Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences.
Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface - p. xvii 7. Chapter One: Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins - p. xviii 8. Chapter Two: Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions - p. 20 9. Chapter Three: Accurate Calculation of Electric Fields Inside Enzymes - p. 43 10. Chapter Four: Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics - p. 72 11. Chapter Five: Modeling Mercury in Proteins - p. 101 12. Chapter Six: Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics - p. 122 13. Chapter Seven: New Algorithms for Global Optimization and Reaction Path Determination - p. 143 14. Chapter Eight: Simulation Studies of Protein and Small Molecule Interactions and Reaction - p. 167 15. Chapter Nine: How to Run FAST Simulations - p. 212 16. Chapter Ten: Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach - p. 225 17. Chapter Eleven: A Networks Approach to Modeling Enzymatic Reactions - p. 248 18. Chapter Twelve: Conformational Sub-states and Populations in Enzyme Catalysis - p. 271 19. Chapter Thirteen: Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites - p. 297 20. Chapter Fourteen: Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation - p. 326 21. Chapter Fifteen: Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands - p. 342 22. Chapter Sixteen: Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation - p. 371 23. Chapter Seventeen: Detecting Allosteric Networks Using Molecular Dynamics Simulation - p. 428 24. Author Index - p. 449 25. Subject Index - p. 479
Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences.
Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study.
1. Cover image - p. iv 2. Title page - p. iv 3. Table of Contents - p. iv 4. Copyright - p. iv 5. Contributors - p. xi 6. Preface - p. xvii 7. Chapter One: Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins - p. xviii 8. Chapter Two: Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions - p. 20 9. Chapter Three: Accurate Calculation of Electric Fields Inside Enzymes - p. 43 10. Chapter Four: Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics - p. 72 11. Chapter Five: Modeling Mercury in Proteins - p. 101 12. Chapter Six: Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics - p. 122 13. Chapter Seven: New Algorithms for Global Optimization and Reaction Path Determination - p. 143 14. Chapter Eight: Simulation Studies of Protein and Small Molecule Interactions and Reaction - p. 167 15. Chapter Nine: How to Run FAST Simulations - p. 212 16. Chapter Ten: Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach - p. 225 17. Chapter Eleven: A Networks Approach to Modeling Enzymatic Reactions - p. 248 18. Chapter Twelve: Conformational Sub-states and Populations in Enzyme Catalysis - p. 271 19. Chapter Thirteen: Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites - p. 297 20. Chapter Fourteen: Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation - p. 326 21. Chapter Fifteen: Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands - p. 342 22. Chapter Sixteen: Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation - p. 371 23. Chapter Seventeen: Detecting Allosteric Networks Using Molecular Dynamics Simulation - p. 428 24. Author Index - p. 449 25. Subject Index - p. 479
