ArticleMolecules (Basel, Switzerland)2024
Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning.
Article in Molecules (Basel, Switzerland), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Mutant-Selective Binding ofInternational journal of molecular sciences · 2026Article
- Molecular Dynamics and Docking Reveal Enhanced Binding of HPV16 E6 Asian American Variants To non-phosphorylated DLG1.Cell biochemistry and biophysics · 2026Article
- Recent Progress and Prospect in Studying Selective Inhibitors Toward Bromodomain Family Members.Molecules (Basel, Switzerland) · 2026Review
- Benchmarking the Ligand-HER2 Interactions Using Machine Learning and Molecular Dynamics Simulations.ACS omega · 2026Article
- Application of chemical similarity and bioisosteres to find allosteric inhibitors of type 2 lipid kinase γ.Scientific reports · 2025Article
- Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling.Protein science : a publication of the Protein Society · 2025Review
- Article
- Binding Mechanism of Inhibitors to CDK6 Deciphered by Multiple Independent Molecular Dynamics Simulations and Free Energy Predictions.Molecules (Basel, Switzerland) · 2025Article
- Structural Dynamics of Rho GTPases.Journal of molecular biology · 2025Review
- Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization.RSC advances · 2025Article
- Development of potent inhibitors against KRAS, its mutant G12R, allosteric and Switch-I/Switch-II site.In silico pharmacology · 2025Article
- Unveiling Allosteric Regulation and Binding Mechanism of BRD9 through Molecular Dynamics Simulations and Markov Modeling.Molecules (Basel, Switzerland) · 2024Article
- Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.Molecules (Basel, Switzerland) · 2024Article
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6 authors.
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Abstract
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg
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