Projets par an
Résumé
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.
langue originale | Anglais |
---|---|
Pages (de - à) | 9771-9784 |
Nombre de pages | 14 |
journal | Journal of physical chemistry B |
Volume | 121 |
Numéro de publication | 42 |
Les DOIs | |
Etat de la publication | Publié - 26 oct. 2017 |
Empreinte digitale Examiner les sujets de recherche de « Reduced Point Charge Models of Proteins - Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems ». Ensemble, ils forment une empreinte digitale unique.
Projets
- 2 Actif
-
-
Analyse multirésolution de potentiels électrostatiques moléculaires de protéines
21/01/08 → …
Projet: Recherche
Équipement
-
Plateforme Technologique Calcul Intensif
Benoît Champagne (!!Manager)
Plateforme technologique Calcul intensifEquipement/installations: Plateforme technolgique
Activités
-
Influence of Protein-Solvent Interactions on the Molecular Dynamics of Reduced Point Charge Models of Proteins - COMP5
Laurence Leherte (Orateur) & Daniel Vercauteren (Orateur)
18 mars 2018Activité: Types de discours ou de présentation › Présentation orale
-
Molecular Dynamics Simulations of Proteins using Reduced Point Charge Models
Laurence Leherte (Orateur)
30 janv. 2018Activité: Types de discours ou de présentation › Discours invité
-
Reduced point charge models of proteins - Influence of protein-solvent interactions
Laurence Leherte (Orateur)
28 août 2017Activité: Types de discours ou de présentation › Présentation orale