Common Motifs and Topological Effects in the Protein Folding Transition State

Journal of Molecular Biology

Volumn 359, Issue 4, 2006, Pages 1075-1085

  Hubner, Isaac A ^a   Lindberg, Magnus ^b   Haglund, Ellinor ^b   Oliveberg, Mikael ^b   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

circular permutant; ensemble; nucleation; protein S6; simulation

Indexed keywords

PROTEIN S6;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENTROPY; MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN TRANSPORT; WILD TYPE;

EID: 33744829290     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.015     Document Type: Article

References (26)

1. Martinez J.C., Viguera A.R., Berisio R., Wilmanns M., Mateo P.L., Filimonov V.V., and Serrano L. Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins. Biochemistry 38 (1999) 549-559
2. Lindberg M.O., Tangrot J., Otzen D.E., Dolgikh D.A., Finkelstein A.V., and Oliveberg M. Folding of circular permutants with decreased contact order: general trend balanced by protein stability. J. Mol. Biol. 314 (2001) 891-900
3. Lindberg M., Tangrot J., and Oliveberg M. Complete change of the protein folding transition state upon circular permutation. Nature Struct. Biol. 9 (2002) 818-822
4. Otzen D.E., and Fersht A.R. Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus. Biochemistry 37 (1998) 8139-8146
5. Li L., and Shakhnovich E.I. Different circular permutations produced different folding nuclei in proteins: a computational study. J. Mol. Biol. 306 (2001) 121-132
6. Clementi C., Jennings P.A., and Onuchic J.N. Prediction of folding mechanism for circular-permuted proteins. J. Mol. Biol. 311 (2001) 879-890
7. Weikl T.R., and Dill K.A. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J. Mol. Biol. 332 (2003) 953-963
8. Onuchic J.N., and Wolynes P.G. Theory of protein folding. Curr. Opin. Struct. Biol. 14 (2004) 70-75
9. Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
10. Hubner I.A., Shimada J., and Shakhnovich E.I. Commitment and nucleation in the protein G transition state. J. Mol. Biol. 336 (2004) 745-761
11. Sosnick T.R., Dothager R.S., and Krantz B.A. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc. Natl Acad. Sci. USA 101 (2004) 17377-17382
12. Vendruscolo M., Paci E., Dobson C.M., and Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature 409 (2001) 641-645
13. Hubner I.A., Oliveberg M., and Shakhnovich E.I. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc. Natl Acad. Sci. USA 101 (2004) 8354-8359
14. Hubner I.A., Edmonds K.A., and Shakhnovich E.I. Nucleation and the transition state of the SH3 domain. J. Mol. Biol. 349 (2005) 424-434
15. Donald J.E., Hubner I.A., Rotemberg V.M., Shakhnovich E.I., and Mirny L.A. CoC: a database of universally conserved residues in protein folds. Bioinformatics 21 (2005) 2539-2540
16. Otzen D.E., and Oliveberg M. Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state. J. Mol. Biol. 317 (2002) 613-627
17. Munoz V. Folding plasticity. Nature Struct. Biol. 9 (2002) 792-794
18. Ternstrom T., Mayor U., Akke M., and Oliveberg M. From snapshot to movie: phi analysis of protein folding transition states taken one step further. Proc. Natl Acad. Sci. USA 96 (1999) 14854-14859
19. Li L., and 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
20. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
21. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
22. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
23. Abdullaev Z.K., Latypov R.F., Badretdinov A.Y., Dolgikh D.A., Finkelstein A.V., Uversky V.N., and Kirpichnikov M.P. S6 permutein shows that the unusual target topology is not responsible for the absence of rigid tertiary structure in de novo protein albebetin. FEBS Letters 414 (1997) 243-246
24. Shimada J., Kussell E.L., and Shakhnovich E.I. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 308 (2001) 79-95
25. Hubner I.A., and Shakhnovich E.I. Geometric and physical considerations for realistic protein models. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 72 (2005) 022901
26. Hubner I.A., Deeds E.J., and Shakhnovich E.I. High-resolution protein folding with a transferable potential. Proc. Natl Acad. Sci. USA 102 (2005) 18914-18919