Theoretical biochemistry: processes and properties of biological systems edited by Leif A Eriksson

Includes index.

Chapter - 1 The Structure and Function of Blue Copper Proteins, Chapter - 2 Myoglobin / D. Karancsi-Menyhard, G. Keseru, G. Naray-Szabo, Chapter - 3 Mechanisms for Enzymatic Reactions Involving Formation or Cleavage of O-O Bonds / P. E. M. Siegbahn, M. R. A. Blomberg, Chapter - 4 Catalytic Reactions of Radical Enzymes / F. Himo, L. A. Eriksson, Chapter - 5 Theoretical Studies of Coenzyme B[subscript 12]-Dependent Carbon-Skeleton Rearrangements / D. M. Smith, S. D. Wetmore, L. Radom, Chapter - 6 Simulations of Enzymatic Systems: Perspectives from Car-Parrinello Molecular Dynamics Simulations / P. Carloni, U. Rothlisberger,
Chapter - 7 Computational Enzymology: Protein Tyrosine Phosphatase Reactions / K. Kolmodin, V. Luzhkov, J. Aqvist, Chapter- 8 Monte Carlo Simulations of HIV-1 Protease Binding Dynamics and Thermodynamics with Ensembles of Protein Conformations: Incorporating Protein Flexibility in Deciphering Mechanisms of Molecular Recognition [et al.] / G. M. Verkhivker, D. Bouzida, D. K. Gehlhaar, Chapter - 9 Modelling G-Protein Coupled Receptors / C. Higgs, C. A. Reynolds, Chapter - 10 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, Chapter - 11 A Multi-Component Model for Radiation Damage to DNA from its Constituents / S. D. Wetmore, L. A. Eriksson, R. J. Boyd, Chapter - 12 New Computational Strategies for the Quantum Mechanical Study of Biological Systems in Condensed Phases [et al.] / C. Adamo, M. Cossi, N. Rega, Chapter - 13 Modelling Enzyme-Ligand Interactions / M. J. Ramos, A. Melo, E. S. Henriques, Chapter - 14 The QM/MM Approach to Enzymatic Reactions / A. J. Mulholland, Chapter - 15 Quinones and Quinoidal Radicals in Photosynthesis / R. A. Wheeler, Author Index, Subject Index

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.