Note: Cover -- Theoretical Biochemistry: Processes and Properties of Biological Systems -- Copyright Page -- Foreword -- Table of Contents -- Chapter 1. The Structure and Function of Blue Copper Proteins -- 1. Introduction -- 2. Methods -- 3. Geometry -- 4. Electronic spectra -- 5. Reorganisation energies -- 6. Reduction potentials -- 7. Related proteins -- 8. Protein strain -- 9. Concluding remarks -- Chapter 2. Myoglobin -- 1. Introduction -- 2. Conformation and structural dynamics -- 3. Complexes with various ligands -- 4. Photodissociation -- 5. Recombination -- 6. Ligand migration -- Chapter 3. Mechanisms for Enzymatic Reactions Involving Formation or Cleavage of O-O Bonds -- 1. Introduction -- 2. Methods and models -- 3. Formation of O2 -- 4. O-O bond cleavage -- 5. Conclusions -- Chapter 4. Catalytic Reactions of Radical Enzymes -- 1. Introduction -- 2. Methodology -- 3. Galactose oxidase -- 4. Pyruvate formate-lyase -- 5. Ribonucleotide reductase -- 6. Concluding remarks -- Chapter 5. Theoretical Studies of Coenzyme B12-Dependent Carbon- Skeleton Rearrangemems -- 1. Introduction -- 2. Background -- 3. Evaluation of theoretical techniques -- 4. 2-Methyleneglutarate mutase -- 5. Methylmalonyl-CoA mutase -- 6. Glutamate mutase -- 7. Comparison of the models for B12-dependent carbon-skeleton mutases -- 8. The partial-proton-transfer concept -- 9. Conclusions -- Chapter 6. Simulations of Enzymatic Systems: Perspectives from Car- Parrinello Molecular Dynamics Simulations -- 1. Introduction -- 2. Principles of the Car-Parrinello method -- 3. Car-Parrinello modeling of biological systems -- 4. Applications to non-enzymatic systems -- 5. Applications to enzymes -- 6. Outlook -- Chapter 7. Computational Enzymology: Protein Tyrosine Phosphatase Reactions -- 1. Introduction -- 2. Protein tyrosine phosphatase reactions. , 3. The empirical valence bond method -- 4. Reaction free energy profile of the LMPTP -- 5. Substrate trapping in cysteine to serine mutated PTPases -- 6. Prediction of a ligand induced conformational change in the active site of CDC25A -- 7. Kinetic isotope effects in phosphoryl transfer reactions -- 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 -- 1. Structural models for molecular recognition -- 2. Structure-based analysis of HIV-1 protease-inhibitor binding -- 3. Structure-based computational models of ligand-protein binding dynamics and molecular docking -- 4. Computer simulations of ligand-protein binding -- 5. Computer simulations of HIV-1 protease-inhibitor binding dynamics and thermodynamics -- 6. Conclusions -- Chapter 9. Modelling G-Protein Coupled Receptors -- 1. Introduction -- 2. Receptor structure and modelling -- 3. Ligand binding -- 4. Structural changes -- 5. Receptor-G-protein interaction -- 6. GPCR dimerisation -- 7. Conclusions -- 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 -- 1. TBP and transcription -- 2. TATA box sequence specific recognition -- 3. Dynamic effects in complex stabilization -- 4. Towards the preinitiation complex assembly -- 5. Concluding remarks -- Chapter 11. A Multi-Component Model for Radiation Damage to DNA from its Constituents -- 1. Introduction -- 2. Characterization of DNA radiation products -- 3. Full DNA studies -- 4. A Multi-component model for DNA radiation damage -- 5. Concluding remarks -- Chapter 12. New Computational Strategies for the Quantum Mechanical Study of Biological Systems in Condensed Phases. , 1. Introduction -- 2. The density functional model -- 3. Vibrational averaging -- 4. Solvent effects -- 5. Applications -- 6. Concluding remarks -- Chapter 13. Modelling Enzyme-Ligand Interactions -- 1. Introduction -- 2. Strategies in enzyme-ligand design -- 3. The enzyme-ligand complex in motion -- 4. A quantum insight into the study of enzyme-ligand interactions -- 5. Conclusions -- Chapter 14. The QM/MM Approach to Enzymatic Reactions -- 1. Introduction -- 2. Theory -- 3. QM/MM methods -- 4. Techniques for reaction modelling -- 5. Practical aspects of modelling enzyme reactions -- 6. Some recent applications -- 7. Conclusions -- Chapter 15. Quinones and Quinoidal Radicals in Photosynthesis -- 1. Introduction -- 2. Tests of computational methods for calculating properties of quinoidal radicals -- 3. Calculated properties of quinoidal radicals important in photosynthesis -- 4. Semiquinone radical anions in plant photosystem II -- 5. Conclusions and future directions -- Author Index -- Subject Index.