Theoretical Biochemistry

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 orCleavage 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 energy profile of the LMPTP. Substrate trapping in cysteine to serine mutated PTPases. Prediction of a ligand induced conformational change in the active site of CDC25A. Kinetic isotope effects in phosphoryl transfer reactions. 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 (G.M. Verkhivker, D. Bouzida, D.K. Gehlhaar, P.A. Rejto, L. Schaffer, S. Arthurs, A.B. Colson, S.T. Freer, V. Larson, B.A: Luty, T. Marrone and P.W. Rose). Structural models for molecular recognition. Structure-based analysis of HIV-1 protease-inhibitor binding. Structure-based computational models of ligand-protein binding dynamics and molecular docking. Computer simulations of ligand-protein binding. Computer simulations of HIV-1 protease-inhibitor binding dynamics and thermodynamics. Conclusions. Modelling G-Protein Coupled Receptors (C. Higgs and C.A. Reynolds). Introduction. Receptor structure and modelling. Ligand binding. Structural changes. Receptor-G-protein interactions. GPCR dimerisation. Conclusions. 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 and H. Weinstein). TBP and transcription. TATA box sequence specific recognition. Dynamics effects in complex stabilization. Towards the preinitiation complex assembly. Concluding remarks. A Multi-Component Model for Radiation Damage to DNAfrom its Components (S.D. Wetmore, L.A. Eriksson and R.J.Boyd). Introduction. Characterization of DNA radiation products. Full DNA studies. Multi-component model for DNA radiation damage. Concluding remarks. New Computational Strategies for the Quantum Mechanical Study of Biological Systems in Condensed Phases (C. Adamo, M. Cossi, N. Rega and V. Barone). Introduction. The density functional model. Vibrational averaging. Solvent effects. Applications. Concluding remarks. Modelling Enzyme-Ligand Interactions (M.J. Ramos, A. Melo and E.S. Henriques). Introduction. Strategies in enzyme-ligand design. The enzyme-ligand complex in motion. A quantum insight into the study of enzyme-ligand interactions. Conclusions. The QM/MM Approach to Enzymatic Reactions (A.J. Mulholland). Introduction. Theory. QM/MM methods. Techniques for reaction modelling. Practical aspects of modelling enzyme reactions. Some recent applications. Conclusions. Quinones and Quinoidal Radicals in Photosynthesis (R.A. Wheeler). Introduction. Tests of computational methods for calculating properties of quinoidal radicals. Calculated properties of quinoidal radicals important in photosynthesis. Semiquinone radical anions in plant photosystem II. Conclusion and future directions. Author Index. Subject Index.