Résumé
| langue | Anglais |
|---|---|
| Pages | 9771-9784 |
| Nombre de pages | 14 |
| journal | Journal of Physical Chemistry B |
| Les DOIs | |
| état | Publié - 2017 |
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Reduced Point Charge Models of Proteins - Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems. / Leherte, Laurence; Vercauteren, Daniel.
Dans: Journal of Physical Chemistry B, 2017, p. 9771-9784.Résultats de recherche: Contribution à un journal/une revue › Article
TY - JOUR
T1 - Reduced Point Charge Models of Proteins - Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems
AU - Leherte,Laurence
AU - Vercauteren,Daniel
PY - 2017
Y1 - 2017
N2 - 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-Owater 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 to weaken 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 to generate stable RPCM trajectories.
AB - 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-Owater 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 to weaken 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 to generate stable RPCM trajectories.
U2 - 10.1021/acs.jpcb.7b06355
DO - 10.1021/acs.jpcb.7b06355
M3 - Article
SP - 9771
EP - 9784
JO - Journal of Physical Chemistry B
T2 - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
SN - 1089-5647
ER -