NDLI: Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

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Evaluation of reduced point charge models of proteins through Molecular Dynamics simulations: application to the Vps27 UIM-1-Ubiquitin complex.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Leherte, Laurence Vercauteren, Daniel P.
Description	Author Affiliation: Leherte L ( Unité de Chimie Physique Théorique et Structurale, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium. Electronic address: laurence.leherte@unamur.be.); Vercauteren DP ( Unité de Chimie Physique Théorique et Structurale, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium.)
Abstract	Reduced point charge models of amino acids are designed, (i) from local extrema positions in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions, and (ii) from local maxima positions in promolecular electron density distribution functions. Corresponding charge values are fitted versus all-atom Amber99 MEPs. To easily generate reduced point charge models for protein structures, libraries of amino acid templates are built. The program GROMACS is used to generate stable Molecular Dynamics trajectories of an Ubiquitin-ligand complex (PDB: 1Q0W), under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a nul mass and radius. The results illustrate how the intra- and inter-molecular H-bond interactions are affected by the degree of reduction of the point charge models and give directions for their implementation; a special attention to the atoms selected to locate the virtual sites and to the Coulomb-14 interactions is needed. Results obtained at various temperatures suggest that the use of reduced point charge models allows to probe local potential hyper-surface minima that are similar to the all-atom ones, but are characterized by lower energy barriers. It enables to generate various conformations of the protein complex more rapidly than the all-atom point charge representation.
File Format	HTM / HTML
ISSN	10933263
Volume Number	47
e-ISSN	18734243
Journal	Journal of Molecular Graphics and Modelling
Language	English
Publisher	Elsevier
Publisher Date	2014-02-01
Publisher Place	United States
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Molecular Biology Molecular Dynamics Simulation Proteins Chemistry Hydrogen Bonding Hydrophobic And Hydrophilic Interactions Molecular Docking Simulation Multiprotein Complexes Protein Binding Protein Conformation Protein Interaction Domains And Motifs Static Electricity Ubiquitin Metabolism Vesicular Transport Proteins Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Computer Graphics and Computer-Aided Design Spectroscopy Materials Chemistry Physical and Theoretical Chemistry

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