Reduced Point Charge Models of Proteins - Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems

Research output: Contribution to journalArticle

Abstract

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W, 2MBB, 2G3Q) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Original languageEnglish
Pages (from-to)9771-9784
Number of pages14
JournalJournal of physical chemistry B
Volume121
Issue number42
DOIs
Publication statusPublished - 26 Oct 2017

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    • 2 Oral presentation
    • 1 Invited talk

    Molecular Dynamics Simulations of Proteins using Reduced Point Charge Models

    Laurence Leherte (Speaker)

    30 Jan 2018

    Activity: Talk or presentation typesInvited talk

    Reduced point charge models of proteins - Influence of protein-solvent interactions

    Laurence Leherte (Speaker)

    28 Aug 2017

    Activity: Talk or presentation typesOral presentation

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