Projets par an
Résumé
A reduced point charge distribution is used to model Ubiquitin and two complexes, Vps27 UIM-1-Ubiquitin and Barnase-Barstar. It is designed from local extrema in charge density distributions obtained from the Poisson equation applied to smoothed molecular electrostatic potentials. A variant distribution is built by locating point charges on atoms. Various charge fitting conditions are selected, i.e. from either electrostatic Amber99 (Assisted Model Building with Energy Refinement) Coulomb potential or forces, considering reference grid points located within various distances from the protein atoms, with or without separate treatment of main and side chain charges. The program GROMACS (Groningen Machine for Chemical Simulations) is used to generate Amber99SB molecular dynamics (MD) trajectories of the solvated proteins modelled using the various reduced point charge models (RPCMs) so obtained. Point charges that are not located on atoms are considered as virtual sites. Some RPCMs lead to stable MD trajectories. They, however, involve a partial loss in the protein secondary structure and lead to a less-structured solute solvation shell. The model built by fitting charges on Coulomb forces calculated at grid points ranging between 1.4 and 2.0 times the van der Waals radius of the atoms, with a separate treatment of main chain and side chain charges, appears to best approximate all-atom MD trajectories.
langue originale | Anglais |
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Pages (de - à) | 289-304 |
Nombre de pages | 16 |
journal | Molecular Simulation |
Volume | 42 |
Numéro de publication | 4 |
Les DOIs | |
Etat de la publication | Publié - 2016 |
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Examiner les sujets de recherche de « Reduced point charge models of proteins: Assessment based on molecular dynamics simulations ». Ensemble, ils forment une empreinte digitale unique.-
Analyse multirésolution de potentiels électrostatiques moléculaires de protéines
Leherte, L. (Chercheur)
21/01/08 → …
Projet: Recherche
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consortium des équipements de calcul intensif
Champagne, B. (Co-investigateur)
1/01/11 → 31/12/22
Projet: Recherche
Équipement
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Plateforme Technologique Calcul Intensif
Champagne, B. (!!Manager)
Plateforme technologique Calcul intensifEquipement/installations: Plateforme technolgique
Activités
- 1 Participation à un Colloque, une journée d'étude
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10th European Conference on Computational Chemistry
Leherte, L. (Poster)
31 août 2015 → 3 sept. 2015Activité: Participation ou organisation d'un événement › Participation à un Colloque, une journée d'étude