Role of enzyme-substrate flexibility in catalytic activity: An evolutionary perspective

Journal of Theoretical Biology

Volumn 194, Issue 2, 1998, Pages 175-194

  Demetrius, Lloyd ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ARTICLE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; EVOLUTION; GENE MUTATION; MODEL; NATURAL SELECTION; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

EID: 0032555892     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1998.0748     Document Type: Article

References (35)

1. ALBERY, W. J. & KNOWLES, J. (1976). Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15, 5631-5640.
2. BENNER, S. A. (1989). Enzyme kinetics and molecular evolution. Chem. Rev. 89, 789-806.
3. CHANDRASEKHARAN, U. M., SANKER, S., GLYNIAS, M. J., KARNICK, S. S. & HUSAIN, A. (1996). Angiotensin II-forming activity in a reconstructed ancestral chymase. Science 271, 502-505.
4. COHEN, P. (1979). Control of Enzyme Activity, Chap. 3. London: Chapman & Hall.
5. CORNISH-BOWDEN, A. (1976). The effect of natural selection on enzyme catalysis. J. Mol. Biol. 101, 1-9.
6. DEMETRIUS, L. (1992). Thermodynamic perturbation of molecular systems. J. Chem. Phys. 97, 6663-6665.
7. DEMETRIUS, L. (1995). Evolutionary dynamics of enzymes. Protein Eng. 8 (8), 541-552.
8. FERSHT, A. R. (1974). Catalysis, binding and enzyme-substrate complemetarity. Proc. R. Soc. Ser. B. 187, 398-407.
9. FERSHT, A. R. (1985). Enzyme Structure and Mechanisms. New York: W. H. Freeman.
10. FRIDOVICH, I. (1975). Superoxide radical and superoxide dismutases. Ann. Rev. Biochem. 64, 97-112.
11. GOLDING, G. B. & DEAN, A. M. (1998). The structural basis of molecular adaption. Mol. Biol. Evol. 15(4), 355-369.
12. GRUNWALD, E. & STEEL, C. (1995). Solvent reorganization and thermodynamic enthalpy and entropy compensation. J. Chem. Soc. 117, 5687-5692.
13. HEINRICH, R. & HOFFMAN, E. (1991). Kinetic parameters of enzymatic reactions in states of maximal activity: an evolutionary approach. J. theor. Biol. 151, 249-288.
14. HERSCHLAG, D. (1988). The role of induced fit and conformational change of enzyme specificity and catalysis. Bioorg. Chem. 16, 62-96.
15. JENCKS, W. J. (1975). Binding energy, specificity and enzyme catalysis - the Circe effect. Adv. Enzymol. 43, 219-419.
16. JERMAN, T. M., OPITZ, J. G., STACKHOUSE, J. & BRENNER, S. (1995). Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57-59.
17. KNOWLES, J. R. (1987). Tinkering with enzymes: what are we learning? Science 236, 1252-1258.
18. KNOWLES, J. R. & ALBERY, W. J. (1977). Perfection in enzyme catalysis: the energetics of triosephosphate isomerase. Acc. Chem. Res. 10, 105-111.
19. KOHNSTAM, G. (1967). Heat capacities of activation and their use in mechanistic studies. In: Advanced Organic Chemistry (Gold, V., ed.) pp. 121-172. London: Academic Press.
20. KOSHLAND, D. E. (1958). Mechanism of transfer enzymes. In: The Enzymes (revised edition) (Boyer, P., et al., eds) pp. 305-346.
21. LIPSCOMB, W. N. (1994). Aspartate transcarbamylase from Escherichia Coli: Activity and regulation. In: Advances in Enzymology, Vol. 68 (Meister, A., ed.) pp. 67-152. Chichester: Wiley.
22. LOLIS, E. & PETSKO, G. A. (1990). Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5 Å resolution: implications for catalysis. Biochemistry 29, 6610-6625.
23. LORSCH, J. & SZOSTAK, J. W. (1996). Chance and necessity in the selection of nucleic acid catalysts. Acc. Chem. Res. 29, 103-110.
24. MCCAMMON, J. A. & HARVEY, S. C. (1989). Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
25. MCDONALD, R. C., STEITZ, T. A. & ENGELMAN, D. M. (1979). Yeast hexokinase in solution exhibits a large conformational change upon binding glucose or glucose 6-phosphate. Biochemistry 18, 338-342.
26. NAKAGAWA, S., HSIANG-AI, Y., KARPLUS, M. & UMEYAMA, H. (1993). Active site dynamics of acyl-chymotrypsin. Protein: Structure, Function and Genetics 16, 172-194.
27. PAGE, M.I. (1987). Theories of enzyme catalysis. In: Enzyme Mechanisms (Page, M. I. & Williams, A; eds) pp. 1-11. London: Royal Society of Chemistry.
28. PETTERSON, G. (1989). Effect of evolution on the kinetic properties of enzymes. Eur. J. Biochem. 184, 561-566.
29. PETTERSON, G. (1992). Evolutionary optimization of the catalytic efficiency of enzymes. Eur. J. Biochem. 206, 289-295.
30. POST, C. B. & RAY, W. J. (1995). Reexamination of induced fit as a determinant of substrate specificity in enzymatic reactions. Biochemistry 34 (49), 15881-15885.
31. RADZICKA, A. & WOLFENDEN, R. (1995). A proficient enzyme Science 367, 90-93.
32. SAMPSON, N. S. & KNOWLES, J. R. (1992). Sequential movement: definition of the structural requirements for looop closure in catalysis by triosephosphate isomerase. Biochemistry 31, 8482-8487.
33. SIMOPOULOS, T. & JENCKS, W. R. (1994). Alkaline phosphatase is an almost perfect enzyme. Biochemistry 33, 10375-10380.
34. TIPPER, D. J. & STROMINGER, J. (1965). Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-alanine. Proc. Natl Acad. Sci. U.S.A. 54, 1133-1141.
35. WAXMAN, D. J. & STROMINGER, J. (1980). Sequence of active site peptides from the penicillin sensitive D-alanine carboxypeptidase of Bacillus subtilis. J. Biol. Chem. 255 (9), 3964-3976.