Approaches to Understanding Enzymes

Biochemistry examines the chemistry of molecules involved in life. These range from small molecules such as carbohydrates to large molecules such as DNA. Much of the chemistry of biological molecules is organic reactions, and so its place within this book is logical. 

As might be expected, computational biochemists have applied the tools and methodologies of quantum chemistry to biological molecules. Many of the same techniques discussed in the previous chapters have been utilized to explicate reaction mechanisms, properties, and structures of a broad range of biomolecules, including proteins, DNA, and RNA. However, the scope of computational biochemistry is enormous, and a reasonable comprehensive coverage of this topic is beyond the scope of this book. 

To provide a flavor of how computational chemistry has been applied to biochemical problems, this chapter focuses on a small subset of computational biochemistry, namely, computational enzymology. Presented here are some examples of how quantum chemical computations have been used to understand the mechanism of catalysis provided by enzymes. The chapter ends with a look at one of the true holy grails of biochemistry the abihty to design an enzyme for a specific purpose, to catalyze a particular reaction where nature provides no such option. 

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Dugas, H., Penney, C. Bioorganic Chemistry, New York, Springer-Verlag 1981 Green, B. S., Ashani, Y., Chipman, D. (eds.) Chemical Approaches to Understanding Enzyme Catalysis, Amsterdam—New York, Elsevier 1982... 

Tabushi, I., Kimura, Y. Yamamura, K. (1982). In Chemical Approaches to Understanding Enzyme Catalysis, ed. G. S. Green, Y. Ashami D. Chipman. Elsevier, Amsterdam. 

Whitten, D. G. Russell, J. C. Foreman, T. K. Schmehl, R. H. Bonilha, J. Braun, A. M. Sobol, W. In "Chemical Approaches to Understanding Enzyme Catalysis Biomimetic Chemistry and Transition-State Analogs" Green, B. S. Ashani, Y. Chipman, D., Eds. Studies in Organic Chemistry, Vol. 10 Elsevier Amsterdam, 1981. 

G. Wulff and A. Sarhan, In Chemical approaches to understanding enzyme catalysis biomimetic chemistry and transition state analogs, B.S. Green, Y. Ashani and D. Chipman Eds, Elsevier, Amsterdam, p. 106 (1982). 

Whitten DG, Russell JC, Foreman TK, Schmehl RH, Bonilha J, Braun AM, Sobol W (1982) In Chemical Approaches to Understanding Enzyme Catalysis Bio-mimetic Chemistry and Transition-State Analogs. Green BS, Ashani Y, Chipman D (eds). Elsevier, Amsterdam... 

G.Wulff, A.Sarhan, "Chemical Approaches to Understanding Enzyme Catalysis Biomimetic Chemistry and Transition-State Analogs", B.S.Green, Y.Ashani, D.Chipman Eds., Elsevier, Amsterdam, 1982,... 

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