Multiple Levels Of Theory Approaches To QM/MM Studies Of Enzyme Mechanisms

Enzyme is an efficient catalysis in living organisms. In most biological systems, enzyme is all very important because it can catalyze most biochemical processes and accelerate the metabolism of living organisms. Intensively understanding the activity of enzymatic mechanism is not only a challenge but a fundamental requirement for quantitatively understanding biochemical processes and further applying enzymatic efficiency, specificities. Experimentally, Great progresses have been achieved both in the analytic techniques for protein structures (such as x-ray, NMR etc) and in the field of gene engineering. However, the correlations between the enzymatic structure and its catalytic functions are not fully clear, and in another aspect, how to validate the right mechanism in a specific catalytic process is also a challenge. In past few decades, computer simulation is playing an increasing role to study enzymatic mechanisms, which compensate the limitation of experimental and theoretical measures.Enzymes are very large and heterogeneous, containing at least thousands of atoms. Its remarkable capability is not only determined by its active site, but also affected by its protein and solvent environment. Therefore, it requires the computational method to take the heterogeneous enzyme environment into account explicitly. Conbined quantum mechanical/molecular mechanical (QM/MM) mechods have become the method of the choice of modelling of reactions in enzyme. In QM/MM simulations of reactions, multiple levels of theory approaches, from semiempirical level to ab initop molecule orbitals and density functional methods, have been used. Ab initio QM/MM is more accurate and relable; however, its computational cost is expensive so that most ab initio QM/MM studies have been limited to determine potential energy surfaces rather than FESs. Calculation of free energy surfaces using ab initio QM/MM are also limited to treat the QM parts by minimizations and the MM parts by sampling. Simultaneous sampling of QM and MM parts has been limited to systems with relatively small QM centers and for which one-dimensional FESs can be envisioned. The computional cost of semiempirical level methods is low, and semiempirical QM/MM is more efficient to calculate FESs and allows simultaneous sampling. It is, however, well-known that the accuracies of semi-empirical models are system-dependent, and results may become unreliable because of large errors. So it is very important to efficiently apply multiple levels of theory approaches to obtain the right potential energy surfaces and free energy surfaces. We have made many efforts to the field including multiple-levels QM/MM studies of enzyme mechanics. In Chapter 2, we detailtedly describes the work for studing enzymatic mechanism. In the work, the catalytic mechanism of a pyridoxal 5'-phosphate-dependent enzyme, L-serine dehydratase, has been investigated using ab initio quantum mechanical/molecular mechanical (QM/MM) methods. New insights into the chemical steps have been obtained, including the chemical role of the substrate carboxyl group in the Schiff base formation step, and a proton-relaying mechanism involving the phosphate of the cofactor in theβ-hydroxyl-leaving step. The latter step is of no barrier and follows sequentially after the elimination of theα-proton, leading to a single but sequentiala,β-elimination step. The rate-limiting transition state is specifically stabilized by the enzyme environment. At this transition state, charges are localized on the substrate carboxyl group, as well as on the amino group of Lys41. Specific interactions of the enzyme environment with these groups are able to lower the activation barrier significantly. One major difficulty associated with studies of complicated enzymatic reactions using ab initio QM/MM models is the appropriate choices of reaction coordinates. In this study, we have made use of efficient semi-empirical QM/MM and pathway optimization techniques to overcome this difficulty.Our effort also involved the methodological development for free energy calculation based on multiple-levels QM/MM. Free energy calculation is the first assignment to achieve the thermodynamical prosperities and is also one of the most difficult fields in computer simulation. In our work, we presented an efficient scheme to calculate multidimensional free energy surface as described in Chapter 3, in which we detailedly described a refined adaptive-umbrella-sampling method presented to explore multidimensional free energy surface for complex chemical reactions in solution and in enzyme. Adaptive umbrella sampling method is an efficient, important tool to sample rare events. To our target, we skillfully designed a so-called refined adaptive umbrella potential to achieve convergent free energy surface. In the scheme, a strictly adaptive umbrella potential and a global background potential are used to fit the system including chemical reaction. Moreover, to overcome the deficiencies of AM1 model, we applied the AM1 model of specific reaction parameters. The formic acid dimer is used to test the scheme. We obtained the convergent free energy surface, which is in accord with the reported results. The solvent effects are analyzed and validated. We hope the scheme can be extensively used in complex chemical reaction in enzyme.