ArticleJournal of computer-aided molecular design2013
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 75 citations in OpenAlex.
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- Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction.Journal of molecular modeling · 2022Article
- It's Getting Complicated-A Fresh Look at p53-MDM2-ARF Triangle in Tumorigenesis and Cancer Therapy.Frontiers in cell and developmental biology · 2022Review
- Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis.Journal of molecular medicine (Berlin, Germany) · 2020Article
- Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.International journal of molecular sciences · 2020Article
- Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water.Frontiers in chemistry · 2019Article
- Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism.International journal of molecular sciences · 2018Article
- Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant.International journal of molecular sciences · 2018Article
- Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations.RSC advances · 2018Article
- Exploration of the binding affinities between ecdysone agonists and EcR/USP by docking and MM-PB/GBSA approaches.Journal of molecular modeling · 2017Article
- Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution.Scientific reports · 2017Article
- Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations.Scientific reports · 2017Article
- Molecular Mechanism and Energy Basis of Conformational Diversity of Antibody SPE7 Revealed by Molecular Dynamics Simulation and Principal Component Analysis.Scientific reports · 2016Article
- Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.Scientific reports · 2016Article
- Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor.International journal of molecular sciences · 2016Article
- Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation.Scientific reports · 2015Article
- Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods.Scientific reports · 2015Article
- Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2015Article
- Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation.Journal of molecular modeling · 2015Article
- Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods.PloS one · 2015Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations followed by principal component analysis were performed to study the conformational change of MDM2 induced by p53 and two inhibitor (P4 and MI63a) bindings. The results show that the hydrophobic cleft of MDM2 is very flexible and adaptive to different structural binding partners. The cleft tends to become wider and more stable as MDM2 binds to the three binding partners, while unbound MDM2 shows a narrower and pretty flexible cleft, which agrees with recent experimental data and theoretical studies. It was also found that the binding of P4 and p53 stabilizes the motion of the loop L2 linking the helix α2 and β strand (β3), but the presence of MI63a makes the motion of L2 disordered. In addition, the binding free energies of the three partners to MDM2 were calculated using molecular mechanics generalized Born surface area to explain the binding modes of these three partners to MDM2. This study will be helpful not only for better understanding the functional, concerted motion of MDM2, but also for the rational design of potent anticancer drugs targeting the p53-MDM2 interaction.
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