Discrete molecular dynamics studies of the folding of a protein-like model

Folding and Design - Tập 3 - Trang 577-587 - 1998
Nikolay V. Dokholyan1, Sergey V. Buldyrev1, H Eugene Stanley1, Eugene I. Shakhnovich2
1Center for Polymer Studies, Physics Department, Boston University, Boston, MA 02215, USA
2Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA

Tài liệu tham khảo

Levinthal, 1968, Are there pathways for protein foldings?, J. Chim. Phys, 65, 44, 10.1051/jcp/1968650044 Go, 1983, Theoretical studies of protein folding, Annu. Rev. Biophys. Bioeng, 12, 183, 10.1146/annurev.bb.12.060183.001151 Karplus, 1994, Protein folding: theoretical studies of thermodynamics and dynamics, 127 Shakhnovich, 1997, Theoretical studies of protein-folding, thermodynamics and kinetics, Curr. Opin. Struct. Biol, 7, 29, 10.1016/S0959-440X(97)80005-X Taketomi, 1975, Studies on protein folding, unfolding and fluctuations by computer simulations, Int. J. Peptide Protein Res, 7, 445, 10.1111/j.1399-3011.1975.tb02465.x Go, 1981, Noninteracting local-structure model of folding and unfolding transition in globular proteins, I. Formulation. Biopolymers, 20, 991 Abe, 1981, Noninteracting local-structure model of folding and unfolding transition in globular proteins. II. Application to two-dimensional lattice proteins, Biopolymers, 20, 1013, 10.1002/bip.1981.360200512 Dill, 1985, Theory for the folding and stability of globular proteins, Biochemistry, 24, 1501, 10.1021/bi00327a032 Bryngelson, 1989, Intermediates and barrier crossing in a random energy model (with applications to protein folding), J. Phys. Chem, 93, 6902, 10.1021/j100356a007 Shakhnovich, 1994, Proteins with selected sequences fold into unique native conformation, Phys. Rev. Lett, 72, 3907, 10.1103/PhysRevLett.72.3907 Abkevich, 1994, Specific nucleus as the transition state for protein folding: evidence from the lattice model, Biochemistry, 33, 10026, 10.1021/bi00199a029 Gutin, 1995, Evolution-like selection of fast-folding model proteins, Proc. Natl Acad. Sci. USA, 92, 1282, 10.1073/pnas.92.5.1282 Shakhnovich, 1996, Conserved residues and the mechanism of protein folding, Nature, 379, 96, 10.1038/379096a0 Dill, 1990, Dominant forces in protein folding, Biochemistry, 29, 7133, 10.1021/bi00483a001 Creighton, 1992 Privaov, 1989, Thermodynamic problems of protein structure, Annu. Rev. Biophys. Chem, 18, 47, 10.1146/annurev.bb.18.060189.000403 Klimov, 1996, Criterion that determines the foldability of proteins, Phys. Rev. Lett, 76, 4070, 10.1103/PhysRevLett.76.4070 Baumgartner, 1987, Simulations of polymer models, 281 Irbäck, 1995, Sequence dependence of self-interacting random chains, J. Phys. A: Math. Gen, 28, 2121, 10.1088/0305-4470/28/8/006 Berriz, 1997, Cooperativity and stability in a Langevin model of protein like folding, J. Chem. Phys, 106, 9276, 10.1063/1.474039 Guo, 1997, Thermodynamics of protein folding: a statistical mechanical study of a small all-β-protein, Biopolymers, 42, 745, 10.1002/(SICI)1097-0282(199712)42:7<745::AID-BIP1>3.0.CO;2-T Zhou, 1997, Equilibrium thermodynamics of homopolymers and clusters: molecular dynamics and Monte-Carlo simulations of system with square-well interactions, J. Chem. Phys, 107, 10691, 10.1063/1.474186 Zhou, 1997, Folding thermodynamics of a three-helix-bundle protein, Proc. Natl Acad. Sci. USA, 94, 14429, 10.1073/pnas.94.26.14429 Doi, 1996 Shakhnovich, 1993, Engineering of stable and fast folding sequences of model proteins, Proc. Natl Acad. Sci. USA, 90, 7195, 10.1073/pnas.90.15.7195 Abkevich, 1996, Improved design of stable and fast-folding model proteins, Fold. Des, 1, 221, 10.1016/S1359-0278(96)00033-8 Alder, 1959, Studies in molecular dynamics. I. General method, J. Chem. Phys, 31, 459, 10.1063/1.1730376 Grosberg, 1997 Allen, 1987, Molecular dynamics, 102 Rapaport, 1997, Step potential, 285 Mirny, 1996, Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model, Fold. Des, 1, 103, 10.1016/S1359-0278(96)00019-3 Landau, 1980 Wetlaufer, 1973, Nucleation, rapid folding, and globular interchain regions in proteins, Proc. Natl Acad. Sci. USA, 70, 691, 10.1073/pnas.70.3.697 Karplus, 1976, Protein-folding dynamics, Nature, 260, 404, 10.1038/260404a0 Abkevich, 1995, Domains in folding of model proteins, Protein Sci, 4, 1167, 10.1002/pro.5560040615 Lazaridis, 1997, “New view” of protein folding reconciled with the old through multiple unfolding simulations, Science, 278, 1928, 10.1126/science.278.5345.1928 Anifsen, 1973, Principles that govern the folding of the protein chains, Science, 181, 223, 10.1126/science.181.4096.223 Tsong, 1978, Effects of solvent viscosity and different guanidine salts on the kinetics of ribonuclease A chain folding, Biopolymers, 17, 1669, 10.1002/bip.1978.360170705 Bai, 1995, Protein folding intermediates: native-state hydrogen exchange, Science, 269, 192, 10.1126/science.7618079 Lacroix, 1997, Amide hydrogen exchange and internal dynamics the chemotactic protein CheY from Escherichia coli, J. Mol Biol, 271, 472, 10.1006/jmbi.1997.1178 Kabsch, 1978, A discussion of the solution for the best rotation to relate two sets of vectors, Acta Crystallogr. A, 34, 827, 10.1107/S0567739478001680 Brooks, 1992, Characterization of “native” apolyglobin by molecular dynamics simulations, J. Mol. Biol, 227, 375, 10.1016/0022-2836(92)90893-O Daggett, 1992, A model of the molten globule state from molecular dynamics simulations, Proc. Natl Acad. Sci. USA, 89, 5142, 10.1073/pnas.89.11.5142 Sheinerman, 1997, A molecular dynamics simulation study of segment B1 of protein G, Proteins, 29, 192, 10.1002/(SICI)1097-0134(199710)29:2<193::AID-PROT7>3.0.CO;2-E