Enzymes modeling reaction mechanisms

METHODS FOR MODELLING ENZYME-CATALYSED REACTION MECHANISMS... 

Mulholland AJ, GH Grant, WG Richards (1993) Computer Modeling of Enzyme Catalyzed Reaction-Mechanisms. Protein Eng. 6 (2) 133—147... 

Despite all the problems inherent to QM/CM approaches, some extremely interesting and perceptive work has been described in the literature recently in which all sorts of approaches have been used, improvements introduced and results obtained ([351, 372] and references therein). The study of enzyme catalysed reaction mechanisms, the calculation of relative binding free energies of substrates and inhibitor, and the determination of proton transfer processes in enzymatic reactions, are all good examples of enzyme-ligand interactions studies. Even though Warshel s EVB method [349] probably remains the most practical QM/CM approach for the study of enzyme catalysis, very useful work has been reported on enzyme catalysed reactions ([381] for an excellent review-[238, 319, 382-384]). This is a consequence of the accuracy of QM to treat the active site and inhibitor/substrate and the viability of classical mechanics to model the bulk of the enzyme not directly involved in the chemical reaction. 

Mulholland, A., J., Grant, G. H. and Richards, W. G. (1993) Computer modelling of enzyme catalysed reaction mechanisms, Protein Engineering 6, 133-147. 

Methods for Modelling Enzyme-Catalysed Reaction Mechanisms. - Perhaps the most obvious challenge in investigating enzyme reactions by computational modelling is posed by the very large size of enzymes, exacerbated by the need to include at least a representative part their environment (i.e. the surrounding solvent, perhaps membrane or other proteins, cofactors or DNA which may be bound to the enzyme). 

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. 

What the mechanistic baseline provided by a model reaction does do is to suggest where molecular evolution may have necessarily started, although it must be remembered that substrates and enzymes have co-evolved so that the chemical scope of a primitive substrate may not be that of a modem substrate. Furthermore, a model-reaction mechanism may indicate what processes it was necessary for an enzyme to avoid in order to open the way for a comparatively unfavorable reaction to be catalyzed. One of the most striking examples is provided by the recent studies of Kluger and his coworkers of the unexpected chemical properties of the cofactor thiamin diphosphate [25-29]. Although this work has nothing explicitly to do with... 

The simplest conclusion is then that tunneling occurs both in enzymic hydride-transfer reactions and in related non-enzymic (model) reactions. It remains to be seen whether enzymic rate acceleration has evolved simply to make the existing tunneling reaction much more efficient or instead to create new tunneling mechanisms distinct from those observed in model systems. 

Reversibly fonned micelles have long been of interest as models for enzymes, since tliey provide an amphipatliic environment attractive to many substrates. Substrate binding (non-covalent), saturation kinetics and competitive inliibition are kinetic factors common to botli enzyme reaction mechanism analysis and micellar binding kinetics. 

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... 

The carboxyl proteases are so called because they have two catalytically essential aspartate residues. They were formerly called acid proteases because most of them are active at low pH. The best-known member of the family is pepsin, which has the distinction of being the first enzyme to be named (in 1825, by T. Schwann). Other members are chymosin (rennin) cathepsin D Rhizopus-pepsin (from Rhizopus chinensis) penicillinopepsin (from Penicillium janthinel-lum) the enzyme from Endothia parasitica and renin, which is involved in the regulation of blood pressure. These constitute a homologous family, and all have an Mr of about 35 000. The aspartyl proteases have been thrown into prominence by the discovery of a retroviral subfamily, including one from HIV that is the target of therapy for AIDS. These are homodimers of subunits of about 100 residues.156,157 All the aspartyl proteases contain the two essential aspartyl residues. Their reaction mechanism is the most obscure of all the proteases, and there are no simple chemical models for guidance. 

A key question in the action of enzymes is the understanding of the mechanisms by which they attain their catalytic rate enhancement relative to the uncatalyzed reactions. Some enzymes have been shown to produce rate accelerations as large as 1019 [1], The theoretical determination of the reaction mechanisms by which enzymes carry out the chemical reactions has been an area of great interests and intense development in recent years [2-11], A common approach for the modeling of enzyme systems is the QM/MM method proposed by Warshel and Levitt [12], In this method the enzyme is divided into two parts. One part includes the atoms or molecules that participate in the chemical process, which are treated by quantum mechanical calculations. The other contains the rest of the enzyme and the solvent, generally thousands of atoms, which is treated by molecular mechanics methods. 

Mulholland AJ (2005) Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discov Today 10 1393-1402... 

Extending Semi-Empirical Calculations to Model Protein Structure and Enzyme Reaction Mechanisms... 

The kinetics of the general enzyme-catalyzed reaction (equation 10.1-1) may be simple or complex, depending upon the enzyme and substrate concentrations, the presence/absence of inhibitors and/or cofactors, and upon temperature, shear, ionic strength, and pH. The simplest form of the rate law for enzyme reactions was proposed by Henri (1902), and a mechanism was proposed by Michaelis and Menten (1913), which was later extended by Briggs and Haldane (1925). The mechanism is usually referred to as the Michaelis-Menten mechanism or model. It is a two-step mechanism, the first step being a rapid, reversible formation of an enzyme-substrate complex, ES, followed by a slow, rate-determining decomposition step to form the product and reproduce the enzyme ... 

Application of CBS extrapolations to the A5-ketosteroid isomerase-catalyzed conversion of A5-androstene-3,17-dione to the A4 isomer (Fig. 4.10) provides a test case for extensions to enzyme kinetics. This task requires integration of CBS extrapolations into multilayer ONIOM calculations [56, 57] of the steroid and the active site combined with a polarizable continuum model (PCM) treatment of bulk dielectric effects [58-60], The goal is to reliably predict absolute rates of enzyme-catalyzed reactions within an order of magnitude, in order to verify or disprove a proposed mechanism. 

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. 

In the absence of definitive information about the structure of the active site theoretical modeling of enzyme catalyzed reactions is difficult but not impossible. These difficulties are caused by the extremely large size of the enzyme-substrate-solvent system which typically comprises thousands or tens of thousands of atoms so that direct theoretical treatment at the microscopic quantum mechanical level is not yet practical. The computational demand is simply too enormous. As a compromise, a scheme generally referred to as QM/MM (quantum mechanics/molecular mechanics) has been devised. In QM/MM calculations, the bulk of the enzyme-solvent system (i.e. most of the atoms) is treated at a low cost, usually at the molecular mechanics (MM) level, while the more nearly correct and much more expensive quantum level (QM) computation is applied only to the reaction center (active site). 

J. R. Alvarez-Idaboy, R. Gonzalez-Jonte, A. Hernandez-Laguna, Y. G. Smeyers, Reaction Mechanism of the Acyl-Enzyme Formation in /3-Lactam Hydrolysis by Means of Quantum Chemical Modeling , J. Mol. Struct. 2000, 204, 13 - 28. 

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