Chapter 8

Where to Start

Zalatan, J. G., and Herschlag, D. 2009. The far reaches of enzymology. Nat. Chem. Biol. 5:516–520.

Hammes, G. G. 2008. How do enzymes really work? J. Biol. Chem. 283:22337–22346.

Koshland, D. E., Jr. 1987. Evolution of catalytic function. Cold Spring Harbor Symp. Quant. Biol. 52:1–7.

Jencks, W. P. 1987. Economics of enzyme catalysis. Cold Spring Harbor Symp. Quant. Biol. 52:65–73.

Lerner, R. A., and Tramontano, A. 1988. Catalytic antibodies. Sci. Am. 258(3):58–70.

Books

Cook, P. F., and Cleland, W. W. 2007. Enzyme Kinetics and Mechanism. Garland Press.

Fersht, A. 1999. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman and Company.

Walsh, C. 1979. Enzymatic Reaction Mechanisms. W. H. Freeman and Company.

Bender, M. L., Bergeron, R. J., and Komiyama, M. 1984. The Bioorganic Chemistry of Enzymatic Catalysis. Wiley-Interscience.

Abelson, J. N., and Simon, M. I. (Eds.). 1992. Methods in Enzymology. Academic Press.

Friedmann, H. C. (Ed.). 1981. Benchmark Papers in Biochemistry, vol. 1, Enzymes. Hutchinson Ross.

Transition-State Stabilization, Analogs, and Other Enzyme Inhibitors

Schramm, V. L. 2007. Enzymatic transition state theory and transition state analog design. J. Biol. Chem. 282:28297–28300.

Pauling, L. 1948. Nature of forces between large molecules of biological interest. Nature 161:707–709.

Leinhard, G. E. 1973. Enzymatic catalysis and transition-state theory. Science 180:149–154.

Kraut, J. 1988. How do enzymes work? Science 242:533–540.

Waxman, D. J., and Strominger, J. L. 1983. Penicillin-binding proteins and the mechanism of action of β-lactam antibiotics. Annu. Rev. Biochem. 52:825–869.

Abraham, E. P. 1981. The β-lactam antibiotics. Sci. Am. 244(6):76–86.

Walsh, C. T. 1984. Suicide substrates, mechanism-based enzyme inactivators: Recent developments. Annu. Rev. Biochem. 53:493–535.

Catalytic Antibodies

Hilvert, D. 2000. Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69:751–794.

Wade, H., and Scanlan, T. S. 1997. The structural and functional basis of antibody catalysis. Annu. Rev. Biophys. Biomol. Struct. 26:461–493.

Lerner, R. A., Benkovic, S. J., and Schultz, P. G. 1991. At the crossroads of chemistry and immunology: Catalytic antibodies. Science 252:659–667.

Cochran, A. G., and Schultz, P. G. 1990. Antibody-catalyzed porphyrin metallation. Science 249:781–783.

Enzyme Kinetics and Mechanisms

Hammes, G. G., Benkovic, S. J., and Hammes-Schiffer, S. 2011. Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis. Biochemistry 50:10422–10430.

Johnson, K. A., and Goody, R. S. 2011. The Original Michaelis Constant: Translation of the 1913 Michaelis−Menten Paper. Biochemistry 50:8264–8269.

Hammes-Schiller, S., and Benkovic, S. J. 2006. Relating protein motion to catalysis. Annu. Rev. Biochem. 75:519–541.

Benkovic, S. J., and Hammes-Schiller, S. 2003. A perspective on enzyme catalysis. Science 301:1196–1202.

Hur, S., and Bruice, T. C. 2003. The near attack conformation approach to the study of the chorismate to prephenate reaction. Proc. Natl. Acad. Sci. U.S.A. 100:12015–12020.

Miles, E. W., Rhee, S., and Davies, D. R. 1999. The molecular basis of substrate channeling. J. Biol. Chem. 274:12193–12196.

Warshel, A. 1998. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J. Biol. Chem. 273:27035–27038.

Cannon, W. R., and Benkovic, S. J. 1999. Solvation, reorganization energy, and biological catalysis. J. Biol. Chem. 273:26257–26260.

Cleland, W. W., Frey, P. A., and Gerlt, J. A. 1998. The low barrier hydrogen bond in enzymatic catalysis. J. Biol. Chem. 273: 25529–25532.

Romesberg, F. E., Santarsiero, B. D., Spiller, B., Yin, J., Barnes, D., Schultz, P. G., and Stevens, R. C. 1998. Structural and kinetic evidence for strain in biological catalysis. Biochemistry 37:14404–14409.

Fersht, A. R., Leatherbarrow, R. J., and Wells, T. N. C. 1986. Binding energy and catalysis: A lesson from protein engineering of the tyrosyl-tRNA synthetase. Trends Biochem. Sci. 11:321–325.

Jencks, W. P. 1975. Binding energy, specificity, and enzymic catalysis: The Circe effect. Adv. Enzymol. 43:219–410.

Knowles, J. R., and Albery, W. J. 1976. Evolution of enzyme function and the development of catalytic efficiency. Biochemistry 15:5631–5640.

Single Molecule Studies

Allewell, N. M. 2010. Thematic Minireview Series: Single-molecule Measurements in Biochemistry and Molecular Biology. J. Biol. Chem. 285:18959–18983. A series of reviews on single-molecule studies.

Min, W., English, B. P., Lou, G., Cherayil, B. J., Kou, S. C., and Xie, X. S. 2005. Fluctuating Enzymes: Lessons from Single-Molecule Studies. Acc. Chem. Res. 38: 923–931.

Xie, X. S., and Lu, H. P. 1999. Single-molecule enzymology. J. Biol. Chem. 274:15967–15970.

Lu, H. P., Xun, L., and Xie, X. S. 1998. Single-molecule enzymatic dynamics. Science 282:1877–1882.