Biological enzyme modeling reaction mechanisms

A reasonable ambition for model reactions is that their mechanisms ought to contain some dues about the mechanism of the enzyme-catalyzed reaction also. It has long been realized that it is fruitless simply to buUd the model-reaction mechanism into an enzyme active site. Such a procedure would entail the view that the factors present and at work in the model system render a complete account of the biological history of the enzyme. There is no reason to expect this to be so, and many reasons to think it would not be so. In the simplest sense, a given enzyme must occupy a niche in a metabolic network that may require its regulation and may influence its structure and mechanistic potentialities in ways that cannot be derived from non-enzymic studies. 

Sjbberg B-M (1997) Ribonucleotide Reductases - A Group of Enzymes with Different Metallosites and a Similar Reaction Mechanism. 88 139-174 Slebodnick C, Hamstra BJ, Pecoraro VL (1997) Modeling the Biological Chemistry of Vanadium Structural and Reactivity Studies Elucidating Biological Function. 89 51-108 Smit HHA, see Thiel RC (1993) 81 1-40... 

Karplus, M. and Post, C. B. (1996). Simulations of lysozyme Internal motions and the reaction mechanism. Lysozymes Model Enzymes in Biochemistry and Biology. Basel, Switzerland, Birkhauser. 

Manganese compounds of biologic importance are examined by pulse radiolysis e.g., the rate of dismutation of radiation-generated Of is catalyzed by Escherichia coli, Mn-containing superoxide dismutase involving electron transfer in which enzymes with Mn(IV), Mn(IIl), Mn(II) and Mn(I) oxidation states are involved. A kinetic model for the reaction mechanism of an Mn dismutase from Bacillus stearothermophilus accounts for the variation of the rate of decay on the concentrations of Oj, enzyme, HjOj, NaNj, KCN and H+. 

Earlier writers have also expressed useful views about proper characteristics of model reactions. In particular, Kosower, in a work that broke new ground in chemical biology ([5], pp. 276-277), suggested the difficulty of achieving the duplication of enzyme mechanisms with model compounds but noted that mechanistic parallels between enzyme and model reactions can nevertheless lead to informative results, culminating in what he denoted congruency between enzyme and model reactions, i.e., a very strong resemblance in terms of reactant structures and of the nature and sequential order of mechanistic events. 

The peroxidase reaction provides another prototype for periodic behaviour and chaos in an enzyme reaction. As noted by Steinmetz et al. (1993), in view of its mechanism based on free radical intermediates, this reaction represents an important bridge between chemical oscillations of the Belousov-Zhabotinsky type, and biological oscillators. In view of the above discussion, it is noteworthy that the model proposed by Olsen (1983), and further analysed by Steinmetz et al. (1993), also contains two parallel routes for the autocatalytic production of a key intermediate species in the reaction mechanism. As shown by experiments and accounted for by theoretical studies, the peroxidase reaction possesses a particularly rich repertoire of dynamic behaviour (Barter et al, 1993) ranging from bistability (Degn, 1968 Degn et al, 1979) to periodic oscillations (Yamazaki et al, 1965 Nakamura et al, 1969 ... 

This CuBr2-bpy/TEMPO-based catalytic system can be considered as the first synthetic functional model of galactose oxidase, as both the achieved chemoselectivity, and the proposed reaction mechanism, resemble that of the biological copper enzyme. Nevertheless, this functional model is not able to compete with the natural enzyme in terms of catalytic efficiency. Indeed, the rate of turnover is only 0.006 s while a TOE of 800 s is reached by GOase for its native substrate. The objective of future research investigations is therefore to enhance the proficiency of the catalyst to obtain an economically interesting system for industrial applications. 

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