Research output per year
Research output per year
Research output: Contribution to journal › Article › peer-review
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 language | English |
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Pages (from-to) | 9771-9784 |
Number of pages | 14 |
Journal | The Journal of Physical Chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical |
Volume | 121 |
Issue number | 42 |
DOIs | |
Publication status | Published - 26 Oct 2017 |
Research output: Contribution in Book/Catalog/Report/Conference proceeding › Conference contribution
Leherte, L. (Researcher)
21/01/08 → …
Project: Research
Champagne, B. (Manager)
Technological Platform High Performance ComputingFacility/equipment: Technological Platform
Leherte, L. (Speaker) & Vercauteren, D. (Speaker)
Activity: Talk or presentation types › Oral presentation
Leherte, L. (Speaker)
Activity: Talk or presentation types › Invited talk
Leherte, L. (Speaker)
Activity: Talk or presentation types › Oral presentation