ArticleScientific reports2016
Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.
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 19 papers.
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Who cites it
19 citing papers in PubMed, 61 citations in OpenAlex.
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- Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations.Journal of computer-aided molecular design · 2023Article
- Modelling of the dynamic polarizability of macromolecules for single-molecule optical biosensing.Scientific reports · 2022Article
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- The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction.Structural dynamics (Melville, N.Y.) · 2018Article
- An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase.Molecules (Basel, Switzerland) · 2018Article
- Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations.RSC advances · 2018Article
- Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques.Bioorganic & medicinal chemistry letters · 2018Article
- Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field.Frontiers in chemistry · 2018Article
- Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field.Scientific reports · 2017Article
- Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.The Journal of chemical physics · 2017Article
- Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.Scientific reports · 2017Article
- Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations.Journal of the American Chemical Society · 2017Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
- Computational Exploration for Lead Compounds That Can Reverse the Nuclear Morphology in Progeria.BioMed research international · 2017Article
- Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field.Frontiers in molecular biosciences · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding.
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