Résultat de recherche par an
Résultat de recherche par an
Résultats de recherche: Contribution à un journal/une revue › Article › Revue par des pairs
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 |
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Pages (de - à) | 9771-9784 |
Nombre de pages | 14 |
journal | The Journal of Physical Chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical |
Volume | 121 |
Numéro de publication | 42 |
Les DOIs | |
Etat de la publication | Publié - 26 oct. 2017 |
Résultats de recherche: Contribution dans un livre/un catalogue/un rapport/dans les actes d'une conférence › Article dans les actes d'une conférence/un colloque
Leherte, L. (Chercheur)
21/01/08 → …
Projet: Recherche
Champagne, B. (Co-investigateur)
1/01/11 → 31/12/22
Projet: Recherche
Champagne, B. (!!Manager)
Plateforme technologique Calcul intensifEquipement/installations: Plateforme technolgique
Leherte, L. (Orateur) & Vercauteren, D. (Orateur)
Activité: Discours ou présentation › Présentation orale
Leherte, L. (Orateur)
Activité: Discours ou présentation › Discours invité
Leherte, L. (Orateur)
Activité: Discours ou présentation › Présentation orale