Computer modeling of enzyme catalysis and

Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry, 40, 201... 

S. Braun-Sand, M. H. M. Olsson, A. Warshel, Adv. Phys. Org. Chem. 40, 201 (2005). Computer Modeling of Enzyme Catalysis and Its Relationship to Concepts in Physical Organic Chemistry. 

Abstract This chapter introduces the basic principles used in applying isotope effects to studies of the kinetics and mechanisms of enzyme catalyzed reactions. Following the introduction of algebraic equations typically used for kinetic analysis of enzyme reactions and a brief discussion of aqueous solvent isotope effects (because enzyme reactions universally occur in aqueous solutions), practical examples illustrating methods and techniques for studying enzyme isotope effects are presented. Finally, computer modeling of enzyme catalysis is briefly discussed. 

As for any catalytic process, the study of enzyme catalysis focuses on the determination of reaction energies and kinetic parameters, which requires understanding ground state and transition state (TS) geometries. Computational methods are valuable in this matter, as the TS is hard to be trapped experimentally due to the short-lived nature of the species. However, the intrinsic complexity of the bio-enzymatic reaction, previously described, as well as the way it influences the kinetics have to be modeled in the calculations. 

Before we proceed, it is important to clarify the procedure of parameter fitting, and its validation. The quantity to be compared in analyzing the origin of enzyme catalysis is the change in free energy of activation in the enzyme relative to an equivalent, uncatalyzed reaction in water. Therefore, it is reasonable to assume that the computational model that is parameterized for the aqueous reaction and can reproduce the reduction of free energy barrier in the enzyme can yield insights on enzyme catalysis. Nevertheless, we emphasize that it is equally critical to validate the computational model... 

In analyzing the origin of enzyme catalysis, Warshel and others have advocated the importance of comparing the enzymatic reaction with a reference reaction in water [32]. In addition, it is also necessary to study the reference reaction in the gas phase in order to understand the intrinsic reactivity and the effect of solvation. Thus, to understand enzyme catalysis fully, we must compare results for the same reaction in the gas phase (intrinsic reactivity), in aqueous solution (solvation effects), and in the enzyme (catalysis). This is not possible when there is no model reaction for the uncatalyzed process in the gas phase and in water, or if the uncatalyzed reaction is a bimolecular process as opposed to a unimolecular reaction in the enzyme active site. None of these problems apply to the ODCase reaction. Furthermore, OMP decarboxylation is a unimolecular process, both in water and the enzyme, providing an excellent opportunity to compare directly the computed free energies of activation [1] this is the approach that we have undertaken [16]. Warshel et al. used an ammonium ion-orotate ion pair fixed at distances of 2.8 or 3.5 A as the reference reaction in water to mimic an active site lysine residue [32]. 

Given recent developments in computer modeling of chemical reactions, there is considerable interest in attempting to develop a mathematical understanding of enzyme catalysis. The sheer complexity of enzymes means that at present, it is possible to apply a strict quantum mechanical approach to only a limited region, such as the active site, and classical molecular mechanics are used to describe the remainder of the molecule. This combined approach had some success in modeling some aspects of enzyme-catalyzed reactions, such as the importance of particular side chains in the catalytic process.However, a complete mathematical description of enzyme catalysis remains a considerable way off. 

It seems to us that the complicated interrelations between structure and function in enzyme catalysis cannot be fully understood without a model that takes all the relevant interactions into account. If one can devise sufficiently accurate schemes for simulating enzymatic reactions and reproducing the observed rate constants, it would be possible to examine the different contributions to the calculated activation energy and evaluate their relative importance. This would also make it possible to explore the detailed mechanisms of enzyme catalysis in a way that is not accessible to direct experimental methods (e.g. with a reliable computational simulation scheme, the relative importance of such factors as strain and electrostatics can be readily evaluated). However, it is, important to realise that in order for a theoretical framework to be really useful in this context, it should be able to give semi-quantitative or quantitative information, rather than just providing an exercise in computational quantum chemistry at the qualitative level. 

One of the most promising approaches for elucidation of enzyme catalytic mechanisms and designing new catalysts is a directed evolution , method of purposeful mutation of non-enzymatic proteins to evolve desired activity mimicking native enzymes. Another important trend in chemical and oizyme catalysis is the growing role of theoretical calculation of thermo mamic parameters of enzyme reactions, conqniter analysis of X-ray structural models, taking from Data Base, computer modeling of structure of chemical catalysts and enzymes and their interaction with substrates and inhibitors, and theoretical construction of transition and pretransitim states of reactions of interest. 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

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