The role of sequence and structure in protein folding kinetics: The diffusion-collision model applied to proteins L and G

Structure

Volumn 12, Issue 10, 2004, Pages 1833-1845

  Islam, Suhail A ^a   Karplus, Martin ^b,c   Weaver, David L ^d  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITÉ LOUIS PASTEUR   (France)

^d TUFTS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN G; PROTEIN L; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CALCULATION; CARBOXY TERMINAL SEQUENCE; DIFFUSION; DIFFUSION COLLISION MODEL; EXPERIMENT; KINETICS; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DIFFUSION; KINETICS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 4644266686     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.06.024     Document Type: Article

References (57)

1. Anfinsen C.B. Principles that govern the folding of protein chains. Science. 181:1973;223-230
2. Baker D. A surprising simplicity to protein folding. Nature. 405:2000;39-42
3. Bashford D., Weaver D.L., Karplus M. Diffusion-collision model for the folding kinetics of the lambda-repressor operator-binding domain. J. Biomol. Struct. Dyn. 1:1984;1243-1255
4. Bashford D., Cohen F.E., Karplus M., Kuntz I.D., Weaver D.L. Diffusion-collision model for the folding kinetics of myoglobin. Proteins. 4:1988;211-227
5. Blanco F.J., Serrano L. Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:1995;634-649
6. Brockwell D.J., Smith D.A., Radford S.E. Protein folding mechanisms. new methods and emerging ideas Curr. Opin. Struct. Biol. 10:2000;16-25
7. Brooks C.L. Helix-coil kinetics. folding time scales for helical peptides from a sequential kinetic model J. Phys. Chem. 100:1996;2546-2549
8. Brown S., Fawzi N.J., Head-Gordon T. Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci. USA. 100:2003;10712-10717
9. Burton R.E., Myers J.K., Oas T.G. Protein folding dynamics. quantitative comparison between theory and experiment Biochemistry. 37:1998;5337-5343
10. Dobson C.M., Sali A., Karplus M. Protein folding. a perspective from theory and experiment Angew. Chem. Int. Ed. Engl. 37:1998;868-893
11. Ferguson N., Capaldi A.P., James R., Kleanthous C., Radford S.E. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. J. Mol. Biol. 266:1999;1597-1608
12. Fersht A.R., Daggett V. Protein folding and unfolding at atomic resolution. Cell. 108:2002;573-582
13. Frank M.K., Clore G.M., Gronenborn A.M. Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci. 4:1995;2605-2615
14. Gallagher T., Alexander P., Bryan P., Gilliland G.L. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry. 33:1994;4721-4729
15. Gorski S.A., Capaldi A.P., Kleanthous C., Radford S.E. Acidic conditions stabilize intermediates populated during the folding of Im7 and Im9. J. Mol. Biol. 312:2001;849-863
16. Grantcharova V., Alm E.J., Baker D., Horwich A.L. Mechanisms of protein folding. Curr. Opin. Struct. Biol. 11:2001;70-82
17. Gu H., Kim D., Baker D. Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. J. Mol. Biol. 274:1997;588-596
18. Guo Z., Thirumalai D. Kinetics of protein folding. nucleation, mechanism, time scales and pathways Biopolymers. 36:1994;83-102
19. Guo Z., Thirumalai D. Kinetics and thermodynamics of folding of a de novo design four-helix bundle protein. J. Mol. Biol. 263:1996;323-343
20. Honeycutt J., Thirumalai D. Metastability of the folded states of globular proteins. Proc. Natl. Acad. Sci. USA. 87:1990;3526-3529
21. Islam S.A., Karplus M., Weaver D.L. Application of the diffusion-collision model to the folding of three-helix bundle proteins. J. Mol. Biol. 318:2002;199-215
22. Jackson S. How do small single-domain proteins fold? Fold. Des. 3:1998;R81-R91
23. Karanicolas J., Brooks C.L. III. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 11:2002;2351-2361
24. Karplus M. The Levinthal paradox. yesterday and today Fold. Des. 2:1997;569-576
25. Karplus M., Weaver D.L. Protein-folding dynamics. Nature. 260:1976;404-406
26. Karplus M., Weaver D.L. Diffusion-collision model for protein folding. Biopolymers. 18:1979;1421-1437
27. Karplus M., Weaver D.L. The diffusion-collision model and experimental data. Protein Sci. 3:1994;650-669
28. Kim D.E., Gu H., Baker D. The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proc. Natl. Acad. Sci. USA. 95:1998;4982-4986
29. Kim D.E., Fisher C., Baker D. A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298:2000;971-984
30. Krantz B.A., Mayne L., Rumbly J., Englander S.W., Sosnick T.R. Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J. Mol. Biol. 324:2002;359-371
31. Kuszewski J., Clore G.M., Gronenborn A.M. The immunoglobulin binding domain of streptococcal protein G. Protein Sci. 3:1994;1945-1952
32. Levinthal, C. (1969). How to Fold Graciously. Paper presented at Mossbauer Spectroscopy in Biological Systems, Allerton House, Monticello, Illinois. (Urbana, IL: University of Illinois Press).
33. Lee S., Karplus M., Bashford D., Weaver D.L. Brownian dynamics simulation of protein folding. a study of the diffusion-collision model Biopolymers. 26:1987;481-506
34. Mayor U., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M.V., Alonso D.O.V., Daggett V., Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds. Nature. 421:2003;863-867
35. Munoz V., Eaton W.A. Folding dynamics and mechanism of beta-hairpin formation. Nature. 390:1997;196-197
36. Munoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat. Struct. Biol. 1:1994;399-409. a
37. Munoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters, II. Helix macro dipole effects and rational modi cation of the helical content of natural peptides. J. Mol. Biol. 245:1994;275-296. b
38. Munoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters III. Temperature and pH dependence J. Mol. Biol. 245:1994;297-308. c
39. Munoz V., Serrano L. Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers. 41:1997;495-509
40. Myers J.K., Oas T.G. Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8:2001;552-558
41. Pappu R.V., Weaver D.L. The early folding kinetics of apomyoglobin. Protein Sci. 7:1998;480-490
42. Park S.-H., Shastry M.C.R., Roder H. Folding dynamics of the B1 domain of protein G explored by ultra rapid mixing. Nat. Struct. Biol. 6:1999;943-947
43. Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998;985-994
44. Plaxco K.W., Millet I.S., Segel D.J., Doniach S., Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat. Struct. Biol. 6:1999;554-556
45. Scally M.L., Yi Q., Gu H., McCormack A., Yates J.R. III, Baker D. Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Biochemistry. 36:1997;3373-3382
46. Sheinerman F.B., Brooks C.L. III. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:1998;439-456. a
47. Sheinerman F.B., Brooks C.L. III. Molecular picture of folding of a small alpha/beta protein. Proc. Natl. Acad. Sci. USA. 95:1998;1562-1567. b
48. 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
49. Sorenson J.M., Head-Gordon T. Matching simulation and experiment. a new simplified model for simulating protein folding J. Comput. Biol. 7:2000;469-481
50. Sorenson J.M., Head-Gordon T. Protein engineering study of protein L by simulation. J. Comput. Biol. 9:2002;35-54
51. Weaver D.L. Microdomain dynamics in folding proteins. Biopolymers. 21:1982;1275-1300
52. Weaver D.L. Alternative pathways in diffusion-collision controlled protein folding. Biopolymers. 23:1984;675-694
53. Weikl T.R., Dill K.A. Folding rates and low-entropy-loss routes of two-state proteins. J. Mol. Biol. 329:2003;585-598
54. Weikl T.R., Palassini M., Dill K.A. Cooperativity in 2-state protein folding kinetics. Protein Sci. 13:2004;822-829
55. Wilkström M., Sjöbring U., Kasten W., Björck L., Drakenberg T., Forsén S. Proton nuclear magnetic resonance sequential assignments of an immunoglobulin light chain-binding domain of protein L. Biochemistry. 32:1993;3381-3386
56. Yapa K., Weaver D.L., Karplus M. Beta-sheet coil transitions in a simple polypeptide model. Proteins. 12:1992;237-265
57. Yi Q., Scalley-Kim M.L., Alm E.J., Baker D. NMR characterization of residual structure in the denatured state of protein L. J. Mol. Biol. 299:2000;1341-1351