First principles prediction of protein folding rates

Journal of Molecular Biology

Volumn 294, Issue 3, 1999, Pages 619-625

  Debe, Derek A ^a   Goddard III, William A ^a  

^a California Institute of Technology   (United States)

Author keywords

Diffusion; Fold topology; Kinetics; Nucleation condensation; Protein folding

Indexed keywords

ALPHA HELIX; ARTICLE; DIFFUSION COEFFICIENT; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE;

EID: 0033521194     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3278     Document Type: Article

References (56)

1. Baldwin R. L. Pulsed H/D-exchange studies of folding intermediates. Curr. Opin. Struct. Biol. 3:1993;84-91.
2. Bhattacharyya R. P., Sosnick T. R. Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil. Biochemistry. 38:1999;2601-2609.
3. Burton R. E., Huang G. S., Daugherty M. A., Fullbright P. W., Oas T. G. Microsecond protein folding through a compact transition state. J. Mol. Biol. 263:1996;311-322.
4. Chan H. S., Dill K. A. The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92:1990;3118-3135.
5. Clarke J., Hamill S. J., Johnson C. M. Folding and stability of a fibronectin type III domain of human tenascin. J. Mol. Biol. 270:1997;771-778.
6. Debe D. A., Carlson M. J., Goddard W. A. The topomer-sampling model of protein folding. Proc. Natl Acad. Sci. USA. 96:1999a;2596-2601.
7. Debe D. A., Carlson M. J., Sadanobu J., Chan S. I., Goddard W. A. Protein fold determination from sparse distance restraints: the restrained generic protein direct Monte Carlo method. J. Phys. Chem. B. 103:1999b;3001-3008.
8. Einstein A. Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen. Ann. Phys. (Leipzig). 17:1905;549-560.
9. 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. 286:1999;1597-1608.
10. Fersht A. R. Optimization of rates of protein-folding - the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA. 92:1995;10869-10873.
11. Flory P. J. Theory of elastic mechanisms in fibrous proteins. J. Am. Chem. Soc. 78:1956;5222-5235.
12. Ghaemmaghami S., Word J. M., Burton R. E., Richardson J. S., Oas T. G. Folding kinetics of a fluorescent variant of monomeric lambda repressor. Biochemistry. 37:1998;9179-9185.
13. Grantcharova V. P., Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 36:1997;15685-15692.
14. Guijarro J. I., Morton C. J., Plaxco K. W., Campbell L. D., Dobson C. M. Folding kinetics of the SH3 domain of PI3 kinase by real-time NMR combined with optical spectroscopy. J. Mol. Biol. 276:1998;657-667.
15. Gutin A. M., Shakhnovich E. I. Statistical-mechanics of polymers with distance constraints. J. Chem. Phys. 100:1994;5290-5293.
16. Hagen S. J., Hofrichter J., Szabo A., Eaton W. A. Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding. Proc. Natl Acad. Sci. USA. 93:1996;11615-11617.
17. Hamill S. J., Meekhof A. E., Clarke J. The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Biochemistry. 37:1998;8071-8079.
18. Huang G. S., Oas T. G. Structure and stability of monomeric lambda-reppressor - NMR evidence for 2-state folding. Biochemistry. 34:1995;3884-3892.
19. Itzhaki L. S., Otzen D. E., Fersht A. R. The structure of the transition-state for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein-folding. J. Mol. Biol. 254:1995;260-288.
20. Jackson S. E. How do small single-domain proteins fold? Fold Design. 3:1998;R81-R91.
21. Jackson S. E., Fersht A. R. Folding of chymotrypsin inhibitor-2.1. Evidence for a 2-state transition. Biochemistry. 30:1991;10428-10435.
22. Jacob M., Schindler T., Balbach J., Schmid F. X. Diffusion control in an elementary protein folding reaction. Proc. Natl Acad. Sci. USA. 94:1997;5622-5627.
23. Karplus M., Weaver D. L. Protein folding dynamics. Nature. 260:1976;404-406.
24. Khorasanizadeh S., Peters I. D., Roder H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nature Struct. Biol. 3:1996;193-205.
25. Kragelund B. B., Robinson C. V., Knudsen J., Dobson C. M., Poulsen F. M. Folding of a 4-helix bundle - studies of acyl-coenzyme-A binding-protein. Biochemistry. 34:1995;7217-7224.
26. Kragelund B. B., Hojrup P., Jensen M. S., Schjerling C. K., Juul E., Knudsen J., Poulsen F. M. Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family. J. Mol. Biol. 256:1996;187-200.
27. Kuhlman B., Luisi D. L., Evans P. A., Raleigh D. P. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9. J. Mol. Biol. 284:1998;1661-1670.
28. Ladurner A. G., Itzhaki L. S., Daggett V., Fersht A. R. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc. Natl Acad. Sci. USA. 95:1998;8473-8478.
29. Lazaridis T., Karplus M. "New-View" of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1997;1928-1931.
30. Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:1976;59-107.
31. Maiorov V. N., Crippen G. M. Size-independent comparison of protein 3-dimensional structures. Proteins: Struct. Funct. Genet. 22:1995;273-283.
32. Miyazawa S., Jernigan R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 218:1985;534-552.
33. O'Connor S. E., Imperiali B. A molecular basis for glycosylation-induced conformational switching. Chem. Biol. 5:1998;427-437.
34. Otzen D. E., Kristensen O., Proctor M., Oliveberg M. Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry. 38:1999;6499-6511.
35. Perl D., Welker C., Schindler T., Schroder K., Marahiel M. A., Jaenicke R., Schmid F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nature Struct. Biol. 5:1998;229-235.
36. Plaxco K. W., Baker D. Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proc. Natl Acad. Sci. USA. 95:1998;13591-13596.
37. Plaxco K. W., Spitzfaden C., Campbell I. D., Dobson C. M. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules. J. Mol. Biol. 270:1997;763-770.
38. Plaxco K. W., Guijarro J. I., Morton C. L., Pitkeathly M., Campbell I. D., Dobson C. M. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry. 37:1998a;2529-2537.
39. Plaxco K. W., Simons K. T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277:1998b;985-994.
40. Plotkin S. S., Wang J., Wolynes P. G. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E. 53:1996;6271-6296.
41. Reid K. L., Rodriguez H. M., Hillier B. J., Gregoret L. M. Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA. Protein Sci. 7:1998;470-479.
42. Robinson C. R., Sauer R. T. Equilibrium stability and sub-millisecond refolding of a designed single-chain arc repressor. Biochemistry. 35:1996;13878-13884.
43. Sato S., Kuhlman B., Wu W. J., Raleigh D. P. Folding of the multidomain ribosomal protein L9: the two domains fold independently with remarkably different rates. Biochemistry. 38:1999;5643-5650.
44. Scalley M. L., Yi Q., Gu H. D., McCormack A., Yates J. R., Baker D. Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L. Biochemistry. 36:1997;3373-3382.
45. Schindler T., Herrler M., Marahiel M. A., Schmid F. X. Extremely rapid protein-folding in the absence of intermediates. Nature Struct. Biol. 2:1995;663-673.
46. Schonbrunner N., Koller K. P., Kiefhaber T. Folding of the disulfide-bonded beta-sheet protein tendamistat: rapid two-state folding without hydrophobic collapse. J. Mol. Biol. 268:1997;526-538.
47. Shoemaker B. A., Wang I., Wolynes P. G. Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble. J. Mol. Biol. 287:1999;675-674.
48. Silow M., Oliveberg M. High-energy channeling in protein folding. Biochemistry. 36:1997;7633-7637.
49. Smith C. K., Bu Z. M., Anderson K. S., Sturtevant J. M., Engelman D. M., Regan L. Surface point mutations that significantly alter the structure and stability of a protein's denatured state. Protein Sci. 5:1996;2009-2019.
50. Taddei N., Chiti F., Paoli P., Fiaschi T., Bucciantini M., Stefani M., Dobson C. M., Ramponi G. Thermodynamics and kinetics of folding of common-type acylphosphatase: comparison to the highly homologous muscle isoenzyme. Biochemistry. 38:1999;2135-2142.
51. van Nuland N. A. L., Chiti F., Taddei N., Raugei G., Ramponi G., Dobson C. M. Slow folding of muscle acylphosphatase in the absence of intermediates. J. Mol. Biol. 283:1998a;883-891.
52. van Nuland N. A. J., Meijberg W., Warner L., Forge V., Scheek R. M., Robillard G. T., Dobson C. M. Slow cooperative folding of a small globular protein HPr. Biochemistry. 37:1998b;622-637.
53. Viguera A. R., Martinez J. C., Filimonov V. V., Mateo P. L., Serrano L. Thermodynamic and kinetic-analysis of the Sh3 domain of spectrin shows a 2-state folding transition. Biochemistry. 33:1994;2142-2150.
54. Viguera A. R., Serrano L., Wilmanns M. Different folding transition states may result in the same native structure. Nature Struct. Biol. 3:1996;874-880.
55. Viguera A. R., Villegas V., Aviles F. X., Serrano L. Favourable native-like helical local interactions can accelerate protein folding. Fold. Design. 2:1997;23-33.
56. Villegas V., Azuaga A., Catasus L., Reverter D., Mateo P. L., Aviles F. X., Serrano L. Evidence for a 2-state transition in the folding process of the activation domain of human procarboxypeptidase-A2. Biochemistry. 34:1995;15105-15110.