메뉴 건너뛰기




Volumn 83, Issue 6, 2002, Pages 3032-3038

Validity of Gō models: Comparison with a solvent-shielded empirical energy decomposition

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE;

EID: 0036928148     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75308-3     Document Type: Article
Times cited : (51)

References (35)
  • 1
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • Alm, E., and D. Baker. 1999. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. U.S.A. 96:11305-11310.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 2
    • 0031160370 scopus 로고    scopus 로고
    • 1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure
    • Blanco, F. J., A. R. Ortiz, and L. Serrano. 1997. 1H and 15N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure. J. Biomol. NMR. 9:347-357.
    • (1997) J. Biomol. NMR , vol.9 , pp. 347-357
    • Blanco, F.J.1    Ortiz, A.R.2    Serrano, L.3
  • 3
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins. 21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 4
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
    • Chan, H. S., and K. A. Dill. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins. 30:2-33.
    • (1998) Proteins , vol.30 , pp. 2-33
    • Chan, H.S.1    Dill, K.A.2
  • 5
    • 0034703474 scopus 로고    scopus 로고
    • Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability
    • Cota, E., S. J. Hamill, S. B. Fowler, and J. Clarke. 2000. Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability. J. Mol. Biol. 302:713-725.
    • (2000) J. Mol. Biol. , vol.302 , pp. 713-725
    • Cota, E.1    Hamill, S.J.2    Fowler, S.B.3    Clarke, J.4
  • 6
    • 0009586942 scopus 로고    scopus 로고
    • Understanding protein folding via free-energy surfaces from theory and experiment
    • Dinner, A. R., A. Sali, L. J. Smith, C. M. Dobson, and M. Karplus. 2000. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25:331-339.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 331-339
    • Dinner, A.R.1    Sali, A.2    Smith, L.J.3    Dobson, C.M.4    Karplus, M.5
  • 7
    • 0033200063 scopus 로고    scopus 로고
    • Protein misfolding, evolution and disease
    • Dobson, C. M. 1999. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24:329-332.
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 329-332
    • Dobson, C.M.1
  • 8
    • 0035961329 scopus 로고    scopus 로고
    • The structural basis of protein folding and its links with human disease
    • Dobson, C. M. 2001. The structural basis of protein folding and its links with human disease. Phil. Trans. R. Soc. Lond. B. 356:133-145.
    • (2001) Phil. Trans. R. Soc. Lond. B. , vol.356 , pp. 133-145
    • Dobson, C.M.1
  • 9
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 12
    • 0033613131 scopus 로고    scopus 로고
    • A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
    • Galzitskaya, O. V., and A. V. Finkelstein. 1999. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Sci. U.S.A. 96:11299-11304.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 11299-11304
    • Galzitskaya, O.V.1    Finkelstein, A.V.2
  • 13
    • 0040974381 scopus 로고    scopus 로고
    • The three-dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen
    • Garcia-Saez, I., D. Reverter, J. Vendrell, F. X. Avilés, and M. Coll. 1997. The three-dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen. EMBO J. 16:6906-6913.
    • (1997) EMBO J. , vol.16 , pp. 6906-6913
    • Garcia-Saez, I.1    Reverter, D.2    Vendrell, J.3    Avilés, F.X.4    Coll, M.5
  • 14
    • 0030584660 scopus 로고    scopus 로고
    • Immunoglobulin-like modules from titin 1-band: Extensible components of muscle elasticity
    • Improta, S., A. S. Politou, and A. Pastore. 1996. Immunoglobulin-like modules from titin 1-band: Extensible components of muscle elasticity. Structure. 4:323-337.
    • (1996) Structure , vol.4 , pp. 323-337
    • Improta, S.1    Politou, A.S.2    Pastore, A.3
  • 15
    • 0030626588 scopus 로고    scopus 로고
    • The Levinthal paradox: Yesterday and today
    • Karplus, M. 1997. The Levinthal paradox: Yesterday and today. Fold. Des. 2:S69-S75.
    • (1997) Fold. Des. , vol.2
    • Karplus, M.1
  • 16
    • 0002770218 scopus 로고
    • Protein folding: Theoretical studies of thermodynamics and dynamics
    • T. E. Creighton, editors. W. H. Freeman & Co., New York
    • Karplus, M., and E. Shakhnovich. 1992. Protein folding: Theoretical studies of thermodynamics and dynamics. In Protein Folding. T. E. Creighton, editors. W. H. Freeman & Co., New York. 127-195.
    • (1992) Protein Folding , pp. 127-195
    • Karplus, M.1    Shakhnovich, E.2
  • 17
    • 0031465967 scopus 로고    scopus 로고
    • "New view" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis, T., and M. Karplus. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 18
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis, T., and M. Karplus. 1999. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288:477-487.
    • (1999) J. Mol. Biol. , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 19
    • 0026490256 scopus 로고
    • Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein
    • Leahy, D. J., W. A. Hendrickson, I. Aukhil, and H. P. Erickson. 1992. Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science. 258:987-991.
    • (1992) Science , vol.258 , pp. 987-991
    • Leahy, D.J.1    Hendrickson, W.A.2    Aukhil, I.3    Erickson, H.P.4
  • 20
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • Li, A., and V. Daggett. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. U.S.A. 91:10430-10434.
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 21
    • 0023652256 scopus 로고
    • Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds
    • McPhalen, C. A., and M. N. James. 1987. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry. 26:261-269.
    • (1987) Biochemistry , vol.26 , pp. 261-269
    • McPhalen, C.A.1    James, M.N.2
  • 22
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • Mufioz, V., and W. A. Eaton. 1999. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. U.S.A. 96:11311-11316.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 11311-11316
    • Mufioz, V.1    Eaton, W.A.2
  • 23
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular dynamics system
    • Neria, E., S. Fischer, and M. Karplus. 1996. Simulation of activation free energies in molecular dynamics system. J. Chem. Phys. 105:1902-1921.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 24
    • 0028865428 scopus 로고
    • Structural factors contributing to the hydrophobic effect: The partly exposed hydrophohic minicore in chymotrypsin inhibitor 2
    • Otzen, D. E., M. Rheinnecker, and A. R. Fersht. 1995. Structural factors contributing to the hydrophobic effect: The partly exposed hydrophohic minicore in chymotrypsin inhibitor 2. Biochemistry. 34:13051-13058.
    • (1995) Biochemistry , vol.34 , pp. 13051-13058
    • Otzen, D.E.1    Rheinnecker, M.2    Fersht, A.R.3
  • 25
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of Φ-values in protein folding kinetics
    • Ozkan, S. B., I. Bahar, and K. A. Dill. 2001. Transition states and the meaning of Φ-values in protein folding kinetics. Nature Struct. Biol. 8:765-769.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 27
    • 0037093654 scopus 로고    scopus 로고
    • Native and non-native interactions along protein folding and unfolding pathways
    • Paci, E., M. Vendruscolo, and M. Karplus. 2002b. Native and non-native interactions along protein folding and unfolding pathways. Proteins. 47:379-392.
    • (2002) Proteins , vol.47 , pp. 379-392
    • Paci, E.1    Vendruscolo, M.2    Karplus, M.3
  • 28
    • 0026522991 scopus 로고
    • Threedimensional structure of acylphosphatase. Refinement and structure analysis
    • Pastore, A., V. Saudek, G. Ramponi, and R. J. Williams. 1992. Threedimensional structure of acylphosphatase. Refinement and structure analysis. J. Mol. Biol. 224:427-440.
    • (1992) J. Mol. Biol. , vol.224 , pp. 427-440
    • Pastore, A.1    Saudek, V.2    Ramponi, G.3    Williams, R.J.4
  • 29
    • 0027220867 scopus 로고
    • α-lactalbumin possesses a distinct zinc binding site
    • Ren, J., K. R. Acharya, and D. I. Stuart. 1993. α-lactalbumin possesses a distinct zinc binding site. J. Biol. Chem. 268:19292-19298.
    • (1993) J. Biol. Chem. , vol.268 , pp. 19292-19298
    • Ren, J.1    Acharya, K.R.2    Stuart, D.I.3
  • 30
    • 0035917318 scopus 로고    scopus 로고
    • The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
    • Shimada, J., E. L. Kussell, and E. I. Shakhnovich. 2001. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 308:79-95.
    • (2001) J. Mol. Biol. , vol.308 , pp. 79-95
    • Shimada, J.1    Kussell, E.L.2    Shakhnovich, E.I.3
  • 31
    • 0032742688 scopus 로고    scopus 로고
    • Gō-ing for the prediction of protein folding mechanisms
    • Takada, S. 1999. Gō-ing for the prediction of protein folding mechanisms. Proc. Natl. Acad. Sci. U.S.A. 96:11698-11700.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 11698-11700
    • Takada, S.1
  • 32
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
    • Taketomi, H., Y. Ueda, and N. Go. 1975. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Pept. Protein Res. 7:445-459.
    • (1975) Int. J. Pept. Protein Res. , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 33
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo, M., E. Paci, C. M. Dobson, and M. Karplus. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 34
    • 0031893269 scopus 로고    scopus 로고
    • The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
    • Xu, J., W. A. Baase, E. Baldwin, and B. W. Matthews. 1998. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Prot. Sci. 7:158-177.
    • (1998) Prot. Sci. , vol.7 , pp. 158-177
    • Xu, J.1    Baase, W.A.2    Baldwin, E.3    Matthews, B.W.4
  • 35
    • 0033598375 scopus 로고    scopus 로고
    • Interpreting the folding kinetics of helical proteins
    • Zhou, Y., and M. Karplus. 1999. Interpreting the folding kinetics of helical proteins. Nature. 401:400-403.
    • (1999) Nature , vol.401 , pp. 400-403
    • Zhou, Y.1    Karplus, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.