Proteins: Energy, Heat and Signal Flow / Edition 1

by David M. Leitner, John E. Straub

Overview

Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redistribution, signaling, and heat transport in proteins and other molecular machines.

The first of four sections of the book address the transport of energy in molecular motors, which function through a combination of chemically driven large-scale conformational changes and charge transport. Focusing on vibrational energy flow in proteins and nanostructures, the next two sections discuss approaches based on molecular dynamics simulations and harmonic analysis. By exploring the flow of free energy in proteins, the last section examines the conformational changes involved in allosteric transitions and the role of coupled protein–solvent dynamics in conformational changes. It also presents computational approaches developed to locate pathways between protein structures.

The integrated presentation of this comprehensive, up-to-date volume emphasizes the interrelations between disparate computational approaches that have contributed to our understanding of energy flow in proteins and its role in protein function. By defining the forefront of research in this area, the book delineates the current challenges and opportunities in developing novel methods and applications for the evolving study of energy flow in molecular machines and nanomaterials.

Product Details

ISBN-13:	9780367385149
Publisher:	Taylor & Francis
Publication date:	10/18/2019
Series:	Computation in Chemistry , #1
Pages:	415
Product dimensions:	6.12(w) x 9.19(h) x (d)

About the Author

David M. Leitner is a Professor of Chemistry at the University of Nevada in Reno.

John E. Straub is a Professor of Chemistry at Boston University in Boston, Massachusetts.

Table of Contents

Series Preface ix

Preface xi

Editors xv

Contributors xvii

Part I Energy Transduction in Molecular Motors

Chapter 1 Energy Balance and Dynamics of Kinesin Motors Changbong Hyeon José N. Onuchic 3

Chapter 2 Mechanochemical Coupling in Molecular Motors: Insights from Molecular Simulations of the Myosin Motor Domain Haibo Yu Yang Yang Liang Ma Qiang Cui 23

Chapter 3 The Chemomechanical Coupling Mechanisms of Kinesin and Dynein Yi Qin Gao Qiang Shao 47

Chapter 4 Electron Transfer Reactions Coupled with Proton Translocation: Cytochrome Oxidase, Proton Pumps, and Biological Energy Transduction Alexei Stuchebrakhov 71

Part II Vibrational Energy Flow in Proteins: Molecular Dynamics-Based Methods

Chapter 5 Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics Akinori Kidera Kei Moritsugu Yasuhiro Matsunaga Hiroshi Fujisaki 107

Chapter 6 Energy Flow Pathways in Photoreceptor Proteins Takahisa Yamato 129

Chapter 7 Nonequilibrium Molecular Dynamics Simulation of Photoinduced Energy Flow in Peptides: Theory Meets Experiment Phuong H. Nguyen Peter Hamm Gerhard Stock 149

Chapter 8 Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood-Buff Theory Masataka Nagaoka Isseki Yu Masayoshi Takayanagi 169

Part III Vibrational Energy Flow in Proteins and Nanostructures: Normal Mode-Based Methods

Chapter 9 Directed Energy Funneling in Proteins: From Structure to Function Yong Zhang John E. Straub 199

Chapter 10 A Minimalist Network Model for Studying Biomolecular Vibration Mingyang Lu Jianpeng Ma 229

Chapter 11 Heat Transport in Proteins David M. Leitner 247

Chapter 12 Heat Transfer in Nanostructures Dvira Segal 271

Part IV Conformational Transitions and Reaction Path Searches in Proteins

Chapter 13 Tubes, Funnels, and Milestones Ron Elber Krzysztof Kuczera Gouri S. Jas 295

Chapter 14 Pathways and Rates for Structural Transformations of Peptides and Proteins David J. Wales Joanne M. Carr Mey Khalili Vanessa K. de Sauza Birgit Strodel Chris S. Whutleston 315

Chapter 15 Energy Flow and Allostery in an Ensemble Vincent J. Hilser Steven T. Whitten 341

Chapter 16 Molecular Dynamics Simulation Studies of Coupled Protein and Water Dynamics Douglas J. Tobias Neelanjana Sengupta Mounir Tarek 361

Index 387

What People are Saying About This

From the Publisher

… a useful guide for practitioners of molecular dynamics, theorists interested in structural biology, and users of modeling software seeking to understand the methods in more depth. The book is well organized, produced, and edited. References are up-to-date and comprehensive.
—Harry A. Stern, University of Rochester, in the Journal of the American Chemical Society

Editorial Reviews

… a useful guide for practitioners of molecular dynamics, theorists interested in structural biology, and users of modeling software seeking to understand the methods in more depth. The book is well organized, produced, and edited. References are up-to-date and comprehensive.
—Harry A. Stern, University of Rochester, in the Journal of the American Chemical Society

From the Publisher