메뉴 건너뛰기




Volumn 283, Issue 2, 1998, Pages 489-506

Principles governing amino acid composition of integral membrane proteins: Application to topology prediction

Author keywords

Distribution of amino acids; Hidden Markov model; Topology prediction for helical transmembrane proteins; Transmembrane helices

Indexed keywords

AMINO ACID; MEMBRANE PROTEIN;

EID: 0032561132     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2107     Document Type: Article
Times cited : (969)

References (57)
  • 2
    • 0027174134 scopus 로고
    • Prediction of proteins secondary structure by the hidden Markov model
    • Asai K., Hayamizu S., Handa K. Prediction of proteins secondary structure by the hidden Markov model. Comp. Appl. Biosci. 9:1993;141-146
    • (1993) Comp. Appl. Biosci. , vol.9 , pp. 141-146
    • Asai, K.1    Hayamizu, S.2    Handa, K.3
  • 3
    • 0025796712 scopus 로고
    • The SWISS-PROT proteins sequence bank
    • Bairoch A., Boeckmann B. The SWISS-PROT proteins sequence bank. Nucl. Acids Res. 19:1991;2247-2249
    • (1991) Nucl. Acids Res. , vol.19 , pp. 2247-2249
    • Bairoch, A.1    Boeckmann, B.2
  • 5
    • 0017396017 scopus 로고
    • Topological asymmetry of phospholipids in membranes
    • Bergelson L., Barsukov L.I. Topological asymmetry of phospholipids in membranes. Science. 197:1977;224-230
    • (1977) Science , vol.197 , pp. 224-230
    • Bergelson, L.1    Barsukov, L.I.2
  • 9
    • 0029670785 scopus 로고    scopus 로고
    • A predictor of transmembrane alpha-helix domains of proteins based on neural networks
    • Casadio R., Fariselli P., Taroni C., Compiani M. A predictor of transmembrane alpha-helix domains of proteins based on neural networks. Eur. Biophys. J. 24:1996;165-178
    • (1996) Eur. Biophys. J. , vol.24 , pp. 165-178
    • Casadio, R.1    Fariselli, P.2    Taroni, C.3    Compiani, M.4
  • 10
    • 0031437768 scopus 로고    scopus 로고
    • Reduction of membrane proteins hydrophobicity by site-directed mutagenesis: Introduction of multiple polar residues in helix d of bacteriorhodopsin
    • Chen G.-Q., Gouaux E. Reduction of membrane proteins hydrophobicity by site-directed mutagenesis introduction of multiple polar residues in helix d of bacteriorhodopsin. Protein Eng. 10:1997;1061-1066
    • (1997) Protein Eng. , vol.10 , pp. 1061-1066
    • Chen, G.-Q.1    Gouaux, E.2
  • 11
    • 0025306403 scopus 로고
    • The use of gene fusions to determine the topology of all of the subunits of the cytochrome o terminal oxidase complex of Escherichia coli
    • Chepuri V., Gennis R.B. The use of gene fusions to determine the topology of all of the subunits of the cytochrome o terminal oxidase complex of Escherichia coli. J. Biol. Chem. 265:1990;12978-12986
    • (1990) J. Biol. Chem. , vol.265 , pp. 12978-12986
    • Chepuri, V.1    Gennis, R.B.2
  • 12
    • 0029051959 scopus 로고
    • A novel approach to predicting protein structural classes in a (20-1)-d amino acid composition space
    • Chou K.C. A novel approach to predicting protein structural classes in a (20-1)-d amino acid composition space. Proteins: Struct. Funct. Genet. 21:1995;319-344
    • (1995) Proteins: Struct. Funct. Genet. , vol.21 , pp. 319-344
    • Chou, K.C.1
  • 13
    • 0023645034 scopus 로고
    • Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
    • Cornette J.L., Cease K.B., Margalit H., Spouge L., Berzofsky J.A., DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195:1987;659-685
    • (1987) J. Mol. Biol. , vol.195 , pp. 659-685
    • Cornette, J.L.1    Cease, K.B.2    Margalit, H.3    Spouge, L.4    Berzofsky, J.A.5    Delisi, C.6
  • 14
  • 15
    • 0030759333 scopus 로고    scopus 로고
    • Prediction of transmembrane alpha-helices in prokariotic membrane proteins: The dense alignment surface method
    • Cserzo M., Wallin E., Simon I., von Heijne G., Elofsson A. Prediction of transmembrane alpha-helices in prokariotic membrane proteins the dense alignment surface method. Protein Eng. 10:1997;673-676
    • (1997) Protein Eng. , vol.10 , pp. 673-676
    • Cserzo, M.1    Wallin, E.2    Simon, I.3    Von Heijne, G.4    Elofsson, A.5
  • 16
    • 0025259440 scopus 로고
    • Epitopes of monoclonal antibodies which inhibit ubiquinol oxidase activity of Escherichia coli cytochrome d complex localize functional domain
    • Dueweke T.J., Gennis R.B. Epitopes of monoclonal antibodies which inhibit ubiquinol oxidase activity of Escherichia coli cytochrome d complex localize functional domain. J. Biol. Chem. 265:1990;4273-4277
    • (1990) J. Biol. Chem. , vol.265 , pp. 4273-4277
    • Dueweke, T.J.1    Gennis, R.B.2
  • 17
    • 0025881879 scopus 로고
    • Proteolysis of the cytochrome d complex with trypsin localizes a quinol oxidase domain
    • Dueweke T.J., Gennis R.B. Proteolysis of the cytochrome d complex with trypsin localizes a quinol oxidase domain. Biochemistry. 30:1991;3401-3406
    • (1991) Biochemistry , vol.30 , pp. 3401-3406
    • Dueweke, T.J.1    Gennis, R.B.2
  • 19
    • 0021691817 scopus 로고
    • Analysis of membrane and surface proteins sequences with the hydrophobic moment plot
    • Eisenberg D., Schwartz E., Komáromy M., Wall R. Analysis of membrane and surface proteins sequences with the hydrophobic moment plot. J. Mol. Biol. 179:1984;125-142
    • (1984) J. Mol. Biol. , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwartz, E.2    Komáromy, M.3    Wall, R.4
  • 20
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman D.M., Steitz T.A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Chem. 15:1986;321-353
    • (1986) Annu. Rev. Biophys. Chem. , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 21
    • 0025371555 scopus 로고
    • A critical evaluation of the hydropathy profile of membrane proteins
    • Esposti M.D., Crimi M., Venturoli G. A critical evaluation of the hydropathy profile of membrane proteins. Eur. J. Biochem. 190:1990;207-219
    • (1990) Eur. J. Biochem. , vol.190 , pp. 207-219
    • Esposti, M.D.1    Crimi, M.2    Venturoli, G.3
  • 22
    • 0031588960 scopus 로고    scopus 로고
    • Proteins topology recognition from secondary structure sequences: Application of the hidden Markov models to the alpha class proteins
    • Francesco V.D., Garnier J., Munson P.J. Proteins topology recognition from secondary structure sequences application of the hidden Markov models to the alpha class proteins. J. Mol. Biol. 267:1997;446-463
    • (1997) J. Mol. Biol. , vol.267 , pp. 446-463
    • Francesco, V.D.1    Garnier, J.2    Munson, P.J.3
  • 23
    • 0023750080 scopus 로고
    • β-galactoside gene fusions as probes for the cytoplasmic regions of subunits I and II of the membrane-bound cytochrome d terminal oxidase from Escherichia coli
    • Georgiou C.D., Dueweke T.J., Gennis R.B. β-galactoside gene fusions as probes for the cytoplasmic regions of subunits I and II of the membrane-bound cytochrome d terminal oxidase from Escherichia coli. J. Biol. Chem. 263:1988;13130-13137
    • (1988) J. Biol. Chem. , vol.263 , pp. 13130-13137
    • Georgiou, C.D.1    Dueweke, T.J.2    Gennis, R.B.3
  • 25
    • 0032518244 scopus 로고    scopus 로고
    • It's not just a phase: Crystallization and x-ray structure determination of bacteriorhodopsin in lipidic cubic phases
    • Gouaux E. It's not just a phase crystallization and x-ray structure determination of bacteriorhodopsin in lipidic cubic phases. Structure. 15:1998;5-10
    • (1998) Structure , vol.15 , pp. 5-10
    • Gouaux, E.1
  • 26
    • 0028919502 scopus 로고
    • Prediction of protein secondary structures from their hydrophobic characteristics
    • Gromiha M.M., Ponnuswamy P.K. Prediction of protein secondary structures from their hydrophobic characteristics. Int. J. Peptide Proteins Res. 45:1995;225-240
    • (1995) Int. J. Peptide Proteins Res. , vol.45 , pp. 225-240
    • Gromiha, M.M.1    Ponnuswamy, P.K.2
  • 28
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: Extension and analysis of the basic method
    • Hughey R., Krogh A. Hidden Markov models for sequence analysis extension and analysis of the basic method. Comp. Appl. Biosci. 12:1996;95-107
    • (1996) Comp. Appl. Biosci , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 29
    • 0028890031 scopus 로고
    • Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans
    • Iwata S., Ostermeier C., Ludwig B., Michel H. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature. 376:1995;660-669
    • (1995) Nature , vol.376 , pp. 660-669
    • Iwata, S.1    Ostermeier, C.2    Ludwig, B.3    Michel, H.4
  • 30
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones D.T., Taylor W.R., Thorton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33:1994;3038-3049
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thorton, J.M.3
  • 32
    • 0027944605 scopus 로고
    • A hidden Markov model that finds genes in E. coli DNA
    • Krogh A., Mian I.S., Haussler D. A hidden Markov model that finds genes in E. coli DNA. Nucl. Acids Res. 22:1994;4768-4778
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4768-4778
    • Krogh, A.1    Mian, I.S.2    Haussler, D.3
  • 34
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 36
    • 0025320805 scopus 로고
    • An Expectation Maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • Lawrence C.E., Reilly A.A. An Expectation Maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Struct. Funct. Genet. 7:1990;41-51
    • (1990) Proteins: Struct. Funct. Genet. , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 37
    • 0028061987 scopus 로고
    • A neural network model for the prediction of membrane-spanning amino acid sequences
    • Lohmann R., Schneider G., Behrens D., Wrede P. A neural network model for the prediction of membrane-spanning amino acid sequences. Protein Sci. 3:1994;1597-1601
    • (1994) Protein Sci. , vol.3 , pp. 1597-1601
    • Lohmann, R.1    Schneider, G.2    Behrens, D.3    Wrede, P.4
  • 38
    • 0028239038 scopus 로고
    • Discrimination of intercellular and extracellular proteins using amino acid composition and residue-pair frequencies
    • Nakashima H., Nishikawa K. Discrimination of intercellular and extracellular proteins using amino acid composition and residue-pair frequencies. J. Mol. Biol. 238:1994;54-61
    • (1994) J. Mol. Biol. , vol.238 , pp. 54-61
    • Nakashima, H.1    Nishikawa, K.2
  • 39
    • 0028279520 scopus 로고
    • Prediction of transmembrane segments in proteins utilising multiple sequence alignments
    • Persson B., Argos P. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol. 237:1994;182-192
    • (1994) J. Mol. Biol. , vol.237 , pp. 182-192
    • Persson, B.1    Argos, P.2
  • 40
    • 0030020734 scopus 로고    scopus 로고
    • Topology prediction of membrane proteins
    • Persson B., Argos P. Topology prediction of membrane proteins. Protein Sci. 5:1996;363-371
    • (1996) Protein Sci. , vol.5 , pp. 363-371
    • Persson, B.1    Argos, P.2
  • 41
    • 0027382240 scopus 로고
    • Prediction of transmembrane helices from hydrophobic characteristics of protein
    • Ponnuswamy P.K., Gromiha M.M. Prediction of transmembrane helices from hydrophobic characteristics of protein. Int. Peptide Protein Res. 42:1993;326-341
    • (1993) Int. Peptide Protein Res. , vol.42 , pp. 326-341
    • Ponnuswamy, P.K.1    Gromiha, M.M.2
  • 42
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner L.R. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE. 77:1989;257-286
    • (1989) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 44
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86% accuracy
    • Rost B., Fariselli P., Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5:1996;1704-1718
    • (1996) Protein Sci. , vol.5 , pp. 1704-1718
    • Rost, B.1    Fariselli, P.2    Casadio, R.3
  • 45
    • 0017356323 scopus 로고
    • Membrane asymmetry
    • Rothman J., Lenard J. Membrane asymmetry. Science. 195:1977;743-753
    • (1977) Science , vol.195 , pp. 743-753
    • Rothman, J.1    Lenard, J.2
  • 46
    • 0027264995 scopus 로고
    • Predicting the topology of eukaryotic membrane proteins
    • Sipos L., von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213:1993;1333-1340
    • (1993) Eur. J. Biochem. , vol.213 , pp. 1333-1340
    • Sipos, L.1    Von Heijne, G.2
  • 48
    • 0027477526 scopus 로고
    • Structural analysis based on state-space modeling
    • Stultz C.M., White J.V., Smith T.F. Structural analysis based on state-space modeling. Protein Sci. 2:1993;305-314
    • (1993) Protein Sci , vol.2 , pp. 305-314
    • Stultz, C.M.1    White, J.V.2    Smith, T.F.3
  • 50
    • 0028978516 scopus 로고
    • Independence divergence-generated binary trees of amino acids
    • Tusnády G.E., Tusnády G., Simon I. Independence divergence-generated binary trees of amino acids. Protein Eng. 8:1995;417-423
    • (1995) Protein Eng. , vol.8 , pp. 417-423
    • Tusnády, G.E.1    Tusnády, G.2    Simon, I.3
  • 51
    • 0026801560 scopus 로고
    • Topology of the membrane-bound alkane hydroxylase of pseudomonas oleovorans
    • van Beilen J., Penninga D., Witholt B. Topology of the membrane-bound alkane hydroxylase of pseudomonas oleovorans. J. Biol. Chem. 267:1992;9194-9201
    • (1992) J. Biol. Chem. , vol.267 , pp. 9194-9201
    • Van Beilen, J.1    Penninga, D.2    Witholt, B.3
  • 52
    • 0030791975 scopus 로고    scopus 로고
    • Anionic phospholipids are determinants of membrane protein topology
    • van Klompenburg W., Nilsson I., von Heijne G., de Kruijff B. Anionic phospholipids are determinants of membrane protein topology. EMBO J. 16:1997;4261-4266
    • (1997) EMBO J. , vol.16 , pp. 4261-4266
    • Van Klompenburg, W.1    Nilsson, I.2    Von Heijne, G.3    De Kruijff, B.4
  • 53
    • 0026716643 scopus 로고
    • Membrane protein structure prediction
    • von Heijne G. Membrane protein structure prediction. J. Mol. Biol. 225:1992;487-494
    • (1992) J. Mol. Biol. , vol.225 , pp. 487-494
    • Von Heijne, G.1
  • 54
    • 0029108665 scopus 로고
    • Membrane protein assembly: Rules of the game
    • von Heijne G. Membrane protein assembly rules of the game. BioEssays. 17:1994;25-30
    • (1994) BioEssays , vol.17 , pp. 25-30
    • Von Heijne, G.1
  • 55
    • 0026737314 scopus 로고
    • Structure of porin refined at 1.8 Å resolution
    • Weiss M., Schulz G. Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227:1992;493-509
    • (1992) J. Mol. Biol. , vol.227 , pp. 493-509
    • Weiss, M.1    Schulz, G.2
  • 56
    • 0028181528 scopus 로고
    • Protein classification by stochastic modeling and optimal filtering of amino-acid sequences
    • White J.V., Stultz C.M., Smith T.F. Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math. Biosci. 119:1993;35-75
    • (1993) Math. Biosci , vol.119 , pp. 35-75
    • White, J.V.1    Stultz, C.M.2    Smith, T.F.3
  • 57
    • 0027484363 scopus 로고
    • Identification of a residue in the translocation pathway of a membrane carrier
    • Yan R., Maloney P. Identification of a residue in the translocation pathway of a membrane carrier. Cell. 75:1993;37-44
    • (1993) Cell , vol.75 , pp. 37-44
    • Yan, R.1    Maloney, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.