By Monika Fuxreiter
This groundbreaking paintings addresses an important paradigm shift in structural molecular biology, illustrating how protein dynamics performs a critical position in a variety of services, together with enzymatic catalysis, protein–protein interactions, and the association of complicated assemblies. The publication offers sleek computational thoughts for the characterization of proteins and their dynamic homes. The computational tools in particular tackle the dynamical elements of protein functionalities, with specified emphasis at the research of complicated assemblies and intrinsically disordered proteins.
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Extra info for Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods
Local motions allow the selection of different side chain conformers (rotamers), which are optimal for binding or chemical conversion of the substrate. Low-frequency motions (20–200 cm–1) enable concerted action of domains and could be conserved across protein families. Enzymatic cataly sis, for example, is coupled to distinct motions of a protein, which are also sampled in a substrate-free form. , deformability). Organisms living in different temperatures have markedly different flexibilities.
Hybrid representation of the solvent by explicit and implicit models greatly increases the exchange probability . Further improvements in REM could be obtained by subjecting only a small part of the system for exchange, for example in partial (RPEMDs) and local replica exchange methods (LREMDs) . These two approaches have been successfully applied to large systems. Simplifying/modifying the potential energy surface. One of the main factors that limits the sampling is the height of saddle points.
There are various disadvantages of implicit models. One of the major bottlenecks is still the estimation of the nonpolar solvation (entropy-related) energy term, which could play a dominant role in target selection, for example in minor groove-binding deoxyribonucleic acid (DNA) proteins. 15 16 Dynamics Estimation of Free Energy Most simulations are validated by comparing observed quantities such as binding or rate constants to the corresponding computed free energies. Free energies are state functions, which—in principle—do not depend on the pathway, just the difference between the two states.
Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods by Monika Fuxreiter