메뉴 건너뛰기




Volumn 27, Issue 3, 1997, Pages 336-344

Mutation matrices and physical-chemical properties: Correlations and implications

Author keywords

hydrophobicity; local propensities; molecular evolution; protein stability; reverse hydrophobic effect

Indexed keywords

PROTEIN;

EID: 0030931016     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199703)27:3<336::AID-PROT2>3.0.CO;2-B     Document Type: Article
Times cited : (46)

References (57)
  • 1
    • 0023643422 scopus 로고
    • Genetic and structural analysis of the protein stability problem
    • Matthews, B.W. Genetic and structural analysis of the protein stability problem. Biochemistry 26:6885-6888, 1987.
    • (1987) Biochemistry , vol.26 , pp. 6885-6888
    • Matthews, B.W.1
  • 3
    • 0024273441 scopus 로고
    • Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles
    • Nicholson, H., Becktel, W.J., Matthews, B.W. Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles. Nature 336:651-656, 1988.
    • (1988) Nature , vol.336 , pp. 651-656
    • Nicholson, H.1    Becktel, W.J.2    Matthews, B.W.3
  • 4
    • 0026766573 scopus 로고
    • Structural and energetic consequences of disruptive mutations in a protein core
    • Lim, W.A., Farruggio, D.C., Sauer, R.T. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry 31:4324-4333, 1992.
    • (1992) Biochemistry , vol.31 , pp. 4324-4333
    • Lim, W.A.1    Farruggio, D.C.2    Sauer, R.T.3
  • 5
    • 0026532266 scopus 로고
    • Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme
    • Hurley, J.H., Baase, W.A., Matthews, B.W. Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme. J. Mol. Biol. 224:1143-1159, 1992.
    • (1992) J. Mol. Biol. , vol.224 , pp. 1143-1159
    • Hurley, J.H.1    Baase, W.A.2    Matthews, B.W.3
  • 6
    • 0026496539 scopus 로고
    • The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions
    • Hellinga, H.W., Wynn, R., Richards, F.M. The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions. Biochemistry 31:11203-11209, 1992.
    • (1992) Biochemistry , vol.31 , pp. 11203-11209
    • Hellinga, H.W.1    Wynn, R.2    Richards, F.M.3
  • 7
    • 0027093322 scopus 로고
    • Multiple alanine replacements within alpha-helix 126-134 of T4 lysozyme have independent, additive effects on both structure and stability
    • Zhang, X.-J., Baase, W.A., Matthews, B.W. Multiple alanine replacements within alpha-helix 126-134 of T4 lysozyme have independent, additive effects on both structure and stability. Protein Sci. 1:761-776, 1992.
    • (1992) Protein Sci. , vol.1 , pp. 761-776
    • Zhang, X.-J.1    Baase, W.A.2    Matthews, B.W.3
  • 8
    • 0027394606 scopus 로고
    • Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences
    • Eriksson, A.E., Baase, W.A., Matthews, B.W. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J. Mol. Biol. 229:747-769, 1993.
    • (1993) J. Mol. Biol. , vol.229 , pp. 747-769
    • Eriksson, A.E.1    Baase, W.A.2    Matthews, B.W.3
  • 9
    • 0028147533 scopus 로고
    • The crystal structure of a mutant protein with altered but improved hydrophobic core packing
    • Lim, W.A., Hodel, A., Sauer, R.T., Richards, F.M. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc. Natl. Acad. Sci. U.S.A. 91:423-427, 1994.
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 423-427
    • Lim, W.A.1    Hodel, A.2    Sauer, R.T.3    Richards, F.M.4
  • 10
    • 0026777217 scopus 로고
    • Contribution of the hydrophobic effect to globular protein stability
    • Pace, C.N. Contribution of the hydrophobic effect to globular protein stability. J. Mol. Biol. 226:29-35, 1992.
    • (1992) J. Mol. Biol. , vol.226 , pp. 29-35
    • Pace, C.N.1
  • 11
    • 0027256739 scopus 로고
    • Hydrogen bonding, hydrophobicity, packing and protein folding
    • Rose, G.D., Wolfenden, R. Hydrogen bonding, hydrophobicity, packing and protein folding. Ann. Rev. Biophys. Biomol. Struct. 22:381-409, 1993.
    • (1993) Ann. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 381-409
    • Rose, G.D.1    Wolfenden, R.2
  • 13
    • 0003218786 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff, M.O., Eck, R.V. (eds.). Silver Spring, MD: National Biomedical Research Foundation
    • Dayhoff, M.O., Eck, R.V. A model of evolutionary change in proteins. In: "Atlas of Protein Sequence and Structure." Vol. 3. Dayhoff, M.O., Eck, R.V. (eds.). Silver Spring, MD: National Biomedical Research Foundation, 1968:33-41.
    • (1968) Atlas of Protein Sequence and Structure , vol.3 , pp. 33-41
    • Dayhoff, M.O.1    Eck, R.V.2
  • 14
    • 0015243774 scopus 로고
    • Tests for comparing related amino-acid sequences
    • McLachlan, A.D. Tests for comparing related amino-acid sequences. J. Mol. Biol. 61:409-424, 1971.
    • (1971) J. Mol. Biol. , vol.61 , pp. 409-424
    • McLachlan, A.D.1
  • 15
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S., Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919, 1992.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 16
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D.T., Taylor, W.R., Thornton, J.M. A new approach to protein fold recognition. Nature 358:86-89, 1992.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 17
    • 0024267619 scopus 로고
    • Amino acid substitutions in structurally related proteins
    • Risler, J.L., Delorme, M.O., Delacroix, H., Henaut, A. Amino acid substitutions in structurally related proteins. J. Mol. Biol. 204:1019-1029, 1988.
    • (1988) J. Mol. Biol. , vol.204 , pp. 1019-1029
    • Risler, J.L.1    Delorme, M.O.2    Delacroix, H.3    Henaut, A.4
  • 18
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S.F. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219:555-565, 1991.
    • (1991) J. Mol. Biol. , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 19
    • 0027062943 scopus 로고
    • Environment-specific amino-acid substitution tables: Tertiary templates and prediction of protein folds
    • Overington, J., Donnelly, D., Johnson, M.S., Šali, A., Blundell, T.L. Environment-specific amino-acid substitution tables: Tertiary templates and prediction of protein folds. Protein Sci. 1:216-226, 1992.
    • (1992) Protein Sci. , vol.1 , pp. 216-226
    • Overington, J.1    Donnelly, D.2    Johnson, M.S.3    Šali, A.4    Blundell, T.L.5
  • 20
    • 0028153788 scopus 로고
    • A mutation data matrix for transmembrane proteins
    • Jones, D.T., Taylor, W.R., Thornton, J.M. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275, 1994.
    • (1994) FEBS Lett. , vol.339 , pp. 269-275
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 21
    • 0023050277 scopus 로고
    • An algorithm for secondary structure determination in proteins based on sequence similarity
    • Levin, J.M., Robson, B., Gamier, J. An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Lett. 205:303-308, 1986.
    • (1986) FEBS Lett. , vol.205 , pp. 303-308
    • Levin, J.M.1    Robson, B.2    Gamier, J.3
  • 22
    • 0013889249 scopus 로고
    • An improved method of testing for evolutionary homology
    • Fitch, W.M. An improved method of testing for evolutionary homology. J. Mol. Biol. 16:9-16, 1966.
    • (1966) J. Mol. Biol. , vol.16 , pp. 9-16
    • Fitch, W.M.1
  • 23
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham, R. Amino acid difference formula to help explain protein evolution. Science 185:862-864, 1974.
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 24
    • 0018415510 scopus 로고
    • Two types of amino acid substitutions in protein evolution
    • Miyata, T., Miyazawa, S., Yasunaga, T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:219-236, 1979.
    • (1979) J. Mol. Evol. , vol.12 , pp. 219-236
    • Miyata, T.1    Miyazawa, S.2    Yasunaga, T.3
  • 25
    • 0021712450 scopus 로고
    • Aligning amino-acid sequences: A comparison of commonly used methods
    • Feng, D.F., Johnson, M.S., Doolittle, R.F. Aligning amino-acid sequences: A comparison of commonly used methods. J. Mol. Evol. 21:112-125, 1985.
    • (1985) J. Mol. Evol. , vol.21 , pp. 112-125
    • Feng, D.F.1    Johnson, M.S.2    Doolittle, R.F.3
  • 26
    • 0023286275 scopus 로고
    • New scoring matrix for amino acid residue exchange based on residue characteristic physical parameters
    • Rao, J.K.M. New scoring matrix for amino acid residue exchange based on residue characteristic physical parameters. Int. J. Pept. Protein Res. 29:276-281, 1987.
    • (1987) Int. J. Pept. Protein Res. , vol.29 , pp. 276-281
    • Rao, J.K.M.1
  • 27
    • 0027191901 scopus 로고
    • Anew substitution matrix for protein sequence searches based on contact frequencies in protein structures
    • Miyazawa, S., Jernigan, R.L. Anew substitution matrix for protein sequence searches based on contact frequencies in protein structures. Protein Eng. 6:267-278, 1993.
    • (1993) Protein Eng. , vol.6 , pp. 267-278
    • Miyazawa, S.1    Jernigan, R.L.2
  • 28
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons
    • Johnson, M.S., Overington, J.P. A structural basis for sequence comparisons. J. Mol. Biol. 233:716-738, 1993.
    • (1993) J. Mol. Biol. , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 29
    • 0028092214 scopus 로고
    • Amino acid substitution during functionally constrained divergent evolution of protein sequences
    • Benner, S.A., Cohen, M.A., Gerloff, D.L. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 7:1323-1332, 1994.
    • (1994) Protein Eng. , vol.7 , pp. 1323-1332
    • Benner, S.A.1    Cohen, M.A.2    Gerloff, D.L.3
  • 30
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices derived using bayesian statistics and phylogenetic trees
    • Koshi, J.M., Goldstein, R.A. Context-dependent optimal substitution matrices derived using bayesian statistics and phylogenetic trees. Protein Eng. 8:641-645, 1995.
    • (1995) Protein Eng. , vol.8 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 31
    • 0030309852 scopus 로고
    • Correlating mutation matrices with thermodynamic and physical-chemical properties
    • Hunter, L., Klein, T. (eds.). Singapore: World Scientific
    • Koshi, J.M., Goldstein, R.A. Correlating mutation matrices with thermodynamic and physical-chemical properties. In: Pacific Symposium on Biocomputing '96. Hunter, L., Klein, T. (eds.). Singapore: World Scientific, 1995:488-499.
    • (1995) Pacific Symposium on Biocomputing '96 , pp. 488-499
    • Koshi, J.M.1    Goldstein, R.A.2
  • 32
    • 0026605537 scopus 로고
    • Clustal v: Improved software for multiple sequence alignment
    • Higgins, D.G., Bleasby, A.J., Fuchs, R. Clustal v: Improved software for multiple sequence alignment. CABIOS 8:189-191, 1992.
    • (1992) CABIOS , vol.8 , pp. 189-191
    • Higgins, D.G.1    Bleasby, A.J.2    Fuchs, R.3
  • 33
    • 0021931978 scopus 로고
    • Statistical analysis of the physical properties of the 20 naturally occurring amino acids
    • Kidera, A., Konishi, Y., Oka, M., Oi, T., Scheraga, H.A. Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J. Protein Chem. 4:23-55, 1985.
    • (1985) J. Protein Chem. , vol.4 , pp. 23-55
    • Kidera, A.1    Konishi, Y.2    Oka, M.3    Oi, T.4    Scheraga, H.A.5
  • 34
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii, K., Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9:27-36, 1996.
    • (1996) Protein Eng. , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 35
    • 0000484499 scopus 로고
    • Hydrophobic parameters of amino acid-side chains from the partitioning of n-acetyl-amino-acid amides
    • Fauchere, J., Pliska, V. Hydrophobic parameters of amino acid-side chains from the partitioning of n-acetyl-amino-acid amides. Eur. J. Med. Chem. 18:369-375, 1983.
    • (1983) Eur. J. Med. Chem. , vol.18 , pp. 369-375
    • Fauchere, J.1    Pliska, V.2
  • 36
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
    • Radzicka, A., Wolfenden, R. Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 27:1664-1670, 1988.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 37
    • 0007544025 scopus 로고
    • Denaturation of proteins and enzymes
    • McElroy, W.D., Glass, B. (eds.). Baltimore: Johns Hopkins Press
    • Kauzmann, W. Denaturation of proteins and enzymes. In: "The Mechanism of Enzyme Action." McElroy, W.D., Glass, B. (eds.). Baltimore: Johns Hopkins Press, 1954:70-120.
    • (1954) The Mechanism of Enzyme Action , pp. 70-120
    • Kauzmann, W.1
  • 38
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann, W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63, 1959.
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 40
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • Richards, F.M. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977.
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 42
    • 0028958462 scopus 로고
    • Conservation of salt bridges in protein families
    • Schueler, O., Margalit, H. Conservation of salt bridges in protein families. J. Mol. Biol. 248:125-135, 1995.
    • (1995) J. Mol. Biol. , vol.248 , pp. 125-135
    • Schueler, O.1    Margalit, H.2
  • 43
    • 0003128793 scopus 로고
    • Prediction of protein structural classes from amino acid compositions
    • Fasman, G.D. (ed.). New York: Plenum Press
    • Chou, P.Y. Prediction of protein structural classes from amino acid compositions. In: "Prediction of Protein Structure and the Principles of Protein Conformation." Fasman, G.D. (ed.). New York: Plenum Press, 1989:549-586.
    • (1989) Prediction of Protein Structure and the Principles of Protein Conformation , pp. 549-586
    • Chou, P.Y.1
  • 44
    • 0028178865 scopus 로고
    • Alpha-helix-forming propensities in peptides and proteins
    • Creamer, T.P., Rose, G.D. Alpha-helix-forming propensities in peptides and proteins. Proteins 19:85-97, 1994.
    • (1994) Proteins , vol.19 , pp. 85-97
    • Creamer, T.P.1    Rose, G.D.2
  • 45
    • 0028176595 scopus 로고
    • Measurement of the beta-sheet-forming propensities of amino acids
    • Minor, D.L., Kim, P.S. Measurement of the beta-sheet-forming propensities of amino acids. Nature 367:660-663, 1994.
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor, D.L.1    Kim, P.S.2
  • 47
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill, K.A. Dominant forces in protein folding. Biochemistry 29:7133-7155, 1990.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 49
    • 0029115970 scopus 로고
    • Optimal local propensities for model proteins
    • Govindarajan, S., Goldstein, R.A. Optimal local propensities for model proteins. Proteins 22:413-418, 1995.
    • (1995) Proteins , vol.22 , pp. 413-418
    • Govindarajan, S.1    Goldstein, R.A.2
  • 50
    • 0030006663 scopus 로고    scopus 로고
    • Constructing amino-acid residue substitution classes maximally indicative of local protein structure
    • Thompson, M.J., Goldstein, R.A. Constructing amino-acid residue substitution classes maximally indicative of local protein structure. Proteins 25:28-37, 1996.
    • (1996) Proteins , vol.25 , pp. 28-37
    • Thompson, M.J.1    Goldstein, R.A.2
  • 51
    • 0025317840 scopus 로고
    • Reverse hydrophobic effects relieved by amino acid substitutions at a protein surface
    • Pakula, A.A., Sauer, R.T. Reverse hydrophobic effects relieved by amino acid substitutions at a protein surface. Nature 344:363-364, 1990.
    • (1990) Nature , vol.344 , pp. 363-364
    • Pakula, A.A.1    Sauer, R.T.2
  • 52
    • 0027464611 scopus 로고
    • Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: Implications for the denatured state
    • Bowler, B.E., May, K., Zaragoza, T., York, P., Dong, A., Caughey, W.S. Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: Implications for the denatured state. Biochemistry 32:183-190, 1993.
    • (1993) Biochemistry , vol.32 , pp. 183-190
    • Bowler, B.E.1    May, K.2    Zaragoza, T.3    York, P.4    Dong, A.5    Caughey, W.S.6
  • 53
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty, A., Kortemme, T., Baldwin, R.L. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 54
    • 0027193828 scopus 로고
    • Effects of alanine substitutions in alpha-helices of sperm whale myoglobin on protein stability
    • Pinker, R.J., Lin, L., Rose, G.D., Kallenback, N.R. Effects of alanine substitutions in alpha-helices of sperm whale myoglobin on protein stability. Protein Sci. 2:1099-1105, 1993.
    • (1993) Protein Sci. , vol.2 , pp. 1099-1105
    • Pinker, R.J.1    Lin, L.2    Rose, G.D.3    Kallenback, N.R.4
  • 55
    • 0028178528 scopus 로고
    • Determination of alpha-helix propensity within the context of a folded protein, sites 44 and 131 in bacteriophage t4 lysozyme
    • Blaber, M., Zhang, X.J., Lindstrom, J.D., Pepiot, S.D., Baase, W.A., Matthews, B.W. Determination of alpha-helix propensity within the context of a folded protein, sites 44 and 131 in bacteriophage t4 lysozyme. J. Mol. Biol. 235:600-624, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 600-624
    • Blaber, M.1    Zhang, X.J.2    Lindstrom, J.D.3    Pepiot, S.D.4    Baase, W.A.5    Matthews, B.W.6
  • 56
    • 0028846974 scopus 로고
    • Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins
    • West, M.W., Hecht, M.H. Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci. 4:2032-2039, 1995.
    • (1995) Protein Sci. , vol.4 , pp. 2032-2039
    • West, M.W.1    Hecht, M.H.2
  • 57
    • 0029064713 scopus 로고
    • Periodicity of polar and non-polar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides
    • Ziong, H., Buckwalter, B.L., Shieh, H., Hecht, M.H. Periodicity of polar and non-polar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. Proc. Natl. Acad. Sci. U.S.A. 92:6349-6353, 1995.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 6349-6353
    • Ziong, H.1    Buckwalter, B.L.2    Shieh, H.3    Hecht, M.H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.