3D-Lattice Monte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics

Biophysical Chemistry

Volumn 106, Issue 1, 2003, Pages 81-89

  Leonhard, K ^a   Prausnitz, J M ^a,b   Radke, C J ^a,b  

^a University of California   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Interaction energies; Lattice simulation; Protein folding; Size effects; Solvation

Indexed keywords

AMINO ACID DERIVATIVE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; KINETICS; MOLECULAR MODEL; MOLECULAR SIZE; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; SIMULATION; THERMODYNAMICS;

EID: 0141627542     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(03)00185-6     Document Type: Article

References (16)

1. Li H., Helling R., Tang C., Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science. 273:1996;666-669.
2. Du R., Pande V.S., Grosberg A.Y., Tanaka T., Shakhnovich E. On the role of conformational geometry in protein folding. J. Chem. Phys. 111:1999;10375-10380.
3. Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:1983;183.
4. Shakhnovich E.I., Gutin A.M. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. 90:1993;7195-7199.
5. Shakhnovich E.I. Proteins with selected sequences fold into unique native conformation. Phys. Rev. Lett. 72:1994;3907-3910.
6. Abkevich V.I., Gutin A.M., Shakhnovich E.I. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:1994;6052-6062.
7. Tiana G., Broglia R.A., Roman H.E., Vigezzi E., Shakhnovich E. Folding and misfolding of designed proteinlike chains with mutations. J. Chem. Phys. 108:1998;757-761.
8. Pande D.S., Vijay S., Rokhsar. Folding pathway of a lattice model for proteins. Proc. Natl. Acad. Sci. 96:1999;1273-1278.
9. Mirny L.A., Abkevich V.I., Shakhnovich E.I. How evolution makes proteins fold quickly. Proc. Natl. Acad. Sci. 95:1998;4976-4981.
10. Crippen G.M., Chhajer M. Lattice models of protein folding permitting disordered native states. J. Chem. Phys. 116:2002;2261-2268.
11. Dinner A.R., Šali A., Karplus M. The folding mechanism of larger model proteins: role of native structure. Proc. Natl. Acad. Sci. 93:1996;8356-8361.
12. Miyazawa S., Jernigan R.L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:1985;534-552.
13. K. Leonhard, J.M. Prausnitz, C.J. Radke, Solvent amino acid interaction energies in 3-D-lattice Monte Carlo simulations of a model 27-mer protein. Folding thermodynamics and kinetics, Protein Sci., submitted for publication.
14. Gruebele M. The fast protein folding problem. Annu. Rev. Phys. Chem. 50:1999;485-516.
15. Boyd R.H., Phillips P.J. The Science of Polymer Molecules. 1993;Cambridge University Press.
16. Kaya H., Chan H.S. Polymer principles of protein calorimetry two-state cooperativity. Proteins: Struct. Func. Gen. 40:2000;637-661.