
    • Helical packing patterns in membrane and soluble proteins
    • DOI 10.1529/biophysj.104.049288
    • Gimpelev, M.; Forrest, L.; Murray, D.; Honig, B. Helical packing patterns in membrane and soluble proteins Biophys. J. 2004, 87, 4075-4086 (Pubitemid 39602911)
    • (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 4075-4086
    • Gimpelev, M.1    Forrest, L.R.2    Murray, D.3    Honig, B.4
  • 33
    • 44649159957 scopus 로고    scopus 로고
    • Coils in the membrane core are conserved and functionally important
    • Kauko, A.; Illergard, K.; Elofsson, A. Coils in the membrane core are conserved and functionally important J. Mol. Biol. 2008, 380, 170-180
    • (2008) J. Mol. Biol. , vol.380 , pp. 170-180
    • Kauko, A.1    Illergard, K.2    Elofsson, A.3
  • 36
    • 12344330612 scopus 로고    scopus 로고
    • A study of the membrane-water interface region of membrane proteins
    • DOI 10.1016/j.jmb.2004.11.036, PII S0022283604014858
    • Granseth, E.; von Heijne, G.; Elofsson, A. A study of the membrane-water interface region of membrane proteins J. Mol. Biol. 2005, 346, 377-385 (Pubitemid 40128328)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.1 , pp. 377-385
    • Granseth, E.1    Von Heijne, G.2    Elofsson, A.3
  • 37
    • 78649770531 scopus 로고    scopus 로고
    • Why are polar residues within the membrane core evolutionary conserved?
    • Illergard, K.; Kauko, A.; Elofsson, A. Why are polar residues within the membrane core evolutionary conserved? Proteins 2011, 79, 79-91
    • (2011) Proteins , vol.79 , pp. 79-91
    • Illergard, K.1    Kauko, A.2    Elofsson, A.3
  • 38
    • 39749132236 scopus 로고    scopus 로고
    • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    • DOI 10.1002/prot.21629
    • Johansson, A.; Lindahl, E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations Proteins 2008, 70, 1332-1344 (Pubitemid 351304093)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.4 , pp. 1332-1344
    • Johansson, A.C.V.1    Lindahl, E.2
  • 39
    • 0026716643 scopus 로고
    • Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
    • von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule J. Mol. Biol. 1992, 225, 487-494
    • (1992) J. Mol. Biol. , vol.225 , pp. 487-494
    • Von Heijne, G.1
  • 40
    • 0024442722 scopus 로고
    • Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues
    • DOI 10.1038/341456a0
    • von Heijne, G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues Nature 1989, 341, 456-458 (Pubitemid 19241917)
    • (1989) Nature , vol.341 , Issue.6241 , pp. 456-458
    • Von Heijne, G.1
  • 42
    • 59149104036 scopus 로고    scopus 로고
    • Signal anchor sequence provides motive force for polypeptide chain translocation through the endoplasmic reticulum membrane
    • Kida, Y.; Morimoto, F.; Sakaguchi, M. Signal anchor sequence provides motive force for polypeptide chain translocation through the endoplasmic reticulum membrane J. Biol. Chem. 2009, 284, 2861-2866
    • (2009) J. Biol. Chem. , vol.284 , pp. 2861-2866
    • Kida, Y.1    Morimoto, F.2    Sakaguchi, M.3
  • 43
    • 0026529067 scopus 로고
    • Different positively charged amino acids have similar effects on the topology of a polytopic transmembrane protein in Escherichia coli
    • Andersson, H.; Bakker, E.; von Heijne, G. Different positively charged amino acids have similar effects on the topology of a polytopic transmembrane protein in Escherichia coli J. Biol. Chem. 1992, 267, 1491-1495
    • (1992) J. Biol. Chem. , vol.267 , pp. 1491-1495
    • Andersson, H.1    Bakker, E.2    Von Heijne, G.3
  • 44
    • 0027263346 scopus 로고
    • Positively charged amino acids placed next to a signal sequence block protein translocation more efficiently in Escherichia coli than in mammalian microsomes
    • Johansson, M.; Nilsson, I.; von Heijne, G. Positively charged amino acids placed next to a signal sequence block protein translocation more efficiently in Escherichia coli than in mammalian microsomes Mol. Gen. Genet. 1993, 239, 251-256 (Pubitemid 23167505)
    • (1993) Molecular and General Genetics , vol.239 , Issue.1-2 , pp. 251-256
    • Johansson, M.1    Nilsson, I.2    Von Heijne, G.3
  • 45
    • 33747879895 scopus 로고    scopus 로고
    • A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops
    • Lasso, G.; Antoniw, J.; Mullins, J. A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops Bioinformatics 2006, 22, e290-7
    • (2006) Bioinformatics , vol.22 , pp. 290-7
    • Lasso, G.1    Antoniw, J.2    Mullins, J.3
  • 46
    • 48249151108 scopus 로고    scopus 로고
    • OCTOPUS: Improving topology prediction by two-track ANNbased preference scores and an extended topological grammar
    • Viklund, H.; Elofsson, A. OCTOPUS: improving topology prediction by two-track ANNbased preference scores and an extended topological grammar Bioinformatics 2008, 24, 1662-1668
    • (2008) Bioinformatics , vol.24 , pp. 1662-1668
    • Viklund, H.1    Elofsson, A.2
  • 47
    • 60849099626 scopus 로고    scopus 로고
    • Prediction of membrane protein structures with complex topologies using limited constraints
    • Barth, P.; Wallner, B.; Baker, D. Prediction of membrane protein structures with complex topologies using limited constraints Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 1409-1414
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 1409-1414
    • Barth, P.1    Wallner, B.2    Baker, D.3
  • 48
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones, D.; Taylor, W.; Thornton, J. A model recognition approach to the prediction of allhelical membrane protein structure and topology Biochemistry 1994, 33, 3038-3049 (Pubitemid 24103366)
    • (1994) Biochemistry , vol.33 , Issue.10 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 49
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • DOI 10.1006/jmbi.2000.4315
    • Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 2001, 305, 567-580 (Pubitemid 33032862)
    • (2001) Journal of Molecular Biology , vol.305 , Issue.3 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.L.4
  • 50
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnady, G.; Simon, I. The HMMTOP transmembrane topology prediction server Bioinformatics 2001, 17, 849-850 (Pubitemid 32970487)
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 849-850
    • Tusnady, G.E.1    Simon, I.2
  • 51
    • 3042579686 scopus 로고    scopus 로고
    • Best α-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • DOI 10.1110/ps.04625404
    • Vviklund, H.; Elofsson, A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information Protein Sci. 2004, 13, 1908-1917 (Pubitemid 38822130)
    • (2004) Protein Science , vol.13 , Issue.7 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2
  • 53
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • DOI 10.1093/bioinformatics/btl677
    • Jones, D. Improving the accuracy of transmembrane protein topology prediction using evolutionary information Bioinformatics 2007, 23, 538-544 (Pubitemid 46522586)
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 538-544
    • Jones, D.T.1
  • 55
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • DOI 10.1016/j.jmb.2004.03.016, PII S0022283604002943
    • Kall, L.; Krogh, A.; Sonnhammer, E. A combined transmembrane topology and signal peptide prediction method J. Mol. Biol. 2004, 338, 1027-1036 (Pubitemid 38542831)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.5 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 56
    • 57249083976 scopus 로고    scopus 로고
    • SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology
    • Viklund, H.; Bernsel, A.; Skwark, M.; Elofsson, A. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology Bioinformatics 2008, 24, 2928-2929
    • (2008) Bioinformatics , vol.24 , pp. 2928-2929
    • Viklund, H.1    Bernsel, A.2    Skwark, M.3    Elofsson, A.4
  • 57
    • 67649472570 scopus 로고    scopus 로고
    • Transmembrane protein topology prediction using support vector machines
    • Nugent, T.; Jones, D. Transmembrane protein topology prediction using support vector machines BMC Bioinform. 2009, 10, 159
    • (2009) BMC Bioinform. , vol.10 , pp. 159
    • Nugent, T.1    Jones, D.2
  • 58
    • 57149112523 scopus 로고    scopus 로고
    • Transmembrane topology and signal peptide prediction using dynamic bayesian networks
    • Reynolds, S.; Kall, L.; Rife, M.; Bilmes, J.; Noble, W. Transmembrane topology and signal peptide prediction using dynamic bayesian networks PLoS Comput. Biol. 2008, 4, e1000213
    • (2008) PLoS Comput. Biol. , vol.4 , pp. 1000213
    • Reynolds, S.1    Kall, L.2    Rife, M.3    Bilmes, J.4    Noble, W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.