Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 7, 2008, Pages 2397-2402

  Yu, Wookyung ^a   Chung, Kwanghoon ^a,e   Cheon, Mookyung ^a,b   Heo, Muyoung ^a,f   Han, Kyou Hoon ^c   Ham, Sihyun ^d   Chang, Iksoo ^a  

^a Pusan National University   (South Korea)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d Sookmyung Women's University   (South Korea)

^e Ministry of Science and Technology   (South Korea)

^f HARVARD UNIVERSITY   (United States)

Author keywords

Global downhill folding; Protein folding mechanism; Protein thermodynamics; Relaxation kinetics of protein

Indexed keywords

BBL PROTEIN; PERIPHERAL SUBUNIT BINDING DOMAIN PROTEIN; PROTEIN; UNCLASSIFIED DRUG; ESCHERICHIA COLI PROTEIN;

ARTICLE; KINETICS; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; THERMODYNAMICS; BIOLOGICAL MODEL; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN DENATURATION; TEMPERATURE;

ESCHERICHIA COLI PROTEINS; KINETICS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING; TEMPERATURE; THERMODYNAMICS;

EID: 40649105020     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0708480105     Document Type: Article

References (40)

1. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230.
2. Dill KA, et al. (1995) Principles of protein folding - A perspective from simple exact models. Protein Sci 4:561-602.
3. Daggett V, Fersht AR (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4:497-502.
4. Shakhnovich EI (2006) Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chem Rev 106:1559-1588.
5. Go N (1983) Theoretical studies of protein folding. Annu Rev Biophys Bioeng 12:183-210.
6. Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84:7524-7528.
7. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167-195.
8. Shakhnovich EI, Gutin AM (1989) Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophys Chem 34:187-199.
9. Matouschek A, Serrano L, Fersht AR (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224:771-782.
10. Abkevich VI, Gutin AM, Shakhnovich EI (1995) Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 252:460-471.
11. Eaton WA (1999) Searching for "downhill scenarios" in protein folding. Proc Natl Acad Sci USA 96:5897-5899.
12. Muñoz V (2002) Thermodynamics and kinetics of downhill protein folding investigated with a simple statistical mechanical model. Int J Quantum Chem 90:1522-1528.
13. Garcia-Mira MM, Sadqi M, Fischer N, Sanchez-Ruiz JM, Muñoz V (2002) Experimental identification of downhill protein folding. Science 298:2191-2195.
14. Oliva FY, Muñoz VA (2004) A simple thermodynamic test to discriminate between two-state and downhill folding. J Am Chem Soc 126:8596-8597.
15. Ferguson N, Schartau PJ, Sharpe TD, Sato S, Fersht AR (2004) One-state downhill versus conventional protein folding. J Mol Biol 344:295-301.
16. Ferguson, N et al. (2005) Ultra-fast barrier-limited folding in the peripheral subunit-binding domain family. J Mol Biol 353:427-446.
17. Fitz-Gibbon ST, et al. (2002) Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci USA 99:984-989.
18. Naganathan AN, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V (2005) Robustness of downhill folding: Guidelines for the analysis of equilibrium folding experiments on small proteins. Biochemistry 44:7435-7449.
19. Sadqi M, Fushman D, Muñoz V (2006) Atom-by-atom analysis of global downhill protein folding. Nature 442:317-321.
20. Ferguson N, Sharpe TD, Johnson CM, Schartau PJ, Fersht AR (2007) Analysis of 'downhill' protein folding. Nature 445:E14-E15.
21. Zhou Z, Bai Y (2007) Analysis of protein-folding cooperativity. Nature 445:E16-E17.
22. Sadqi M, Fushman D, Muñoz V (2007) Sadqi et al. reply. Nature 445:E17-E18.
23. Muñoz V, Sanchez-Ruiz JM (2004) Exploring protein-folding ensembles: A variable-barrier model for the analysis of equilibrium unfolding experiments. Proc Natl Acad Sci USA 101:17646-17651.
24. Huang F, Sato S, Sharpe TD, Ying L, Fersht AR (2007) Distinguishing between cooperative and unimodal downhill protein folding. Proc Natl Acad Sci USA 104:123-127.
25. Kelly JW (2006) Proteins downhill all the way. Nature 442:255-256.
26. Muñoz V, Eaton WA (1999) A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 96:11311-11316.
27. Henry ER, Eaton WA (2004) Combinatorial modeling of protein folding kinetics: Free energy profiles and rates. Chem Phys 307:163-185.
28. Case DA, et al. (2004) AMBER 8 (Univ of California, San Francisco).
29. Bruscolini P, Pelizzola A (2002) Exact solution of the Muñoz-Eaton model for protein folding. Phys Rev Lett 88:258101.
30. Chang I, Cieplak M, Banavar JR, Maritan A (2004) What can one learn from experiments about the elusive transition state? Protein Sci 13:2446-2457.
31. Binder K, Heermann DW (2002) Monte Carlo Simulation in Statistical Physics (Springer, Berlin).
32. Leeson DT, Gai F, Rodriguez HM, Gregoret LM, Dyer RB (2000) Protein folding and unfolding on a complex energy landscape. Proc Natl Acad Sci USA 97:2527-2532.
33. Shakhnovich E, Farztdinov G, Gutin AM, Karplus M (1991) Protein folding bottlenecks: A lattice Monte Carlo simulation. Phys Rev Lett 67:1665-1668.
34. Camacho CJ, Thirumalai D (1993) Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 90:6369-6372.
35. Chan CK, et al. (1997) Submillisecond protein folding kinetics studied by ultrarapid mixing. Proc Natl Acad Sci USA 94:1779-1784.
36. Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich E (1998) Temperature dependence of the folding rate in a simple protein model: Search for a glass transition. Chem Phys 108:6466-6483.
37. Liu Z, Chan HS (2005) Solvation and desolvation effects in protein folding: Native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions. Phys Biol 2:S75-S85.
38. Kaya H, Chan HS (2000) Polymer principles of protein calorimetric two-state cooperativity. Proteins 40:637-661.
39. Li L, Mirny LA, Shakhnovich EI (2000) Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 7:336-342.
40. Klimov DK, Thirumalai D (2001) Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 43:465-475.