Computational approaches for studying enzyme mechanism. Part A / edited by Gregory A. Voth.

Format:

Book

Contributor:

Voth, Gregory A., editor.

Series:

Methods in enzymology ; Volume 577.

Methods in enzymology ; Volume 577

Language:

English

Subjects (All):

Enzymology.

Enzymes--Analysis.

Enzymes.

Enzymes--Synthesis.

Physical Description:

1 online resource (560 p.)

Edition:

First edition.

Place of Publication:

Amsterdam, [Netherlands] : Academic Press, 2016.

Summary:

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.

Contents:

Front Cover; Computational Approaches for Studying Enzyme Mechanism Part A; Copyright; Contents; Contributors; Preface; Chapter One: The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis; 1. Introduction; 2. Method; 2.1. Umbrella Sampling; 2.2. Steered MD; 3. Applications; 3.1. Protein Farnesyltransferase; 3.1.1. Understanding the Conformational Activation of FPP; 3.1.2. Identification of the Mg2+ Binding Site in FTase; 3.1.3. Simulating the Farnesylation Reaction; 3.2. Aromatic Prenyltransferase NphB

3.2.1. Identifying the Product Regioselectivity Associated with NphB Catalysis3.2.2. Elucidating the Reaction Mechanism with QM/MM PMF Simulations; 3.3. Aspergillus Fumigatus Prenyltransferase; 3.3.1. Regioselectivity of WT FtmPT1; 3.3.2. Regioselectivity of G115T Mutant; 3.4. Cytochrome P450s; 4. Summary; Acknowledgments; References; Chapter Two: Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins; 1. Introduction; 2. Computational Approaches; 2.1. Adiabatic Reactive Molecular Dynamics; 2.2. Multisurface ARMD; 2.3. Empirical Valence Bond; 3. Applications

3.1. Rebinding Dynamics in MbNO3.2. NO Detoxification Reaction in trHbN; 3.3. Competitive Ligand Binding in trHbN; 4. Outlook; Acknowledgments; References; Chapter Three: Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways; 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

2.1. The Pseudobond Approach to Describe the QM/MM Boundary Across Covalent Bonds2.2. A Dual Focal aiQM/MM-PME Potential with the Periodic Boundary Condition; 2.3. Microiterative Optimization and Reaction Coordinate Driving; 2.4. Born-Oppenheimer aiQM/MM-MD with Umbrella Sampling; 2.5. Implementation; 3. Examples; 3.1. Dissociation of tert-Butyl Chloride in Water; 3.2. First Step of Acylation Reaction for a Serine Protease; 4. Enzyme Simulation Protocol; 5. Conclusion; Acknowledgments; References; Chapter Six: QM/MM Calculations on Proteins; 1. Introduction; 2. Methods; 2.1. QM Methods

2.2. MM Methods

Notes:

Description based upon print version of record.

Includes bibliographical references at the end of each chapters and index.

Description based on online resource; title from PDF title page (ebrary, viewed September 1, 2016).

Description based on publisher supplied metadata and other sources.

ISBN:

9780128053638

0128053631

9780128053478

012805347X

OCLC:

956648619