Protein conformational dynamics
Author(s)
Bibliographic Information
Protein conformational dynamics
（Advances in experimental medicine and biology, v. 805）
Springer, c2014
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression.
On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function.
On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Table of Contents
1. Protein Folding Simulations by Generalized-ensemble Algorithms
Takao Yoda, Yuji Sugita & Yuko Okamoto
2. Application of Markov State Models to Simulate Long Timescale Dynamics of Biological Macromolecules
Lin-Tai Da, Fu Kit Sheong, Daniel-Adriano Silva & Xuhui Huang
3. Understanding Protein Dynamics Using Conformational Ensembles
X. Salvatella
4. Generative Models of Conformational Dynamics
Christopher James Langmead
5. Generalized Spring Tensor Models for Protein Fluctuation Dynamics and Conformation Changes
Hyuntae Na, Tu-Liang Lin & Guang Song
6. The Joys and Perils of Flexible Fitting
Niels Volkmann
7. Coarse-Grained Models of the Proteins Backbone: Conformational Dynamics
Tap Ha-Duong
8. Simulating Protein Folding in Different Environmental Conditions
Dirar Homouz
9. Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model
Jian Song & Wei Zhuang
10. The Dilemma of Conformational Dynamics in Enzyme Catalysis: Perspectives from
Theory and Experiment
Urmi Doshi & Donald Hamelberg
11. Exploiting Protein Intrinsic Flexibility in Drug Design
Suryani Lukman, Chandra S. Verma, & Gloria Fuentes
12. NMR and Computational Methods in the Structural and Dynamic Characterization of Ligand-receptor Interactions
Michela Ghitti, Giovanna Musco & Andrea Spitaler
13. Molecular Dynamics Simulation of Membrane Proteins
Jingwei Weng & Wenning Wang
14. Free-energy Landscape of Intrinsically Disordered Proteins Investigated by All-atom Multicanonical Molecular Dynamics
Junichi Higo & Koji Umezawa
15. Coordination and Control Inside Simple Biomolecular Machines
Jin Yu
16. Multi-state Targeting Machinery Govern the Fidelity and Efficiency of Protein Localization
Ming-jun Yang, Xueqin Pang & Ke-li Han
17. Molecular Dynamics Simulations of F1-ATPase
Yuko Ito & Mitsunori Ikeguchi
18. Chemosensorial G-proteins-coupled Receptors: A Perspective from Computational Methods
Francesco Musiani, Giulia Rossetti, Alejandro Giorgetti & Paolo Carloni
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