Commitment and Nucleation in the Protein G Transition State

Journal of Molecular Biology

Volumn 336, Issue 3, 2004, Pages 745-761

  Hubner, Isaac A ^a   Shimada, Jun ^a,b   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

^b 19034   (United States)

Author keywords

Nucleation; Protein folding; Protein G; Transition state ensemble; value

Indexed keywords

PROTEIN G;

ARTICLE; ATOM; CALCULATION; CONFORMATION; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN FOLDING; VALIDATION PROCESS;

EID: 0842332830     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.032     Document Type: Article

References (46)

1. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. 1999;W.H. Freeman, New York.
2. Fersht A.R., Matouschek A., Serrano L. The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224:1992;771-782.
3. Galzitskaya O.V., Ivankov D.N., Finkelstein A.V. Folding nuclei in proteins. FEBS Letters. 489:2001;113-118.
4. Li A., Daggett V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275:1998;677-694.
5. Daggett V., Li A.J., Fersht A.R. Combined molecular dynamics and phi-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. 120:1998;12740-12754.
6. Vendruscolo M., Paci E., Dobson C.M., Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:2001;641-645.
7. Paci E., Vendruscolo M., Dobson C.M., Karplus M. Determination of a transition state at atomic resolution from protein engineering data. J. Mol. Biol. 324:2002;151-163.
8. Paci E., Clarke J., Steward A., Vendruscolo M., Karplus M. Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proc. Natl Acad. Sci. USA. 100:2003;394-399.
9. Davis R., Dobson C.M., Vendruscolo M. Determination of the structures of distinct transition state ensembles for a beta-sheet peptide with parallel folding pathways. J. Chem. Phys. 117:2002;9510-9517.
10. Shimada J., Shakhnovich E.I. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl Acad. Sci. USA. 99:2002;11175-11180.
11. Li L., Shakhnovich E.I. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl Acad. Sci. USA. 98:2001;13014-13018.
12. Gsponer J., Caflisch A. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl Acad. Sci. USA. 99:2002;6719-6724.
13. Park S.H., Shastry M.C., Roder H. Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing. Nature Struct. Biol. 6:1999;943-947.
14. Du R., Pande V.S., Grosberg A.Y., Tanaka T., Shakhnovich E.S. On the transition coordinate for protein folding. J. Chem. Phys. 108:1998;334-350.
15. Bolhuis P.G., Chandler D., Dellago C., Geissler P.L. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53:2002;291-318.
16. Bolhuis P.G., Dellago C., Chandler D. Reaction coordinates of biomolecular isomerization. Proc. Natl Acad. Sci. USA. 97:2000;5877-5882.
17. Geissler P.L., Dellago C., Chandler D., Hutter J., Parrinello M. Autoionization in liquid water. Science. 291:2001;2121-2124.
18. Bolhuis P.G. Transition-path sampling of beta-hairpin folding. Proc. Natl Acad. Sci. USA. 100:2003;12129-12134.
19. Dellago C., Bolhuis P.G., Chandler D. Efficient transition path sampling: application to Lennard-Jones cluster rearrangements. J. Chem. Phys. 108:1998;9236-9245.
20. Bryant Z., Pande V.S., Rokhsar D.S. Mechanical unfolding of a beta-hairpin using molecular dynamics. Biophys. J. 78:2000;584-589.
21. Binder K., Heermann D.W. Monte Carlo Simulation in Statistical Physics: An Introduction. 4th English edit. Springer Series in Solid-State Sciences. vol. 80:2002;Springer, Berlin.
22. Shimada J., Kussell E.L., Shakhnovich E.I. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 308:2001;79-95.
23. Gerstein M., Tsai J., Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249:1995;955-966.
24. Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:1983;183-210.
25. Maiorov V.N., Crippen G.M. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. J. Mol. Biol. 235:1994;625-634.
26. Maiorov V.N., Crippen G.M. Size-independent comparison of protein three-dimensional structures. Proteins: Struct. Funct. Genet. 22:1995;273-283.
27. Shea J.E., Brooks C.L. III. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:2001;499-535.
28. Zhou Y., Karplus M. Interpreting the folding kinetics of helical proteins. Nature. 401:1999;400-403.
29. Galzitskaya O.V., Finkelstein A.V. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl Acad. Sci. USA. 96:1999;11299-11304.
30. Alm E., Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl Acad. Sci. USA. 96:1999;11305-11310.
31. Munoz V., Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA. 96:1999;11311-11316.
32. Takada S. Go-ing for the prediction of protein folding mechanisms. Proc. Natl Acad. Sci. USA. 96:1999;11698-11700.
33. Kussell E., Shimada J., Shakhnovich E.I. Side-chain dynamics and protein folding. Proteins: Struct. Funct. Genet. 52:2003;303-321.
34. Ferguson N., Fersht A.R. Early events in protein folding. Curr. Opin. Struct. Biol. 13:2003;75-81.
35. McCallister E.L., Alm E., Baker D. Critical role of beta-hairpin formation in protein G folding. Nature Struct. Biol. 7:2000;669-673.
36. Munoz V., Thompson P.A., Hofrichter J., Eaton W.A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390:1997;196-199.
37. Kuszewski J., Clore G.M., Gronenborn A.M. Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G. Protein Sci. 3:1994;1945-1952.
38. Mirny L.A., Shakhnovich E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291:1999;177-196.
39. Plaxco K.W., Larson S., Ruczinski I., Riddle D.S., Thayer E.C., Buchwitz B., et al. Evolutionary conservation in protein folding kinetics. J. Mol. Biol. 298:2000;303-312.
40. Mirny L., Shakhnovich E. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308:2001;123-129.
41. 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. 254:1995;260-288.
42. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
43. Sanchez I.E., Kiefhaber T. Origin of unusual phi-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334:2003;1077-1085.
44. Nauli S., Kuhlman B., Baker D. Computer-based redesign of a protein folding pathway. Nature Struct. Biol. 8:2001;602-605.
45. Jackson S.E., Fersht A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry. 30:1991;10428-10435.
46. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14:1996;33-38. see also pp. 27-28.