On the relationship between folding and chemical landscapes in enzyme catalysis

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

Volumn 105, Issue 37, 2008, Pages 13877-13882

  Roca, Maite ^a   Messer, Benjamin ^a   Hilvert, Donald ^b   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b ETH ZURICH   (Switzerland)

Author keywords

Chorismate mutase; Dynamics; Induced fit; Molten globule; Preorganization

Indexed keywords

CHORISMIC ACID; ENZYME;

ARTICLE; CATALYSIS; CHEMICAL PROCEDURES; ENZYME ACTIVATION; ENZYME ANALYSIS; ENZYME ENGINEERING; ENZYME STRUCTURE; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING;

CATALYSIS; CHORISMATE MUTASE; COMPUTER SIMULATION; DIMERIZATION; KINETICS; METHANOCOCCUS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY;

EID: 52949128744     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0803405105     Document Type: Article

References (29)

1. Marti S, et al. (2004) Theoretical insights in enzyme catalysis. Chem Soc Rev 33:98-107.
2. Warshel A, et al. (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210-3235.
3. Onuchic JN, Wolynes PG (2004) Theory of protein folding. Curr Opin Struct Biol 14:70-75.
4. Xiang Y, Goodman MF, Beard WA, Wilson SH, Warshel A (2008) Exploring the role of large conformational changes in the fidelity of DNA polymerase β. Proteins 70:231-247.
5. Benkovic SJ, Hammes GG, Hammes-Schiffer S (2008) Free-energy landscape of enzyme catalysis. Biochemistry 47:3317-3321.
6. Prakash MK, Marcus RA (2007) An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations. Proc Natl Acad Sci USA 104:15982-15987.
7. Min W, Xie XS, Bagchi B (2008) Two-dimensional reaction free energy surfaces of catalytic reaction: Effects of protein conformational dynamics on enzyme catalysis. J Phys Chem B 112:454-466.
8. Liu H, Warshel A (2007) The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry 46:6011-6025.
9. Vamvaca K, Vögeli B, Kast P, Pervushin K, Hilvert D (2004) An enzymatic molten globule: Efficient coupling of folding and catalysis. Proc Natl Acad Sci USA 101:12860-12864.
10. Pervushin K, Vamvaca K, Vögeli B, Hilvert D (2007) Structure and dynamics of amolten globular enzyme. Nat Struct Mol Biol 14:1202-1206.
11. Gajewski JJ, et al. (1987) On the mechanism of rearrangement of chorismic acid and related compounds. J Am Chem Soc 109:1170-1186.
12. Lee AY, Karplus PA, Ganem B, Clardy J (1995) Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase. J Am Chem Soc 117:3627-3628.
13. Fersht AR (2000) Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism. Proc Natl Acad Sci USA 97:1525-1529.
14. Shea JE, Onuchic JN, Brooks CL (2002) Probing the folding free-energy landscape of the src-SH3 protein domain. Proc Natl Acad Sci USA 99:16064-16068.
15. MacBeath G, Kast P, Hilvert D (1998) Redesigning enzyme topology by directed evolution. Science 279:1958-1961.
16. Hammes-Schiffer S, Benkovic SJ (2006) Relating protein motion to catalysis. Annu Rev Biochem 75:519-541.
17. Roca M, Liu H, Messer B, Warshel A (2007) On the relationship between thermal stability and catalytic power of enzymes. Biochemistry 46:15076-15088.
18. Prakash MK, Marcus RA (2007) An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations. Proc Natl Acad Sci USA 104:15982-15987.
19. Ishikita H, Warshel A (2008) Predicting drug-resistant mutations of HIV protease. Angew Chem Int Ed 47:697-700.
20. Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253:694-698.
21. Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84:7524-7528.
22. Hinds DA, Levitt M (1992) A lattice model for protein-structure prediction at low resolution. Proc Natl Acad Sci USA 89:2536-2540.
23. Shakhnovich E, Abkevich V, Ptitsyn O (1996) Conserved residues and the mechanism of protein folding. Nature 379:96-98.
24. Dill KA (1990) Dominant forces in protein folding. Biochemistry 29:7133-7155.
25. Olszewski KA, Kolinski A, Skolnick J (1996) Folding simulations and computer redesign of protein A three-helix bundle motifs. Proteins 25:286-299.
26. Fan ZZ, Hwang JK, Warshel A (1999) Using simplified protein representation as a reference potential for all-atom calculations of folding free energy. Theor Chem Acc 103:77-80.
27. Lee FS, Chu ZT, Warshel A (1993) Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the Polaris and Enzymix programs. J Comput Chem 14:161-185.
28. Warshel A (1991) Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley, New York).
29. Strajbl M, Shurki A, Kato M, Warshel A (2003) Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. J Am Chem Soc 125:10228-10237.