Theoretical Biochemistry Processess and Properties of Biological Systems

About this book

Theoretical chemistry has been an area of tremendous expansion and development over the past decade; from an approach where we were able to treat only a few atoms quantum mechanically or make fairly crude molecular dynamics simulations, into a discipline with an accuracy and predictive power that has rendered it an essential complementary tool to experiment in basically all areas of science. This volume gives a flavour of the types of problems in biochemistry that theoretical calculations can solve at present, and illustrates the tremendous predictive power these approaches possess. 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-Parinello QM-MD and novel hybrid QM/MM studies are covered. 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.

Contents

The structure and function of blue copper proteins, (U. Ryde et al.). Myoglobin (D. Karancsi-Menhard et al.). Mechanisms for enzymatic reaction involviing formation or cleavage of O-O bonds (P.E.M. Siegbahn et al.). Catalytic reactions of radical enzymes (F Himo, L.A. Eriksson). Theoretical studies of coenzyme B12-dependant carbon-skeleton rearrangements (D.M. Smith et al.). Simulations of enzymatic systems: perspectives form Car-Parinello molecular dynamics simulations(P. Carloni, U. Rothlisberger). Computational enzymology: protein tyrosine phospatase reactions (K. Kolmodoin et al.). Monte Carlo simulations of HIV-1 protease binding dynamics and thermodynamics with ensembles of protein conformations: incorporating protein flexibility in decipherine mechanisms of molecular recognition (G.M. Verkhivker et al.). Modelling G-protein coupled receptors (C. Higgs, C.A. Reynolds). Protein-DNA interactions in the initiation of transcription: the role of flexibility and dynamics of the TATA recognition sequence and the TATA box binding protein (N. Pastor, H. Weinstein). A multi-component model for radiation damage to DNA from its components (S.D. Wetmore et al..). New computational strategies for the quantum mechanical study of biological systems in condensed phases (C. Adamo et al.). Modelling enzyme-ligand interactions (M.J. Ramos et al.). The QM/CM approach to enzymatic reactions (A.J. Mulholland). Quinones and quinoidal radicals in photosynthesis (R.A. Wheeler). Author index. Subject index.

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