Theoretical Biochemistry - Processes and Properties of Biological Systems
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Table of contents
- Table of Contentsvii
- Chapter 1. The Structure and Function of Blue Copper Proteins1
- 1. Introduction1
- 2. Methods2
- 3. Geometry6
- 4. Electronic spectra17
- 5. Reorganisation energies26
- 6. Reduction potentials28
- 7. Related proteins32
- 8. Protein strain42
- 9. Concluding remarks46
- Chapter 2. Myoglobin57
- 1. Introduction57
- 2. Conformation and structural dynamics58
- 3. Complexes with various ligands66
- 4. Photodissociation73
- 5. Recombination79
- 6. Ligand migration86
- Chapter 3. Mechanisms for Enzymatic Reactions Involving Formation or Cleavage of O-O Bonds95
- 1. Introduction95
- 2. Methods and models97
- 3. Formation of O299
- 4. O-O bond cleavage107
- 5. Conclusions137
- Chapter 4. Catalytic Reactions of Radical Enzymes145
- 1. Introduction145
- 2. Methodology147
- 3. Galactose oxidase149
- 4. Pyruvate formate-lyase158
- 5. Ribonucleotide reductase169
- 6. Concluding remarks177
- Chapter 5. Theoretical Studies of Coenzyme B12-Dependent Carbon- Skeleton Rearrangemems183
- 1. Introduction183
- 2. Background184
- 3. Evaluation of theoretical techniques190
- 4. 2-Methyleneglutarate mutase193
- 5. Methylmalonyl-CoA mutase197
- 6. Glutamate mutase200
- 7. Comparison of the models for B12-dependent carbon-skeleton mutases205
- 8. The partial-proton-transfer concept206
- 9. Conclusions209
- Chapter 6. Simulations of Enzymatic Systems: Perspectives from Car- Parrinello Molecular Dynamics Si215
- 1. Introduction215
- 2. Principles of the Car-Parrinello method216
- 3. Car-Parrinello modeling of biological systems218
- 4. Applications to non-enzymatic systems219
- 5. Applications to enzymes220
- 6. Outlook243
- Chapter 7. Computational Enzymology: Protein Tyrosine Phosphatase Reactions253
- 1. Introduction253
- 2. Protein tyrosine phosphatase reactions254
- 3. The empirical valence bond method256
- 4. Reaction free energy profile of the LMPTP263
- 5. Substrate trapping in cysteine to serine mutated PTPases274
- 6. Prediction of a ligand induced conformational change in the active site of CDC25A276
- 7. Kinetic isotope effects in phosphoryl transfer reactions279
- Chapter 8. Monte Carlo Simulations of HIV-1 Protease Binding Dynamics and Thermodynamics with Ensemb289
- 1. Structural models for molecular recognition .289
- 2. Structure-based analysis of HIV-1 protease-inhibitor binding293
- 3. Structure-based computational models of ligand-protein binding dynamics and molecular docking298
- 4. Computer simulations of ligand-protein binding302
- 5. Computer simulations of HIV-1 protease-inhibitor binding dynamics and thermodynamics312
- 6. Conclusions327
- Chapter 9. Modelling G-Protein Coupled Receptors341
- 1. Introduction341
- 2. Receptor structure and modelling342
- 3. Ligand binding351
- 4. Structural changes356
- 5. Receptor-G-protein interaction359
- 6. GPCR dimerisation363
- 7. Conclusions366
- Chapter 10. Protein-DNA Interactions in the Initiation of Transcription: The Role of Flexibility and377
- 1. TBP and transcription377
- 2. TATA box sequence specific recognition382
- 3. Dynamic effects in complex stabilization398
- 4. Towards the preinitiation complex assembly400
- 5. Concluding remarks401
- Chapter 11. A Multi-Component Model for Radiation Damage to DNA from its Constituents409
- 1. Introduction409
- 2. Characterization of DNA radiation products411
- 3. Full DNA studies437
- 4. A Multi-component model for DNA radiation damage456
- 5. Concluding remarks458
- Chapter 12. New Computational Strategies for the Quantum Mechanical Study of Biological Systems in C467
- 1. Introduction467
- 2. The density functional model469
- 3. Vibrational averaging488
- 4. Solvent effects496
- 5. Applications507
- 6. Concluding remarks532
- Chapter 13. Modelling Enzyme-Ligand Interactions539
- 1. Introduction539
- 2. Strategies in enzyme-ligand design540
- 3. The enzyme-ligand complex in motion555
- 4. A quantum insight into the study of enzyme-ligand interactions568
- 5. Conclusions578
- Chapter 14. The QM/MM Approach to Enzymatic Reactions597
- 1. Introduction597
- 2. Theory603
- 3. QM/MM methods614
- 4. Techniques for reaction modelling618
- 5. Practical aspects of modelling enzyme reactions625
- 6. Some recent applications631
- 7. Conclusions646
- Chapter 15. Quinones and Quinoidal Radicals in Photosynthesis655
- 1. Introduction655
- 2. Tests of computational methods for calculating properties of quinoidal radicals659
- 3. Calculated properties of quinoidal radicals important in photosynthesis670
- 4. Semiquinone radical anions in plant photosystem II683
- 5. Conclusions and future directions684
- Author Index691
- Subject Index695
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.
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.