ArticleScientific reports2016
On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 15 citations in OpenAlex.
- Design of Mimetic Antibodies Targeting the SARS-CoV-2 Spike Glycoprotein Based on the GB1 Domain: A Molecular Simulation and Experimental Study.Biochemistry · 2025Article
- Impact of water models on the structure and dynamics of enzyme tunnels.Computational and structural biotechnology journal · 2024Article
- Enthalpic Classification of Water Molecules in Target-Ligand Binding.Journal of chemical information and modeling · 2024Article
- The oxidation of the [4Fe-4S] cluster of DNA primase alters the binding energies with DNA and RNA primers.Biophysical journal · 2024Article
- LAWS: Local alignment for water sites-Tracking ordered water in simulations.Biophysical journal · 2023Article
- Critical test of isotropic periodic sum techniques with group-based cut-off schemes.Scientific reports · 2018Article
- The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.Frontiers in molecular biosciences · 2018Article
- Dynamics of Hydration Water Plays a Key Role in Determining the Binding Thermodynamics of Protein Complexes.Scientific reports · 2017Article
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4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior. We characterize the waters at the interface and in the core of the Maxi protein by the statistics of correctly predicted positions with respect to crystallographic water positions in the PDB files as well as the dynamic measures of diffusion constants and position lifetimes. Our approach provides a methodology for the evaluation of predicted interfacial water positions through an investigation of water-mediated inter-chain contacts. While our results show satisfactory behaviour for molecular dynamics simulation, they also highlight the need for improvement of continuum methods.
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