BookKe-li Han, Xin Zhang, Ming-jun Yang, editors.
Summary: "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"--Publisher's description.
Contents:
Protein folding simulations by generalized-ensemble algorithms
Application of Markov state models to simulate long timescale dynamics of biological macromolecules
Understanding protein dynamics using conformational ensembles
Generative models of conformational dynamics
Generalized spring tensor models for protein fluctuation dynamics and conformational changes
The joys and perils of flexible fitting
Coarse-grained models of the proteins backbone conformational dynamics
Simulating protein folding in different environmental conditions
Simulating the peptide folding kinetic related spectra based on the Markov state model
The dilemma of conformational dynamics in enzyme catalysis: perspectives from theory and experiment
Exploiting intrinsic flexibility in drug design
NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions
Molecular dynamics simulation of membrane proteins
Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics
Coordination and control inside simple biomolecular machines
Multi-state targeting machinery govern the fidelity and efficiency of protein localization
Molecular dynamics simulations of F1-ATPase
Chemosensorial G-proteins-coupled receptors: a perspective from computational methods.
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