Enzymatic reactions computational study

Computer simulation techniques offer the ability to study the potential energy surfaces of chemical reactions to a high degree of quantitative accuracy [4]. Theoretical studies of chemical reactions in the gas phase are a major field and can provide detailed insights into a variety of processes of fundamental interest in atmospheric and combustion chemistry. In the past decade theoretical methods were extended to the study of reaction processes in mesoscopic systems such as enzymatic reactions in solution, albeit to a more approximate level than the most accurate gas-phase studies. 

In order to use the stopped-flow technique, the reaction under study must have a convenient absorbance or fluorescence that can be measured spectrophotometri-cally. Another method, called rapid quench or quench-flow, operates for enzymatic systems having no component (reactant or product) that can be spectrally monitored in real time. The quench-flow is a very finely tuned, computer-controlled machine that is designed to mix enzyme and reactants very rapidly to start the enzymatic reaction, and then quench it after a defined time. The time course of the reaction can then be analyzed by electrophoretic methods. The reaction time currently ranges from about 5 ms to several seconds. 

For heavy atom isotope effects tunneling is relatively unimportant and the TST model suffices. As an example the dehalogenation of 1,2-dichloroethane (DCE) to 2-chloroethanol catalyzed by haloalkane dehalogenase DhlA is discussed below. This example has been chosen because the chlorine kinetic isotope effect for this reaction has been computed using three different schemes, and this system is among the most thoroughly studied examples of heavy atom isotope effects in enzymatic reactions. 

The Intention of this volume is to give a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and to illustrate the tremendous predictive power these approaches possess. With these aspects in mind, I have tried to gather some of the leading scientists in the field of theoretical/computational biochemistry and let them present their work. You will hence find a wide range of computational approaches, from classical MD and Monte Carlo methods, via semi-empirical and DFT approaches on isolated model systems, to Car-Parrinello QM-MD and novel hybrid QM/MM studies. The systems investigated also cover a broad range from membrane-bound proteins to various types of enzymatic reactions as well as inhibitor studies, cofactor properties, solvent effects, transcription and radiation damage to DNA. 

The information about the existence of the multiple intermediate conformational states involving the enzymatic active complex formation and a detailed characterization of the energy landscape (Fig. 24.7) of the complex formation process cannot be obtained either by only an ensemble-averaged experiment, only a single-molecule experiment, or a solely computational approach. The combined approach demonstrated here is essential to achieve the potential of both single-molecule spectroscopy and MD simulations for studies of slow enzymatic reactions and protein conformational change dynamics. 

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. 

Dealing with complex systems (two or more coupled enzymatic reactions or reactions with coenzyme regeneration) a complete kinetic investigation and computer simulation of the reaction system is very helpful to achieve the desired selectivity and yield of reaction (e. g. by choosing a sensible substrate and coenzyme concentration, enzyme ratio and reaction time). A case study is available[42, 431 exemplifying the production of L-tert-leucine by reductive animation and simultaneous coenzyme regeneration. 

Wolfgang Pauli once stated that the surface was invented by the devil, illustrating the complexity and difficulty of studying the surfaces of materials. This prompts a fundamental question What is the surface of a material The simplest definition is that the surface is the boundary at which the atoms that make up one material terminate and interface with the atoms of a new material. If the surface is considered to be just the outermost layer of atoms of a material, then it comprises on average only 10 atoms per square centimeter (1 square centimeter equals 0.155 square inch), as compared to the bulk of the material, which consists of approximately 10 atoms per cubic centimeter. Surface chemistry is important in many critical chemical processes, such as enzymatic reactions at biological interfaces found in cell walls and membranes, in electronics at the surfaces and interfaces of microchips used in computers, and the heterogeneous catalysts found in the catalytic converter used for cleaning emissions in automobile exhausts. 

Density functional theory (DFT) is today a very powerful tool in the study of electronic structures of molecules. Advancements in DFT, in particular the development of Becke s 3-parameter functional (B3LYP), together with the nearly exponential growth of computer power, have made it possible to treat ever larger systems at a reasonable level of accuracy. Using the B3LYP with a medium-sized basis set, one can routinely handle systems containing more than 100 atoms today, a development that has opened the door for many applications. One of the fields that quantum chemical methods have had very positive impacts on in recent years is the study of enzymatic reaction mechanisms. 

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