Enzyme mechanisms case studies

The balance of this chapter will be devoted to several classic and representative enzyme mechanisms. These particular cases are well understood, because the three-dimensional structures of the enzymes and the bound substrates are known at atomic resolution, and because great efforts have been devoted to kinetic and mechanistic studies. They are important because they represent reaction types that appear again and again in living systems, and because they demonstrate many of the catalytic principles cited above. Enzymes are the catalytic machines that sustain life, and what follows is an intimate look at the inner workings of the machinery. 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

Haldane is also valid for the ordered Bi Bi Theorell-Chance mechanism and the rapid equilibrium random Bi Bi mechanism. The reverse reaction of the yeast enzyme is easily studied an observation not true for the brain enzyme, even though both enzymes catalyze the exact same reaction. A crucial difference between the two enzymes is the dissociation constant (i iq) for Q (in this case, glucose 6-phosphate). For the yeast enzyme, this value is about 5 mM whereas for the brain enzyme the value is 1 tM. Hence, in order for Keq to remain constant (and assuming Kp, and are all approximately the same for both enzymes) the Hmax,f/f max,r ratio for the brain enzyme must be considerably larger than the corresponding ratio for the yeast enzyme. In fact, the differences between the two ratios is more than a thousandfold. Hence, the Haldane relationship helps to explain how one enzyme appears to be more kmeticaUy reversible than another catalyzing the same reaction. 

Later, we shall discuss several examples of the successful application of transient kinetics to the solution of enzyme mechanisms (Chapter 7) and to protein folding (Chapters 18 and 19). Here, we briefly describe some of the strategies and tactics used by the kineticist to initiate a transient kinetic study. On many occasions, steady state kinetics and other studies have set kineticists a well-defined and specific question to answer. At other times, they just wish to study a particular system to gather information. In both cases there is no substitute for... 

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