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Computational approaches for studying enzyme mechanism
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.Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins / N.A. Baker -- 1.Introduction -- 2.Biomolecular Structure and Flexibility -- 3.Solvent Models or: How I Learned to Stop Worrying and Love the Dielectric Coefficient -- 4.Modeling Ion-Solute Interactions -- 5.Force Field and Parameter Choices -- 6.Conclusions -- Acknowledgments -- References -- 2.Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions / S.D. Schwartz -- 1.Introduction -- 2.Transition Path Sampling: A New Paradigm for the Study of Enzymatic Mechanism -- 3.New Methods for Calculation of Values Relevant to Enzyme Mechanism -- 4.Conclusion -- References -- 3.Accurate Calculation of Electric Fields Inside Enzymes / J.Z.H. Zhang -- 1.Introduction -- 2.Theoretical Methods -- Acknowledgments -- References -- 4.Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics / W.J. Shaw -- 1.Hydrogenases -- 2.Proton Transport -- 3.Computational Strategy -- 4.Proton Transport in Hydrogenase -- 5.Proton Transport in Hydrogenase Mimics -- 6.Summary -- Acknowledgments -- References -- 5.Modeling Mercury in Proteins / J.C. Smith -- 1.Introduction -- 2.Microbial Interactions with Hg -- 3.Future Perspectives -- Acknowledgments -- References -- 6.Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics / A.E. Roitberg -- 1.Introduction -- 2.Discussion -- 3.Methodology -- References -- 7.New Algorithms for Global Optimization and Reaction Path Determination / B. Engels -- 1.Introduction -- 2.Global Optimization of Aqueous Systems -- 3.Optimization of Water Clusters (H2O)20, (H2O)30, and (H2O)40 -- 4.Illustrating the Basic Concepts of PO -- 5.Summary -- References -- 8.Simulation Studies of Protein and Small Molecule Interactions and Reaction / Y.Q. Gao -- 1.Conformation Sampling of Small Molecules and Proteins -- 2.Transportation of Small Molecules In Proteins -- 3.QM/MM MD Simulations of Enzymatic Reactions -- 4.Summary -- References -- 9.How to Run FAST Simulations / G.R. Bowman -- 1.Introduction -- 2.FAST Algorithm -- 3.FAST Sampling Parameters -- 4.Applications -- Acknowledgment -- References -- 10.Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach / S. Sacquin-Mora -- 1.Introduction -- 2.Material and Methods -- 3.Results and Discussion -- 4.Concluding Remarks -- References -- 11.A Networks Approach to Modeling Enzymatic Reactions / P. Imhof -- 1.Introduction -- 2.Networks of Reaction Pathways -- 3.Conclusion -- Acknowledgment -- References -- 12.Conformational Sub-states and Populations in Enzyme Catalysis / C. Narayanan -- 1.Introduction -- 2.Theoretical Conceots -- 3.Ascertaining Conformational Sub-states and Populations from Relaxation Dispersion NMR -- 4.Obtaining Conformational Sub-states from Simulations -- 5.Anharmonic Conformational Analysis -- 6.Examples of Conformational Sub-states in Enzyme Catalysis -- 7.Summary and Conclusions -- Acknowledgments -- References -- 13.Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites / J. Blumberger -- 1.Introduction -- 2.Methodology -- 3.Applications -- 4.Concluding Remarks -- Acknowledgments -- References -- 14.Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation / J.-W. Chu -- 1.Introduction -- 2.Calculation of Protein Fluctuograms -- 3.Implementation Considerations -- 4.Discussion -- Acknowledgments -- References -- 15.Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands / X. Huang -- 1.Introduction -- 2.Methodology to Elucidate Long-Timescale Dynamics of Enzymes -- 3.Case Studies -- 4.Remarks and Future Perspectives -- Acknowledgments -- References -- 16.Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation / E. Tajkhorshid -- 1.Nanoscale Effects Governing Membrane Transporter Function -- 2.Modeling Membrane Transporters in Their Native Environment -- 3.Modeling Substrate Binding and Unbinding Processes in Membrane Transporters -- 4.Emerging Techniques to Simulate Large-Scale Structural Transitions in Membrane Transporters -- 5.The Direction of Future Membrane Protein Studies -- Acknowledgments -- References -- 17.Detecting Allosteric Networks Using Molecular Dynamics Simulation / J. Wereszczynski -- 1.Introduction -- 2.Theory -- 3.Methods -- 4.Results and Discussion -- 5.Conclusion -- Acknowledgments -- References.
Includes bibliographical references and indexes.
Computational approaches for studying enzyme mechanism. Part B