Computational Approaches for Studying Enzyme Mechanism Part A, Volume 577

• Preface
• Chapter One: The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis
  • Abstract
  • 1 Introduction
  • 2 Method
  • 3 Applications
  • 4 Summary
  • Acknowledgments
• Chapter Two: Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins
  • Abstract
  • 1 Introduction
  • 2 Computational Approaches
  • 3 Applications
  • 4 Outlook
  • Acknowledgments
• Chapter Three: Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways
  • Abstract
  • 1 Introduction
  • 2 Collective Variable and Reaction Order Parameter
  • 3 Traditional Importance Sampling vs GE Sampling
  • 4 Dimensionality Limit
  • 5 One of the First Metadynamics-Based Enzyme Reaction Studies
  • 6 GE-Based String Optimization: The OTPRW Method
  • 7 OTPRW Study of a Substrate-Assisted Glycosylation Reaction
  • 8 Final Remarks
  • Acknowledgments
• Chapter Four: Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis
  • Abstract
  • 1 Introduction
  • 2 Alchemical FES
  • 3 Reaction Profiles
  • Acknowledgment
  • Appendix
• Chapter Five: Born–Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions
  • Abstract
  • 1 Introduction
  • 2 Methods
  • 3 Examples
  • 4 Enzyme Simulation Protocol
  • 5 Conclusion
  • Acknowledgments
• Chapter Six: QM/MM Calculations on Proteins
  • Abstract
  • 1 Introduction
  • 2 Methods
  • 3 Applications
  • 4 Suggested Approach for QM/MM Investigations
  • Acknowledgments
• Chapter Seven: Enzymatic Cleavage of Glycosidic Bonds: Strategies on How to Set Up and Control a QM/MM Metadynamics Simulation
  • Abstract
  • 1 Introduction
  • 2 Carbohydrate Structures and Glycoside Hydrolases
  • 3 QM/MM Molecular Dynamics Simulation of the Catalytic Mechanism
  • 4 Conclusions
  • Acknowledgments
• Chapter Eight: Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method
  • Abstract
  • 1 Introduction
  • 2 Biological Questions
  • 3 QM/MM Simulations of the ABC-Transporter HlyB
  • 4 Computational Challenges
  • 5 A Multiscale QM/MM Method: RP–FM
  • 6 Concluding Remarks
  • Acknowledgments
• Chapter Nine: QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes
  • Abstract
  • 1 Introduction
  • 2 Background on Computational Methods
  • 3 Case Study: The Transition State of AP
  • 4 Summary/Conclusions
  • Acknowledgments
• Chapter Ten: Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions
  • Abstract
  • 1 Introduction
  • 2 Enzyme System Modeling
  • 3 The Potential Energy Surface
  • 4 Reaction Coordinates and Classical Free Energy Simulations
  • 5 Concluding Words
  • Acknowledgments
• Chapter Eleven: Examinations of the Chemical Step in Enzyme Catalysis
  • Abstract
  • 1 Introduction
  • 2 KIEobs vs KIEint
  • 3 The Northrop Method
  • 4 Case Study 1: TSase
  • 5 Case Study 2: DHFR
  • 6 Summary
  • Acknowledgments
• Chapter Twelve: Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes
  • Abstract
  • 1 Introduction
  • 2 Overview of QM/DMD
  • 3 Setting Up QM/DMD
  • 4 Running QM/DMD and Details of the Procedure
  • 5 Conclusions
• Chapter Thirteen: Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange
  • Abstract
  • 1 Introduction
  • 2 Methodology
  • 3 Implementation
  • 4 Applications of AP Schemes
  • 5 Summary
  • Acknowledgments
• Chapter Fourteen: Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory
  • Abstract
  • 1 Introduction
  • 2 Methods
  • 3 Illustrative Examples
  • 4 Concluding Remarks
  • Acknowledgment
• Chapter Fifteen: Simulating Nuclear and Electronic Quantum Effects in Enzymes
  • Abstract
  • 1 Introduction
  • 2 Electronic Quantum Effects in Biological Systems
  • 3 Incorporating NQEs in AIMD Simulations
  • 4 Outlook
  • Acknowledgments
• Chapter Sixteen: Using Molecular Simulation to Study Biocatalysis in Ionic Liquids
  • Abstract
  • 1 Introduction
  • 2 Methods for Simulating Biomolecules in ILs
  • 3 Perspective: Challenges and Future Directions
• Chapter Seventeen: The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes
  • Abstract
  • 1 Introduction
  • 2 Methods
  • 3 EXAFS Simulations
  • 4 MOD-QM/MM Models of DNA Quadruplexes
  • 5 Conclusions
  • Acknowledgments
• Author Index
• Subject Index

Computational Approaches for Studying Enzyme Mechanism Part A, is the first of  two volumes in the Methods in Enzymology series, focusses 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 life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, and genetics to name a few.

• Focuses on computational approaches for studying enzyme mechanism
• Continues the legacy of this premier serial with quality chapters authored by leaders in the field
• Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists