Native geometry and the dynamics of protein folding

Biophysical Chemistry

Volumn 115, Issue 2-3 SPEC. ISS., 2005, Pages 169-175

  Faisca, P F N ^a   Telo Da Gama, M M ^a  

^a UNIVERSITY OF LISBON   (Portugal)

Author keywords

Contact order; Cooperativity; Kinetics; Lattice models; Long range contacts; Protein folding

Indexed keywords

AMINO ACID;

CONFERENCE PAPER; CONFORMATION; CORRELATION ANALYSIS; DYNAMICS; GEOMETRY; KINETICS; MATHEMATICAL MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN FOLDING; STATISTICAL SIGNIFICANCE;

EID: 14744273112     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2004.12.022     Document Type: Conference Paper

References (27)

1. S.E. Jackson How do small protein molecules fold? Fold. Des. 3 1998 81 91
2. K.W. Plaxco, K.T. Simmons, and D. Baker Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 1998 985 994
3. H. Kaya, and H.S. Chan Simple two-state protein folding kinetics requires near-levinthal thermodynamic cooperativity Proteins 52 2003 510 523
4. J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proc. Natl. Acad. Sci. U. S. A. 84 1987 7524 7528
5. P.E. Leopold, M. Montal, and J.N. Onuchic Protein folding funnels-a kinetic approach to the sequence structure relationship Proc. Natl. Acad. Sci. U. S. A. 89 1992 8721 8725
6. K.W. Plaxco, I.S. Millet, D.J. Segel, S. Doniach, and D. Baker Polypeptide chain collapse can occur concomitantly with the rate limiting step in protein folding Nat. Struct. Biol. 6 1999 554 557
7. B. Gillespie, and K.W. Plaxco Non-glassy kinetics in the folding of a simple single domain protein Proc. Natl. Acad. Sci. U. S. A. 97 2000 12014 12019
8. P. Wittung-Stafshede, J.C. Lee, J.R. Winkler, and H.B. Gray Cytochrome b(562) folding triggered by electron transfer: approaching the speed limit for formation of a four-helix-bundle protein Proc. Natl. Acad. Sci. U. S. A. 96 1999 6587 6590
9. N.A.J. van Nuland, F. Chiti, N. Taddei, G. Raugei, G. Ramponi, and C.M. Dobson Slow folding of muscle acylphosphatase in the absence of intermediates J. Mol. Biol. 283 1998 883 891
10. K.W. Plaxco, K.T. Simmons, I. Ruczinski, and D. Baker Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics Biochemistry 39 2000 11177 11183
11. N. Gō, and H. Taketomi Respective role of short- and long-range interactions in protein folding Proc. Natl. Acad. Sci. U. S. A. 75 1978 559 563
12. V.I. Abkevich, A.M. Gutin, and E.I. Shakhnovich Impact of local and non-local interactions on thermodynamics and kinetics of protein folding J. Mol. Biol. 252 1995 460 471
13. R. Doyle, K. Simmons, H. Qian, and D. Baker Local interactions and the optimization of protein folding Proteins 29 1997 282 291
14. M.M. Gromiha, and S. Selvaraj Importance of long-range interactions in protein folding Biophys. Chem. 77 1999 49 68
15. D.B. Wetlaufer Nucleation, rapid folding, and globular intrachain regions in proteins Proc. Natl. Acad. Sci. U. S. A. 70 1973 697 701
16. R. Unger, and J. Moult Local Interactions dominate folding in a simple lattice protein model J. Mol. Biol. 259 1996 988 994
17. M.M. Gromiha, and S. Selvaraj Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding prediction J. Mol. Biol. 310 2001 27 32
18. L. Mirny, and E.I. Shakhnovich R.A. Broglia E.I. Shakhnovich Proceedings of the International School of Physics Enrico Fermi, Course CXLV Protein Folding Evolution Design 2001 IOS Press Ohmusha 38
19. S. Miyazawa, and R.L. Jernigan Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation Macromolecules 18 1985 534 552
20. N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller Equation of state calculations by fast computing machines J. Chem. Phys. 21 1953 1087 1092
21. D.P. Landau, and K. Binder A guide to Monte Carlo simulations in statistical physics 2000 Cambridge University Press
22. E.I. Shakhnovich, and A.M. Gutin Engineering of stable and fast-folding sequences of model proteins Proc. Natl. Acad. Sci. U. S. A. 90 1993 7195 7199
23. P.F.N. Faisca, and R.C. Ball Thermodynamic control and dynamical regimes in protein folding J. Chem. Phys. 116 2002 7231 7238
24. P.F.N. Faisca, and R.C. Ball Topological complexity, contact order and protein folding rates J. Chem. Phys. 117 2002 8587 8591
25. A.I. Jewett, V.S. Pande, and K.W. Plaxco Cooperativity, smooth energy landscapes and the origins of topology-dependent kinetics protein folding rates J. Mol. Biol. 326 2003 247 253
26. H. Kaya, and H.S. Chan Contact order dependent protein folding rates: kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences Proteins 52 2003 524 533
27. P.F.N. Faisca, M.M. Telo da Gama, and R.C. Ball Folding and form: insights from lattice simulations Phys. Rev. E 69 2004 51917