Protein Conformational Dynamics

ISBN-13: 9783319029696 / Angielski / Twarda / 2014 / 488 str.

Ke-Li Han;Xin Zhang;Ming-Jun Yang

Opis

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 inthis 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.

Spis treści

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