Computational Approaches for Studying Enzyme Mechanism Part B

1st Edition, Volume 578 - August 2, 2016
Editor: Gregory Voth
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 1 1 1 0 7 - 9
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 1 1 1 0 8 - 6

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 study… Read more

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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.

Preface
Chapter One: Continuum Electrostatics Approaches to Calculating pK_as and E_ms in Proteins
- Abstract
- 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
Chapter Two: Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions
- Abstract
- 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
Chapter Three: Accurate Calculation of Electric Fields Inside Enzymes
- Abstract
- 1 Introduction
- 2 Theoretical Methods
- Acknowledgments
Chapter Four: Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics
- Abstract
- 1 Hydrogenases
- 2 Proton Transport
- 3 Computational Strategy
- 4 Proton Transport in Hydrogenase
- 5 Proton Transport in Hydrogenase Mimics
- 6 Summary
- Acknowledgments
Chapter Five: Modeling Mercury in Proteins
- Abstract
- 1 Introduction
- 2 Microbial Interactions with Hg
- 3 Future Perspectives
- Acknowledgments
Chapter Six: Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics
- Abstract
- 1 Introduction
- 2 Discussion
- 3 Methodology
Chapter Seven: New Algorithms for Global Optimization and Reaction Path Determination
- Abstract
- 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
Chapter Eight: Simulation Studies of Protein and Small Molecule Interactions and Reaction
- Abstract
- 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
Chapter Nine: How to Run FAST Simulations
- Abstract
- 1 Introduction
- 2 FAST Algorithm
- 3 FAST Sampling Parameters
- 4 Applications
- Acknowledgment
Chapter Ten: Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach
- Abstract
- 1 Introduction
- 2 Material and Methods
- 3 Results and Discussion
- 4 Concluding Remarks
Chapter Eleven: A Networks Approach to Modeling Enzymatic Reactions
- Abstract
- 1 Introduction
- 2 Networks of Reaction Pathways
- 3 Conclusion
- Acknowledgment
Chapter Twelve: Conformational Sub-states and Populations in Enzyme Catalysis
- Abstract
- 1 Introduction
- 2 Theoretical Concepts
- 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
Chapter Thirteen: Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites
- Abstract
- 1 Introduction
- 2 Methodology
- 3 Applications
- 4 Concluding Remarks
- Acknowledgments
Chapter Fourteen: Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation
- Abstract
- 1 Introduction
- 2 Calculation of Protein Fluctuograms
- 3 Implementation Considerations
- 4 Discussion
- Acknowledgments
Chapter Fifteen: Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands
- Abstract
- 1 Introduction
- 2 Methodology to Elucidate Long-Timescale Dynamics of Enzymes
- 3 Case Studies
- 4 Remarks and Future Perspectives
- Acknowledgments
Chapter Sixteen: Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation
- Abstract
- 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
Chapter Seventeen: Detecting Allosteric Networks Using Molecular Dynamics Simulation
- Abstract
- 1 Introduction
- 2 Theory
- 3 Methods
- 4 Results and Discussion
- 5 Conclusion
- Acknowledgments
Author Index
Subject Index

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Gregory Voth