메뉴 건너뛰기




Volumn 256, Issue 3, 1996, Pages 623-644

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading

Author keywords

Contact energy; Hydrophobicity; Residue packing energy; Sequence sampling weights; Sequence threading

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DATA BASE; ENERGY; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

EID: 0029919190     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0114     Document Type: Article
Times cited : (1077)

References (37)
  • 2
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J. U., Lüthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 4
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
    • (1993) Proteins: Struct. Funct. Genet. , vol.16 , pp. 92-112
    • Bryant, S.H.1    Lawrence, C.E.2
  • 5
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • Bryngelson, J. D. & Wolynes, P. G. (1987). Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA, 84, 7524-7528.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 7
    • 0025319917 scopus 로고
    • Conformations of folded proteins in restricted spaces
    • Covell, D. G. & Jernigan, R. L. (1990). Conformations of folded proteins in restricted spaces. Biochemistry, 29, 3287-3294.
    • (1990) Biochemistry , vol.29 , pp. 3287-3294
    • Covell, D.G.1    Jernigan, R.L.2
  • 8
    • 0025851973 scopus 로고
    • Prediction of protein folding from amino acid sequence over discrete conformation spaces
    • Crippen, G. M. (1991). Prediction of protein folding from amino acid sequence over discrete conformation spaces. Biochemistry, 30, 4232-4237.
    • (1991) Biochemistry , vol.30 , pp. 4232-4237
    • Crippen, G.M.1
  • 9
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • (Dayhoff, M. O., ed.), National Biomedical Research Foundation, Washington, DC
    • Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978). A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure 1978 (Dayhoff, M. O., ed.), vol. 3. suppl. 5, pp. 345-352, National Biomedical Research Foundation, Washington, DC.
    • (1978) Atlas of Protein Sequence and Structure 1978 , vol.3 , Issue.5 SUPPL. , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 10
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson, A. E., Baase, W A., Zhang, X.-J., Heinz, D. W., Blaber, M., Baldwin, E. P. & Matthews, B. W (1992). Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science, 255, 178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1    Baase, W.A.2    Zhang, X.-J.3    Heinz, D.W.4    Blaber, M.5    Baldwin, E.P.6    Matthews, B.W.7
  • 11
    • 0000484499 scopus 로고
    • Hydrophobic parameters π of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchère, V. L. & Pliška, V. (1983). Hydrophobic parameters π of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 18, 369-375.
    • (1983) Eur. J. Med. Chem. , vol.18 , pp. 369-375
    • Fauchère, V.L.1    Pliška, V.2
  • 12
    • 85030196110 scopus 로고    scopus 로고
    • A 3-D sequence independent representation of the protein databank
    • in the press
    • Fischer, D., Tsai, C. J., Nussinov, R. & Wolfson, H. J. (1996). A 3-D sequence independent representation of the protein databank. Protein Eng., in the press.
    • (1996) Protein Eng.
    • Fischer, D.1    Tsai, C.J.2    Nussinov, R.3    Wolfson, H.J.4
  • 13
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Go, N. (1983). Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12, 183-210.
    • (1983) Annu. Rev. Biophys. Bioeng. , vol.12 , pp. 183-210
    • Go, N.1
  • 14
    • 0343426297 scopus 로고
    • Why are the statistics of globular protein structures Boltzmann-like?
    • Gutin, A. M., Badretdinov, A. Y. & Finkelstein A. V. (1992). Why are the statistics of globular protein structures Boltzmann-like? Mol. Biol. (USSR), 26, 94-102.
    • (1992) Mol. Biol. (USSR) , vol.26 , pp. 94-102
    • Gutin, A.M.1    Badretdinov, A.Y.2    Finkelstein, A.V.3
  • 15
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models; the calculation of low energy conformations from potentials of mean force
    • Hendlich, M., Lackner, P., Weitckus, S., Floechner, H., Froschauer, R., Gottsbachner, K., Casari, G. & Sippl, M. J. (1990). Identification of native protein folds amongst a large number of incorrect models; the calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.
    • (1990) J. Mol. Biol. , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floechner, H.4    Froschauer, R.5    Gottsbachner, K.6    Casari, G.7    Sippl, M.J.8
  • 17
  • 18
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 19
    • 0027522362 scopus 로고
    • Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size
    • Lee, B. (1993). Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size. Protein Sci. 2, 733-738.
    • (1993) Protein Sci. , vol.2 , pp. 733-738
    • Lee, B.1
  • 20
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Lüthy R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 21
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov, V. N. & Crippen, G. M. (1992). Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227, 876-888.
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 22
    • 0023741058 scopus 로고
    • Hydrophobic stabilization in t4 lysozyme deter mined directly by multiple substitutions of ile3
    • Matsumura, M., Becktel, W. J. & Matthews, B. W. (1988). Hydrophobic stabilization in T4 lysozyme deter mined directly by multiple substitutions of Ile3. Nature, 334, 406-410.
    • (1988) Nature , vol.334 , pp. 406-410
    • Matsumura, M.1    Becktel, W.J.2    Matthews, B.W.3
  • 23
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 24
    • 0028075953 scopus 로고
    • Protein stability for single substitution mutants and the extent of local compactness in the denatured state
    • Miyazawa, S. & Jernigan, R. L. (1994). Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng. 7, 1209-1220.
    • (1994) Protein Eng. , vol.7 , pp. 1209-1220
    • Miyazawa, S.1    Jernigan, R.L.2
  • 25
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequences of two proteins
    • Needleman, S. B. & Wunsch, C. B. (1970). A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.B.2
  • 26
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 27
    • 0027504808 scopus 로고
    • Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
    • Nishikawa, K. & Matsuo, Y. (1993). Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng. 6, 811-820.
    • (1993) Protein Eng. , vol.6 , pp. 811-820
    • Nishikawa, K.1    Matsuo, Y.2
  • 28
    • 0021691918 scopus 로고
    • An analysis of incorrectly folded protein models; implications for structure predictions
    • Novotny J., Bruccoleri, R. E. & Karplus, M. (1984). An analysis of incorrectly folded protein models; implications for structure predictions. J. Mol. Biol. 177, 787-818.
    • (1984) J. Mol. Biol. , vol.177 , pp. 787-818
    • Novotny, J.1    Bruccoleri, R.E.2    Karplus, M.3
  • 29
    • 0015217634 scopus 로고
    • The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; establishment of a hydrophobicity scale
    • Nozaki, Y. & Tanford, C. (1971). The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxine solutions; establishment of a hydrophobicity scale. J. Biol. Chem. 246, 2211-2217.
    • (1971) J. Biol. Chem. , vol.246 , pp. 2211-2217
    • Nozaki, Y.1    Tanford, C.2
  • 30
    • 0027220647 scopus 로고
    • Identification and classification of protein fold families
    • Orengo, C. A., Flores, T. P., Taylor, W. R., & Thornton, J. M. (1993). Identification and classification of protein fold families. Protein Eng. 6, 485-500.
    • (1993) Protein Eng. , vol.6 , pp. 485-500
    • Orengo, C.A.1    Flores, T.P.2    Taylor, W.R.3    Thornton, J.M.4
  • 31
    • 0026777217 scopus 로고
    • Contribution of the hydrophobic effect to globular protein stability
    • Pace, C. N. (1992). Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 226, 29-35.
    • (1992) J. Mol. Biol. , vol.226 , pp. 29-35
    • Pace, C.N.1
  • 32
    • 0028270634 scopus 로고
    • Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
    • Sǎli, A., Shakhnovich, E. & Karplus, M. (1994). Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235, 1614-1636.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Sǎli, A.1    Shakhnovich, E.2    Karplus, M.3
  • 33
    • 0026076664 scopus 로고
    • Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
    • Sharp, K. A., Nicholls, A., Friedman, R. & Honig, B. (1991). Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry, 30, 9686-9697.
    • (1991) Biochemistry , vol.30 , pp. 9686-9697
    • Sharp, K.A.1    Nicholls, A.2    Friedman, R.3    Honig, B.4
  • 34
    • 0025005525 scopus 로고
    • Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
    • Shortle, D., Sites, W. E. & Meeker, A. K. (1990). Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry, 29, 8033-8041.
    • (1990) Biochemistry , vol.29 , pp. 8033-8041
    • Shortle, D.1    Sites, W.E.2    Meeker, A.K.3
  • 35
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force
    • Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 213, 859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 36
    • 0026704815 scopus 로고
    • Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
    • Sippl, M. J. & Weitckus, S. (1992). Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins: Struct. Funct. Genet. 13, 258-271.
    • (1992) Proteins: Struct. Funct. Genet. , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 37
    • 0023368698 scopus 로고
    • Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase a subunit
    • Yutani, K., Ogasawara, K., Tsujita, T. & Sugino, Y (1987). Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase a subunit. Proc. Natl Acad. Sci. USA, 84, 4441-4444.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 4441-4444
    • Yutani, K.1    Ogasawara, K.2    Tsujita, T.3    Sugino, Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.