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Volumn 287, Issue 3, 1999, Pages 675-694

Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble

Author keywords

Extrathermodynamic free energy relations; Folding kinetics; Protein structure; Transition state ensemble

Indexed keywords

CHYMOTRYPSIN INHIBITOR;

EID: 0033515615     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2613     Document Type: Article
Times cited : (101)

References (34)
  • 1
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: An evidence from the lattice model
    • Abkevich V. I., Gutin A. M., Shakhnovich E. I. Specific nucleus as the transition state for protein folding: an evidence from the lattice model. Biochemistry. 33:1994;10026-10036.
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 2
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • Bryngelson J. D., Wolynes P. G. Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA. 84:1987;7524-7528.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 3
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson J. D., Wolynes P. G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93:1989;6902-6915.
    • (1989) J. Phys. Chem. , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 6
    • 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. 3:1994;843-852.
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 7
    • 0029981188 scopus 로고    scopus 로고
    • Structure of the transition state for folding of a protein derived from experiment and simulation
    • Daggett V., Li A., Itzhaki L. S., Otzen D. E., Fersht A. R. Structure of the transition state for folding of a protein derived from experiment and simulation. J. Mol. Biol. 257:1996;430-440.
    • (1996) J. Mol. Biol. , vol.257 , pp. 430-440
    • Daggett, V.1    Li, A.2    Itzhaki, L.S.3    Otzen, D.E.4    Fersht, A.R.5
  • 8
    • 0032584281 scopus 로고    scopus 로고
    • Movement of the intermediate and rate determining transition state of barnase on the energy landscape with changing temperature
    • Dalby P. A., Oliveberg M., Fersht A. R. Movement of the intermediate and rate determining transition state of barnase on the energy landscape with changing temperature. Biochemistry. 37:1998;4674-4679.
    • (1998) Biochemistry , vol.37 , pp. 4674-4679
    • Dalby, P.A.1    Oliveberg, M.2    Fersht, A.R.3
  • 9
    • 0029781355 scopus 로고    scopus 로고
    • The folding mechanism of larger model proteins: Role of native structure
    • Dinner A. R., Šali A., Shakhnovich M. K. E. The folding mechanism of larger model proteins: role of native structure. Proc. Natl. Acad. Sci. USA. 93:1996;8356-8361.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 8356-8361
    • Dinner, A.R.1    Šali, A.2    Shakhnovich, M.K.E.3
  • 11
    • 0028856785 scopus 로고
    • Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
    • Fersht A. R. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA. 92:1995a;10869-10873.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 12
    • 0028958601 scopus 로고
    • Characterizing transition states in protein folding: An essential step in the puzzle
    • Fersht A. R. Characterizing transition states in protein folding: an essential step in the puzzle. Curr. Opin. Struct. Biol. 5:1995b;79-84.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 79-84
    • Fersht, A.R.1
  • 13
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht A. R. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7:1997;3-9.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 14
    • 0030623529 scopus 로고    scopus 로고
    • Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
    • Finkelstein A. V., Badretdinov A. Y. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. Fold. Design. 2:1997;115-121.
    • (1997) Fold. Design , vol.2 , pp. 115-121
    • Finkelstein, A.V.1    Badretdinov, A.Y.2
  • 15
    • 33947466111 scopus 로고
    • Theory of elastic mechanisms in fibrous proteins
    • Flory P. J. Theory of elastic mechanisms in fibrous proteins. J. Am. Chem. Soc. 78:1956;5222-5235.
    • (1956) J. Am. Chem. Soc. , vol.78 , pp. 5222-5235
    • Flory, P.J.1
  • 17
    • 0028935887 scopus 로고
    • Structure and stability of monomeric λ repressor: NMR evidence for two-state folding
    • Huang G. S., Oas T. G. Structure and stability of monomeric λ repressor: NMR evidence for two-state folding. Biochemistry. 34:1995;3884-3892.
    • (1995) Biochemistry , vol.34 , pp. 3884-3892
    • Huang, G.S.1    Oas, T.G.2
  • 18
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor-2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
    • Itzhaki L. S., Otzen D. E., Fersht A. R. The structure of the transition state for folding of chymotrypsin inhibitor-2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254:1995;260-288.
    • (1995) J. Mol. Biol. , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 19
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. i. the theory of linear systems
    • Jacobson H., Stockmayer W. H. Intramolecular reaction in polycondensations. i. the theory of linear systems. J. Chem. Phys. 18:1950;1600-1606.
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 20
    • 0031296703 scopus 로고    scopus 로고
    • Strain in the folding nucleus of chymotrypsin inhibitor 2
    • Ladurner A. G., Itzhaki L. S., Fersht A. R. Strain in the folding nucleus of chymotrypsin inhibitor 2. Fold. Des. 2:1997;363-368.
    • (1997) Fold. Des. , vol.2 , pp. 363-368
    • Ladurner, A.G.1    Itzhaki, L.S.2    Fersht, A.R.3
  • 21
    • 0026723063 scopus 로고
    • Protein folding funnels-a kinetic appoach to the sequence structure relationship
    • Leopold P. E., Montal M., Onuchic J. N. Protein folding funnels-a kinetic appoach to the sequence structure relationship. Proc. Natl Acad. Sci. USA. 89:1992;8721-8725.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 23
    • 0030334834 scopus 로고    scopus 로고
    • Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2
    • López-Hernándex E., Serrano L. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold. Design. 1:1996;43-55.
    • (1996) Fold. Design , vol.1 , pp. 43-55
    • López-Hernándex, E.1    Serrano, L.2
  • 24
    • 0001143109 scopus 로고
    • Helix-coil, liquid crystal, and spin glass transitions of a collapsed heteropolymer
    • Luthey-Schulten Z. A., Ramirez B. E., Wolynes P. G. Helix-coil, liquid crystal, and spin glass transitions of a collapsed heteropolymer. J. Phys. Chem. 99:1995;2177-2185.
    • (1995) J. Phys. Chem. , vol.99 , pp. 2177-2185
    • Luthey-Schulten, Z.A.1    Ramirez, B.E.2    Wolynes, P.G.3
  • 25
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S., Jernigan R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 218:1985;534-552.
    • (1985) Macromolecules , vol.218 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 26
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S., Jernigan R. L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:1996;623-644.
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 27
    • 0028447768 scopus 로고
    • Elucidating the folding problem of helical peptides using empirical parameters
    • Mu ñ V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nature Struct. Biol. 1:1994;399-409.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 399-409
    • Mu Ñ., V.1    Serrano, L.2
  • 30
    • 0001482546 scopus 로고    scopus 로고
    • Non-markovian configurational diffusion and reaction coordinates for protein folding
    • Plotkin S. S., Wolynes P. G. Non-markovian configurational diffusion and reaction coordinates for protein folding. Phys. Rev. Letters. 80:1998;5015-5018.
    • (1998) Phys. Rev. Letters , vol.80 , pp. 5015-5018
    • Plotkin, S.S.1    Wolynes, P.G.2
  • 31
    • 0033515614 scopus 로고    scopus 로고
    • Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble
    • Shoemaker B. A., Wolynes P. G. Exploring structures in protein folding funnels with free energy functionals: The denatured ensemble. J. Mol. Biol. 287:1999;657-674.
    • (1999) J. Mol. Biol. , vol.287 , pp. 657-674
    • Shoemaker, B.A.1    Wolynes, P.G.2
  • 33
    • 0000710672 scopus 로고    scopus 로고
    • Diffusive dynamics of the reaction coordinate for protein folding funnels
    • Socci N. D., Onuchic J. N., Wolynes P. G. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem.Phys. 104:1996;5860-5868.
    • (1996) J. Chem.Phys. , vol.104 , pp. 5860-5868
    • Socci, N.D.1    Onuchic, J.N.2    Wolynes, P.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.