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.
… 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
ENERGY TRANSDUCTION IN MOLECULAR MOTORS
Energy Balance and Dynamics of Kinesin Motors, Changbong Hyeon and José N. Onuchic
Mechanochemical Coupling in Molecular Motors: Insights from Molecular Simulations of the Myosin Motor Domain, Haibo Yu, Yang Yang, Liang Ma, and Qiang Cui
The Chemomechanical Coupling Mechanisms of Kinesin and Dynein, Yi Qin Gao and Qiang Shao
Electron Transfer Reactions Coupled with Proton Translocation: Cytochrome Oxidase, Proton Pumps, and Biological Energy Transduction, Alexei Stuchebrukhov
VIBRATIONAL ENERGY FLOW IN PROTEINS: MOLECULAR DYNAMICS-BASED METHODS
Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics, Akinori Kidera, Kei Moritsugu, Yasuhiro Matsunaga, and Hiroshi Fujisaki
Energy Flow Pathways in Photoreceptor Proteins, Takahisa Yamato
Nonequilibrium Molecular Dynamics Simulation of Photoinduced Energy Flow in Peptides: Theory Meets Experiment, Phuong H. Nguyen, Peter Hamm, and Gerhard Stock
Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations: Time-Resolved Vibrational Analysis and Surficial Kirkwood–Buff Theory, Masataka Nagaoka, Isseki Yu, and Masayoshi Takayanagi
VIBRATIONAL ENERGY FLOW IN PROTEINS AND NANOSTRUCTURES: NORMAL MODE-BASED METHODS
Directed Energy Funneling in Proteins: From Structure to Function, Yong Zhang and John E. Straub
A Minimalist Network Model for Studying Biomolecular Vibration, Mingyang Lu and Jianpeng Ma
Heat Transport in Proteins, David M. Leitner
Heat Transfer in Nanostructures, Dvira Segal
CONFORMATIONAL TRANSITIONS AND REACTION PATH SEARCHES IN PROTEINS
Tubes, Funnels, and Milestones, Ron Elber, Krzysztof Kuczera, and Gouri S. Jas
Pathways and Rates for Structural Transformations of Peptides and Proteins, David J. Wales, Joanne M. Carr, Mey Khalili, Vanessa K. de Souza, Birgit Strodel, and Chris S. Whittleston
Energy Flow and Allostery in an Ensemble, Vincent J. Hilser and Steven T. Whitten
Molecular Dynamics Simulation Studies of Coupled Protein and Water Dynamics, Douglas J. Tobias, Neelanjana Sengupta, and Mounir Tarek