The Gō model revisited: Native structure and the geometric coupling between local and long-range contacts

Proteins: Structure, Function and Genetics

Volumn 60, Issue 4, 2005, Pages 712-722

  Faísca, Patrícia F N ^a   Telo Da Gama, Margarida M ^a   Nunes, Ana ^a  

^a UNIVERSITY OF LISBON   (Portugal)

Author keywords

Folding kinetics; Lattice models; Monte Carlo simulation; Native geometry

Indexed keywords

POLYMER;

ARTICLE; CRYSTAL STRUCTURE; ENERGY TRANSFER; GEOMETRY; KINETICS; MOLECULAR INTERACTION; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

BINDING SITES; COMPUTER SIMULATION; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEINS;

EID: 24644503109     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20521     Document Type: Article

References (35)

1. Plaxco KW, Simmons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
2. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhanovich E. On the role of conformational geometry in protein folding. J Chem Phys 1999;111:10375-13080.
3. Baker D. A surprinsing simplicity to protein folding. Nature 2000;405:39-42.
4. Dokholyan NV, Li L, Ding F, Shakhnovich EI. Topological determinants of protein folding. Proc Natl Acad Sci USA 2002;99:8637-8641.
5. Miller EJ, Fischer KE, Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc Natl Acad Sci USA 2002;99:13059-10363.
6. Faisca PFN, Ball RC. Topological complexity, contact order and protein folding rates, J Chem Phys 2002;117:8587-8591.
7. Weikl TR, Dill KA. Folding rates and low entropy routes of two-state proteins. J Mol Biol 2003;329:585-598.
8. Kaya H, Chan HS. Contact order dependent protein folding rates: kinetics consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins 2003;52:524-533.
9. Faisca PFN, Telo da Gama MM, Ball RC. Folding and form: insights from lattice simulations. Phys Rev E 2004;69:051917.
10. Plaxco KW, Simmons KT, Ruczinski I, Baker D. Topology, stability, sequence and length: defining the determinants of two-state protein folding kinetics. Biochemistry 2000;39:11177-11183.
11. Gō N, Taketomi H. Respective roles of short- and long-range interactions in protein folding. Proc Natl Acad Sci USA 1978;75:559-563.
12. Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 1995;252:460-471.
13. Doyle R, Simons K, Qian H, Baker D. Local interactions and the optimization of protein folding. Proteins 1997;29:282-291.
14. Gromiha MM and Selvaraj S. Importance of long-range interactions in protein folding. Biophys Chem 1997;77:49-68.
15. Unger E, Moult J. Local interactions dominate folding in a simple protein model. J Mol Biol 1996;259:988-994.
16. Govindarajan S, Goldstein RA. Optimal local propensities for model proteins. Proteins 1995;22:413-418.
17. Gromiha MM, Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state folders: application of long-range order to folding rate prediction. J Mol Biol 2001;310:27-32.
18. Gutin AM, Abkevich VI, Shakhnovich, EI. Chain length scaling of protein folding. Phys Rev Lett 1996;77:5433-5436.
19. Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: search for a "glass" transition. J Chem Phys 1998;108:6466-6483.
20. Cieplak M, Hoang TX, Li MS. Scaling of folding properties in simple models of proteins. Phys Rev Lett 1999;83:1684-1687.
21. Faisca, PFN, Ball RC. Thermodynamic control and dynamical regimes in protein folding. J Chem Phys 2002;116:7231-7238.
22. Gillespie B, Plaxco KW. Nonglassy kinetics in the folding of a simple single-domain protein. Proc Natl Acad Sci USA 2000;97:12014-12019.
23. Shea JE, Onuchic JN, Brooks CL. Probing the folding free energy landscape of the src-SH3 protein domain. Proc Natl Acad Sci USA 2002;99:16064-16068.
24. Landau DP, Binder K. A Guide to Monte Carlo simulations in statistical physics. Cambridge: Cambridge University Press; 2000.
25. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1092.
26. Saitoh S, Nakai T, Nishikawa K. A geometric constraint approach for reproducing the native backbone conformation of a protein. Proteins 1993;15:191-204.
27. Fan K, Wang J, Wang W. Modeling two-state cooperativity in protein folding. Phys Rev E 2001;041907.
28. Jewett AI, Pande VS, Plaxco KW. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J Mol Biol 2003;326:247-253.
29. Chan HS, Dill KA. Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics. Proteins 1998;30:2-33.
30. Chan HS, Shimizu S, Kaya H. Cooperativity principles in protein folding. Methods Enzymol 2004;380:350-379.
31. Makarov DE, Plaxco KW. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci 2003;12:17-26.
32. Debe DA, Carlson MJ, Goddard WA. The topomer-sampling model of protein folding. Proc Natl Acad Sci USA 1999;96:2596-2601.
33. Makarov DE, Metiu H. A model for the kinetics of protein folding: kinetic Monte Carlo simulations and analytical results. J Chem Phys 2002;116:5205-5216.
34. Maritan A, Micheletti C, Banavar, JR. Role of secondary motifs in fast folding polymers: a dynamical variational principle. Phys Rev Lett 2000;3009-3012.
35. Micheletti C, Banavar JR, Maritan A, Seno F. Protein structures and optimal folding from a geometrical principle. Phys Rev Lett 1999;3372-3375.