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Volumn 36, Issue 3, 1999, Pages 332-339

Estimates of the loss of main-chain conformational entropy of different residues on protein folding

Author keywords

Conformation; Conformational entropy; Hydrophobicity; Protein engineering; Protein folding

Indexed keywords

ALANINE; GLYCINE; PROTEIN;

EID: 0033566618     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990815)36:3<332::AID-PROT7>3.0.CO;2-H     Document Type: Article
Times cited : (23)

References (44)
  • 1
    • 0024745871 scopus 로고
    • The price of lost freedom: Entropy of bimolecular complex formation
    • Finkelstein AV, Janin J. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng 1989;3:1-3.
    • (1989) Protein Eng , vol.3 , pp. 1-3
    • Finkelstein, A.V.1    Janin, J.2
  • 2
    • 0030961726 scopus 로고    scopus 로고
    • Entropy in protein folding and in protein-protein interactions
    • Brady GP, Sharp KA. Entropy in protein folding and in protein-protein interactions. Curr Opin Struct Biol 1997;7:215-221.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 215-221
    • Brady, G.P.1    Sharp, K.A.2
  • 3
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1-63.
    • (1959) Adv Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 4
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible surface area in proteins
    • Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature (London) 1974;248:338-339.
    • (1974) Nature (London) , vol.248 , pp. 338-339
    • Chothia, C.1
  • 5
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 6
    • 0024199422 scopus 로고
    • Stability of protein structure and hydrophobic interaction
    • Privalov PL, Gill SJ. Stability of protein structure and hydrophobic interaction. Adv Protein Chem 1988;39:191-234.
    • (1988) Adv Protein Chem , vol.39 , pp. 191-234
    • Privalov, P.L.1    Gill, S.J.2
  • 7
    • 0023645034 scopus 로고
    • Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
    • Cornette JL, Cease KB, Margalit H, Spouge JL, Berzsofsky JA, DeLisi C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J Mol Biol 1987;195: 659-685.
    • (1987) J Mol Biol , vol.195 , pp. 659-685
    • Cornette, J.L.1    Cease, K.B.2    Margalit, H.3    Spouge, J.L.4    Berzsofsky, J.A.5    DeLisi, C.6
  • 8
    • 0000181415 scopus 로고
    • The influence of amino acid side-chains on the free energy of helix-coil transitions
    • Nemethy G, Leach SJ, Scheraga HA. The influence of amino acid side-chains on the free energy of helix-coil transitions. J Phys Chem 1966;70:998-1004.
    • (1966) J Phys Chem , vol.70 , pp. 998-1004
    • Nemethy, G.1    Leach, S.J.2    Scheraga, H.A.3
  • 9
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981;14:325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 10
    • 0001064378 scopus 로고
    • Free energy determination of polypeptide conformations generated by molecular dynamics
    • Di Nola A, Berendsen HJC, Edholm O. Free energy determination of polypeptide conformations generated by molecular dynamics. Macromolecules 1984;17:2044-2050.
    • (1984) Macromolecules , vol.17 , pp. 2044-2050
    • Di Nola, A.1    Berendsen, H.J.C.2    Edholm, O.3
  • 11
    • 0000349059 scopus 로고
    • Configuration entropy of the alanine dipeptide in vacuum and in solution: A molecular dynamics study
    • Brady J, Karplus M. Configuration entropy of the alanine dipeptide in vacuum and in solution: a molecular dynamics study. J Am Chem Soc 1985;107:6013-6015.
    • (1985) J Am Chem Soc , vol.107 , pp. 6013-6015
    • Brady, J.1    Karplus, M.2
  • 13
    • 0024362070 scopus 로고
    • On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3 and Hy-HEL-5
    • Novotny J, Bruccoleri RE, Saul FA. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3 and Hy-HEL-5. Biochemistry 1989;28:4735-4749.
    • (1989) Biochemistry , vol.28 , pp. 4735-4749
    • Novotny, J.1    Bruccoleri, R.E.2    Saul, F.A.3
  • 14
    • 0026665778 scopus 로고
    • Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix forming propensities
    • Creamer TP, Rose GD. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix forming propensities. Proc Natl Acad Sci USA 1992;89:5937-5941.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 5937-5941
    • Creamer, T.P.1    Rose, G.D.2
  • 15
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJE. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
    • (1993) J Mol Biol , vol.231 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.E.2
  • 16
    • 0027991081 scopus 로고
    • Estimation of changes in side-chain configurational entropy in binding and folding: General methods and application to helix formation
    • Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side-chain configurational entropy in binding and folding: General methods and application to helix formation. Proteins 1994;20:68-84.
    • (1994) Proteins , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 17
    • 0028178528 scopus 로고
    • Determination of α-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme
    • Blaber M, Zhang X, Lindstorm JD, Pepiot SD, Baase WA, Mathews BW. Determination of α-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. J Mol Biol 1994;235:600-624.
    • (1994) J Mol Biol , vol.235 , pp. 600-624
    • Blaber, M.1    Zhang, X.2    Lindstorm, J.D.3    Pepiot, S.D.4    Baase, W.A.5    Mathews, B.W.6
  • 18
    • 0028343413 scopus 로고
    • Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
    • Koehl P, Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994;239:249-275.
    • (1994) J Mol Biol , vol.239 , pp. 249-275
    • Koehl, P.1    Delarue, M.2
  • 19
    • 0028174101 scopus 로고
    • Protein side-chain conformational entropy derived from fusion data - Comparison with other empirical scales
    • Sternberg MJE, Chickos JS. Protein side-chain conformational entropy derived from fusion data - comparison with other empirical scales. Protein Eng 1994;7:149-155.
    • (1994) Protein Eng , vol.7 , pp. 149-155
    • Sternberg, M.J.E.1    Chickos, J.S.2
  • 20
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding
    • D'Aquino JA, Gomes J, Hilser VJ, Lee KH, Amzel LM, Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins 1996;25:143-156.
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1    Gomes, J.2    Hilser, V.J.3    Lee, K.H.4    Amzel, L.M.5    Freire, E.6
  • 21
    • 0031842913 scopus 로고    scopus 로고
    • Main-chain conformational features at different conformations of the side-chains in proteins
    • Chakrabarti P, Pal D. Main-chain conformational features at different conformations of the side-chains in proteins. Protein Eng 1998;11:631-647.
    • (1998) Protein Eng , vol.11 , pp. 631-647
    • Chakrabarti, P.1    Pal, D.2
  • 22
    • 0027160197 scopus 로고
    • Backbone dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack Jr RL, Karplus M. Backbone dependent rotamer library for proteins: application to side-chain prediction. J Mol Biol 1993;230:543-571.
    • (1993) J Mol Biol , vol.230 , pp. 543-571
    • Dunbrack R.L., Jr.1    Karplus, M.2
  • 23
    • 0028429178 scopus 로고
    • Conformational analysis of the backbone dependent rotamer preferences of protein side-chains
    • Dunbrack Jr RL, Karplus M. Conformational analysis of the backbone dependent rotamer preferences of protein side-chains. Nature Struct Biol 1994;1:334-340.
    • (1994) Nature Struct Biol , vol.1 , pp. 334-340
    • Dunbrack R.L., Jr.1    Karplus, M.2
  • 24
    • 0029063337 scopus 로고
    • Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone
    • Stites WE, Pranata J. Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone. Proteins 1995;22:132-140.
    • (1995) Proteins , vol.22 , pp. 132-140
    • Stites, W.E.1    Pranata, J.2
  • 28
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 29
    • 0023769808 scopus 로고
    • Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system
    • Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, Wolff J, Genest M, Hagler AT. Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins 1988;4:31-47.
    • (1988) Proteins , vol.4 , pp. 31-47
    • Dauber-Osguthorpe, P.1    Roberts, V.A.2    Osguthorpe, D.J.3    Wolff, J.4    Genest, M.5    Hagler, A.T.6
  • 30
    • 0023430560 scopus 로고
    • Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding
    • Matthews BW, Nicholson H, Becktel WJ. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci USA 1987;84:6663-6667.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6663-6667
    • Matthews, B.W.1    Nicholson, H.2    Becktel, W.J.3
  • 31
    • 0025065382 scopus 로고
    • Glycine to alanine substitutions in helices of glyceraldehyde-3-phosphate dehydrogenase: Effects on stability
    • Ganter C, Plückthun A. Glycine to alanine substitutions in helices of glyceraldehyde-3-phosphate dehydrogenase: effects on stability. Biochemistry 1990;29:9395-9402.
    • (1990) Biochemistry , vol.29 , pp. 9395-9402
    • Ganter, C.1    Plückthun, A.2
  • 32
    • 0026755510 scopus 로고
    • Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: Evidence for mutational effects on the free energy of the denatured state
    • Green SM, Meeker AK, Shortle D. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state. Biochemistry 1992;31:5717-5728.
    • (1992) Biochemistry , vol.31 , pp. 5717-5728
    • Green, S.M.1    Meeker, A.K.2    Shortle, D.3
  • 33
    • 0022965255 scopus 로고
    • Stabilization of λ repressor against thermal denaturation by site-directed Gly → Ala changes in α-helix
    • Hecht MH, Sturtevant JM, Sauer RT. Stabilization of λ repressor against thermal denaturation by site-directed Gly → Ala changes in α-helix. Proteins 1986;1:43-46.
    • (1986) Proteins , vol.1 , pp. 43-46
    • Hecht, M.H.1    Sturtevant, J.M.2    Sauer, R.T.3
  • 34
    • 0023038088 scopus 로고
    • A new way of enhancing the thermostability of proteases
    • Imanaka T, Shibazaki M, Takagi M. A new way of enhancing the thermostability of proteases. Nature (London) 1986;324:695-697.
    • (1986) Nature (London) , vol.324 , pp. 695-697
    • Imanaka, T.1    Shibazaki, M.2    Takagi, M.3
  • 35
    • 0026728020 scopus 로고
    • Cumulative stabilizing effects of glycine to alanine substitutions in Bacillus subtilis neutral protease
    • Margarit I, Campagnoli S, Frigerio F, Grandi G, De FV, Fontana A. Cumulative stabilizing effects of glycine to alanine substitutions in Bacillus subtilis neutral protease. Protein Eng 1992;5:543-550.
    • (1992) Protein Eng , vol.5 , pp. 543-550
    • Margarit, I.1    Campagnoli, S.2    Frigerio, F.3    Grandi, G.4    De, F.V.5    Fontana, A.6
  • 36
    • 0025005525 scopus 로고
    • Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
    • Shortle D, Stites WE, Meeker AK. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 1990;29:8033-8041.
    • (1990) Biochemistry , vol.29 , pp. 8033-8041
    • Shortle, D.1    Stites, W.E.2    Meeker, A.K.3
  • 37
    • 0024448349 scopus 로고
    • Addition of a methyl group changes both catalytic velocity and thermostability of the neutral protease from Bacillus stearothermophilus
    • Takagi M, Imanaka T. Addition of a methyl group changes both catalytic velocity and thermostability of the neutral protease from Bacillus stearothermophilus. FEBS Lett 1989;254:43-46.
    • (1989) FEBS Lett , vol.254 , pp. 43-46
    • Takagi, M.1    Imanaka, T.2
  • 38
    • 0000859498 scopus 로고
    • Glycyl residues in proteins and peptides: An analysis
    • Ramakrishnan C, Srinivasan N. Glycyl residues in proteins and peptides: an analysis. Curr Sci 1990;59:851-861.
    • (1990) Curr Sci , vol.59 , pp. 851-861
    • Ramakrishnan, C.1    Srinivasan, N.2
  • 39
    • 0031008576 scopus 로고    scopus 로고
    • Hydrophobicity regained
    • Karplus PA. Hydrophobicity regained. Protein Sci 1997;6:1302-1307.
    • (1997) Protein Sci , vol.6 , pp. 1302-1307
    • Karplus, P.A.1
  • 40
    • 0000484499 scopus 로고
    • Hydrophobic parameters π of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides
    • Fauchère J, Pliska V. Hydrophobic parameters π of amino acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 1983;18:369-375.
    • (1983) Eur J Med Chem , vol.18 , pp. 369-375
    • Fauchère, J.1    Pliska, V.2
  • 41
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 42
  • 43
    • 0019333534 scopus 로고
    • Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins
    • Ponnuswamy PK, Prabhakaran M, Manavalan P. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. Biochim Biophys Acta 1980;623:301-316.
    • (1980) Biochim Biophys Acta , vol.623 , pp. 301-316
    • Ponnuswamy, P.K.1    Prabhakaran, M.2    Manavalan, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.