On the precision of experimentally determined protein folding rates and φ-values

Protein Science

Volumn 15, Issue 3, 2006, Pages 553-563

  De Los Rios, Miguel A ^a   Muralidhara, B K ^b,f   Wildes, David ^c   Sosnick, Tobin R ^d   Marqusee, Susan ^c   Wittung Stafshede, Pernilla ^b   Plaxco, Kevin W ^a   Ruczinski, Ingo ^e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b RICE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CHICAGO   (United States)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^f University of Texas Medical Branch School of Medicine   (United States)

Author keywords

values; FynSH3 domain; Protein folding; Stopped flow mixing

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; CONFIDENCE INTERVAL; ENERGY; LABORATORY; MONITORING; MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; REPRODUCIBILITY;

FLUOROMETRY; KINETICS; OBSERVER VARIATION; POINT MUTATION; PROTEIN FOLDING; PROTO-ONCOGENE PROTEINS C-FYN; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 33644541811     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.051870506     Document Type: Article

References (24)

1. Alm, E., Morozov, A.V., Kortemme, T., and Baker, D. 2002. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322: 463-476.
2. Clementi, C., Garcia, A.E., and Onuchic, J.N. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L. J. Mol. Biol. 326: 933-954.
3. Daggett, V. and Fersht, A. 2003. The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4: 497-502.
4. Daggett, V., Li, A.J., and Fersht, A.R. 1998. Combined molecular dynamics and φ-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.
5. de los Rios, M.A. and Plaxco, K.W. 2005. Apparent Debye-Huckle electrostatic effects in the folding of a simple, single-domain protein. Biochemistry 44: 1243-1250.
6. Ejtehadi, M.R., Avall, S.P., and Plotkin, S.S. 2004. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc. Natl. Acad. Sci. 101: 15088-15093.
7. Fersht, A.R. and Sato, S. 2004. φ-value analysis and the nature of protein-folding transition states. Proc. Natl. Acad. Sci. 101: 7976-7981.
8. Friel, C.T., Capaldi, A.P., and Radford, S.E. 2003. Structural analysis of the rate-limiting transition states in the folding of Im7 and Im9: Similarities and differences in the folding of homologous proteins. J. Mol. Biol. 326: 293-305.
9. Garbuzynskiy, S.O., Finkelstein, A.V., and Galzitskaya, O.V. 2004. Outlining folding nuclei in globular proteins. J. Mol. Biol. 336: 509-525.
10. Garcia-Mira, M.M., Bohringer, D., and Schmid, F.X. 2004. The folding transition of the cold shock protein is strongly polarized. J. Mol. Biol. 339: 555-569.
11. Garvey, E.P. and Matthews, C.R. 1989. Effects of multiple replacements at a single position on the folding and stability of dihydrofolate reductase from Escherichia coli. Biochemistry 28: 2083-2093.
12. Goldenberg, D.P., Frieden, R.W., Haack, J.A., and Morrison, T.B. 1989. Mutational analysis of a protein-folding pathway. Nature 338: 127-132.
13. Hamill, S.J., Steward, A., and Clarke, J. 2000. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297: 165-178.
14. Marianayagam, N.J. and Jackson, S.E. 2004. The folding pathway of ubiquitin from all-atom molecular dynamics simulations. Biophys. J. 111: 159-171.
15. Matouschek, A., Kellis, J.T., Serrano, L., and Fersht, A.R. 1989. Mapping the transition-state and pathway of protein folding by protein engineering. Nature 340: 122-126.
16. Maxwell, K.L., Wildes, D., Zarrine-Afsar, A., de los Rios, M.A., Brown, A.G., Friel, C.T., Hedberg, L., Horng, J.-C., Bona, D., Miller, E.J., et al. 2005. Protein folding: Defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci. 14: 602-616.
17. Mok, Y.K., Elisseeva, E.L., Davidson, A.R., and Forman-Kay, J.D. 2001. Dramatic stabilization of an SH3 domain by a single substitution: Roles of the folded and unfolded states. J. Mol. Biol. 307: 913-928.
18. Northey, J.G., Maxwell, J.L., and Davidson, A.R. 2002. Protein folding kinetics beyond the f value: Using multiple amino acid substitution to investigate the structure of the SH3 domain folding transition state. J. Mol. Biol. 320: 389-402.
19. Nozaki, Y. 1972. The preparation of guanidine hydrochloride. Methods Enzymol. 26: 43-50.
20. Plaxco, K.W., Guijarro, J.I., Morton, C.J., Pitkeathly, M., Campbell, I.D., and Dobson, C.M. 1998. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry 37: 2529-2537.
21. Riddle, D.S., Grantcharova, V.P., Santiago, J.V., Alm, E., Ruczinski, I., and Baker, D. 1999. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 6: 1016-1024.
22. Sanchez, I.E. and Kiefhaber, T. 2003. Origin of unusual φ-values in protein folding: Evidence against specific nucleation sites. J. Mol. Biol. 334: 1077-1085.
23. Settanni, G., Rao, F., and Caflish, A. 2005. φ-Value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. 102: 628-633.
24. Zarrine-Afsar, A. and Davidson, A.R. 2004. The analysis of protein folding kinetic data produced in protein engineering experiments. Methods 34: 41-50.