Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

Nature Structural Biology

Volumn 7, Issue 4, 2000, Pages 336-342

  Li, Lewyn ^a   Mirny, Leonid A ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

M PROTEIN;

ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; KINETICS; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BINDING SITES; COMPUTER SIMULATION; CONSERVED SEQUENCE; ENZYME STABILITY; EVOLUTION, MOLECULAR; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; MUTATION; PROTEIN FOLDING; PROTEINS; PROTO-ONCOGENE PROTEINS PP60(C-SRC); SEQUENCE ALIGNMENT; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 0034112774     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/74111     Document Type: Article

References (39)

1. nd edition (W.H. Freeman and Company, New York; 1993).
2. Li, A. & Daggett, V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275, 677-694 (1998).
3. Duan, Y. & Kollman, P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740-744 (1998).
4. Lazaridis, T. S Karplus, M. 'New view1 of protein folding reconciled with the old through multiple unfolding simulations. Science 278,1928-1931 (1997).
5. Abkevich, V.l., Gutin, A.M. & Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: evidence from lattice model. Biochemistry 33, 10026-10036 (1994).
6. Klimov, D.K. & Thirumalai, D. Cooperativity in protein folding, from lattice models with sidechains to real proteins. Folding Design 3, 127-139 (1998).
7. Socci, N.D., Onuchic, J.N. & Wolynes, P.G. Protein folding mechanisms and the multidimensional folding funnel. Proteins 32, 135-158 (1998).
8. Hao, M-H & Scheraga, H.A. Molecular mechanisms for cooperative folding of proteins. J. Mol. Biol. 277, 973-983 (1998).
9. Kolinski, A. & Skolnick. J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18,338-352 (1994).
10. Berriz, G.F., Gutin, A.M. & Shakhnovich, E.I. Cooperativity and stability in a Langevin model of proteinlike folding. J. Chem. Phys. 106, 9276-9285 (1997).
11. Guo, Z. & Brooks III, C.L. Thermodynamics of protein folding: a statistical mechanical study of a small all-p protein. Biopolymers 42, 745-757 (1997).
12. Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E. & Shakhnovich, E.I. Identifying the protein folding nucleus using molecular dynamics. J. Mol. Biol. 296, 1183-1188 (2000).
13. Itzhaki, L.S., Otzen. D.E. & Fersht, A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288(1995).
14. Lopez-Hernandez, E. & Serrano, L. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, Cl-2. Folding Design 1, 43-55 (1996).
15. Martinez, J.C., Pisabarro, M.T. & Serrano, L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Struct. Biol. 5, 721-729 (1998).
16. Martinez, J.C. & Serrano, L. The folding transition state between SH3 domains is conformationally restricted and evolutionary conserved. Nature Struct Biol. 6, 1010-1015 (1999).
17. Grantcharova, V.P., Riddle, D.S., Santiago, J.V. & Baker, D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Struct. Biol. 5, 714-720 (1998).
18. Riddle, D.S. et al. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct. Biol. 6, 1016-1024 (1999).
19. Fulton, K.F., Main, E.R.G., Daggett, V. & Jackson, S.E. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J. Mol. Biol. 291, 445-461 (1999).
20. Bromberg, S. & Dill, K.A. Side-chain entropy and packing in proteins. Protein Sci. 3, 997-1009 (1994).
21. Hart, W.E. & Istrail, S. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better the 86% of optimal. J. Camp. Biol. 4, 241-259 (1997).
22. Villegas, V.. Martinez. J.C.. Aviles. F.X. & Serrano, L. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283,1027-1036 (1998).
23. Dobson. CM. et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Struct. Biol. 6,1005-1009 (1999).
24. Daggett, V., Li, A. & Fersht, A.R. Combined molecular dynamics and O-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: structural basis of Hammond and anti-Hammond effects. J. Am. Chem. Soc. 120, 12740-12754(1998).
25. Klimov, O.K. & Thirumalai, D. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J. Mol. Biol. 282,471-492 (1998).
26. Gutin, A.M., Abkevich, V.l. & Shakhnovich, E.I. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Folding Design 3,183-194(1998).
27. Matouschek, A., Kellis. J.T., Serrano L. & Fersht, A.R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340, 122-126 (1989).
28. Fersht, A.R.. Itzhaki, L.S., ElMasry, N.F., Matthews, J.M. & Otzen, D.E. Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc. Natl Acad. Sci USA 91, 10426-10429 (1994).
29. ali. A., Shakhnovich, E. & Karplus, M. How does a protein fold? Nature 369, 248-251 (1994).
30. Mirny, L.A., Abkevich, V.l. & Shakhnovich, E.I. How evolution makes proteins fold quickly. Proc. Natl Acad. Sci. USA 95, 4976-4981 (1998).
31. Mirny, L.A. & Shakhnovich, E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291, 177-196 (1999).
32. Miyazawa, S. & Jernigan, R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromo/ecu/es 18,534-552 (1985).
33. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. & Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092 (1953).
34. Abkevich, V.l., Gutin, A.M. & Shakhnovich, E.I. Improved design of stable and fast-folding model proteins. Folding Design 1,221-230 (1996).
35. Dodge, C, Schneider, R. & Sander, C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26, 313-315 (1998).
36. Holm, L. & Sander, C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24, 206-209 (1996).
37. Shakhnovich, E.I. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Folding Design 3, R108-R111 (1998).
38. Per, J.K. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. App. Crystallogr. 24, 946-950 (1991).
39. Merrit, E.A. & Bacon, D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505-524 (1997).