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  SPECIFICATION
COMPUTATIONAL APPROACHES TO PROTEIN DYNAMICS: FROM QUANTUM TO COARSE-GRAINED METHODS(pb) 2018
Author: FUXREITER
ISBN: 9781138198883
Year: 2018
Publisher: CRC PRESS
Category: PHYSICS
Edition: 1
Format: Paperback
Language: English
Pages: 479
 ABOUT THE TITLE
Features
•Focuses on the dynamical aspects of biological functions with a special emphasis on IDPs and complex assemblies
•Describes the methods and results of enzyme catalysis, including the work of the 2013 Nobel Prize co-winner in chemistry Arieh Warshel
•Explains how to apply computational techniques to tackle biological problems involving IDPs
•Discusses the experimental characterization of IDPs
•Gives a historical overview and description of major directions for improving biological simulations
Summary
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.

Editor(s) Bio
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.




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 TABLE OF CONTENTS
Introduction
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
Index
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