Computational Approaches to Protein Dynamics : From Quantum to Coarse-Grained Methods book cover
1st Edition

Computational Approaches to Protein Dynamics
From Quantum to Coarse-Grained Methods

ISBN 9781466561571
Published December 24, 2014 by CRC Press
479 Pages 10 Color & 96 B/W Illustrations

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Book Description

The Latest Developments on the Role of Dynamics in Protein Functions

Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles.

The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues:

  • Is there a quantitative relationship between enzymatic catalysis and protein dynamics?
  • Which are the functionally relevant motions of proteins?
  • How can structural properties and partner recognition mechanisms of IDPs be simulated?
  • How can we speed up molecular dynamics?
  • How can we describe conformational ensembles by the synergistic effort of computations and experiments?

While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

Table of Contents

Dynamics: A Key to Protein Function Mónika Fuxreiter

Enzymatic Catalysis: Multiscale QM/MM Calculations
Adaptive and Accurate Force-Based QM/MM Calculations Noam Bernstein, Iván Solt, Letif Mones, Csilla Várnai, Steven A. Winfield, and Gábor Csányi
Conformational and Chemical Landscapes of Enzyme Catalysis Alexandra T.P. Carvalho, Fernanda Duarte, Konstantinos Vavitsas, and Shina Caroline Lynn Kamerlin
Interplay between Enzyme Function and Protein Dynamics: A Multiscale Approach to the Study of the NAG Kinase Family and Two Class II Aldolases Enrique Marcos, Melchor Sanchez-Martinez, and Ramon Crehuet

Protein Motions: Flexibility Analysis
Simplified Flexibility Analysis of Proteins Yves-Henri Sanejouand

Approaches to Intrinsically Disordered Proteins
ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins Anuradha Mittal, Rahul K. Das, Andreas Vitalis, and Rohit V. Pappu
Intrinsically Disordered Protein: A Thermodynamic Perspective Jing Li, James O. Wrabl, and Vincent J. Hilser
Long Molecular Dynamics Simulations of Intrinsically Disordered Proteins Reveal Preformed Structural Elements for Target Binding Elio Cino, Mikko Karttunen, and Wing-Yiu Choy
Multiscale Simulations of Large Conformational Changes of Disordered and Ordered Proteins Induced by Their Partners Yong Wang, Xiakun Chu, and Jin Wang
Coarse-Grained Simulation of Intrinsically Disordered Proteins David de Sancho, Christopher M. Baker, and Robert B. Best
Natural and Directed Evolution of Intrinsically Disordered Proteins Tali H. Reingewertz and Eric J. Sundberg

Large-Scale Dynamics
Discrete Molecular Dynamics: Foundations and Biomolecular Applications Pedro Sfriso, Agustí Emperador, Josep Lluis Gelpí, and Modesto Orozco

Ensemble Methods
Use of Ensemble Methods to Describe Biomolecular Dynamics by Small Angle X-Ray Scattering Giancarlo Tria, Dmitri I. Svergun, and Pau Bernadó
Bridging Experiments and Simulations: Structure Calculations with a Dynamical Touch Florian Heinkel, Alexander Cumberworth, and Jörg Gsponer


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Mónika Fuxreiter is head of the Laboratory of Protein Dynamics in the Department of Biochemistry and Molecular Biology at the University of Debrecen. She received her MSc and PhD from the Eötvös Loránd University of Sciences, and was a postdoctoral fellow at the University of Southern California under Arieh Warshel. Dr. Fuxreiter has 20 years of experience working on state-of-the-art approaches for biological systems, including partner recognition mechanisms of IDPs and unique regulatory mechanisms of fuzzy complexes and relationships to context-dependence.


"The modeling of biological systems and processes has advanced remarkably in recent years, gradually becoming a legitimate field of research. It has also started to be clear that … structural and kinetic findings emerging from experimental work should be augmented by computer simulations. Some of the progress in the field has been described in the scholarly articles compiled in this book. … the reader should look at the present publication as a report that reflects the current developments in the field, and then make sure when picking a particular approach that this approach actually reproduces ‘reality’."
—From the Foreword by Nobel Laureate Ariel Warshel, Distinguished Professor of Chemistry and Biochemistry, University of Southern California

"The book is conveniently structured to simplify the preparation of a new graduate course on biomolecular simulations."
—Jan Florián, Department of Chemistry and Biochemistry, Loyola University Chicago

"… a comprehensive assessment of the methods for modeling protein dynamics and conformational heterogeneity across multiple spatial and time scales. Each contribution attempts to point the way toward connecting dynamics and heterogeneity to molecular function, thus making for a compelling read."
—Rohit V. Pappu, Department of Biomedical Engineering, Washington University, St. Louis