Theoretical Biochemistry, Volume 9

1st Edition

Processes and Properties of Biological Systems

Authors: Leif A. Eriksson
Hardcover ISBN: 9780444502926
eBook ISBN: 9780080542706
Imprint: Elsevier Science
Published Date: 19th February 2001
Page Count: 720
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Table of Contents

The Structure and Function of Blue Copper Proteins (U. Ryde, M.H.M. Olsson and K. Pierloot). Introduction. Methods. Geometry. Electronic spectra. Reorganisation energies. Reduction potentials. Related proteins. Protein strain. Concluding remarks.

Myoglobin (D. Karancsi-Menyhárd, G. Keserü and G. Náray-Szabó). Introduction. Conformation and structural dynamics. Complexes with various ligands. Photodissociation. Recombination. Ligand migration. Mechanisms for Enzymatic Reactions Involving Formation or Cleavage of O-O Bonds (P.E.M. Siegbahn and M.R.A. Blomberg). Introduction. Methods and models. Formation of O2. O-O bond cleavage. Conclusions. Catalytic Reactions of Radical Enzymes (F. Himo and L.A. Eriksson). Introduction. Methodology. Galactose oxidase. Pyruvate formate-lyase. Ribonucleotide reductase. Concluding remarks. Theoretical Studies of Coenzyme B12-Dependent Carbon-Skeleton Rearrangements (D.M. Smith, S.D. Wetmore and L. Radom). Introduction. Background. Evaluation of theoretical techniques. 2-Methyleneglutarate mutase. Methylmalonyl-CoA mutase. Glutamate mutase. Comparison of the models for B12-dependent carbon-skeleton mutases. The partial-proton-transfer concept. Conclusions. Simulations of Enzymatic Systems: Perspectives from Car-Parinello Molecular Dynamics Simulations (P. Carloni and U. Rothlisberger). Introduction. Principles of the Car-Parinello method. Car-Parinello modelling of biological systems. Applications to non-enzymatic systems. Applications to enzymes. Outlook. Computational Enzymology: Protein Tyrosine Phosphatase Reactions (K. Kolmodin, V. Luzhkov and J. Åqvist). Introduction. Protein tyrosine phosphatase reactions. The empirical valence bond method. Reaction free ene


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.


For experimental and research chemists and biochemists who use theoretical and computational techniques in their work.


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© Elsevier Science 2001
Elsevier Science
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@from:A.S. Edison, University of Florida @qu:"Researchers working on any of the applications covered in the book will find very stimulating chapters that do a fine job of demonstrating the power of combining theory with experiment." @source:Journal of the American Chemical Society, 2002

About the Authors

Leif A. Eriksson Author

Affiliations and Expertise

Department of Quantum Chemistry, Uppsala University, Box 518, 751 20 Uppsala, Sweden