ArticleMolecules (Basel, Switzerland)2022
Deciphering Conformational Changes of the GDP-Bound NRAS Induced by Mutations G13D, Q61R, and C118S through Gaussian Accelerated Molecular Dynamic Simulations.
Article in Molecules (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 16 citations in OpenAlex.
- Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics.Molecules (Basel, Switzerland) · 2024Article
- Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.Journal of enzyme inhibition and medicinal chemistry · 2023Article
- Binding selectivity-dependent molecular mechanism of inhibitors towards CDK2 and CDK6 investigated by multiple short molecular dynamics and free energy landscapes.Journal of enzyme inhibition and medicinal chemistry · 2023Article
- Identification Mechanism of BACE1 on Inhibitors Probed by Using Multiple Separate Molecular Dynamics Simulations and Comparative Calculations of Binding Free Energies.Molecules (Basel, Switzerland) · 2023Article
- Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies.Molecules (Basel, Switzerland) · 2023Review
- Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA.Molecules (Basel, Switzerland) · 2023Article
- Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2023Article
- Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations.Molecules (Basel, Switzerland) · 2023Article
- Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2023Article
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Authors and funding
4 authors at 2 institutions in 1 country.
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Abstract
The conformational changes in switch domains significantly affect the activity of NRAS. Gaussian-accelerated molecular dynamics (GaMD) simulations of three separate replicas were performed to decipher the effects of G13D, Q16R, and C118S on the conformational transformation of the GDP-bound NRAS. The analyses of root-mean-square fluctuations and dynamics cross-correlation maps indicated that the structural flexibility and motion modes of the switch domains involved in the binding of NRAS to effectors are highly altered by the G13D, Q61R, and C118Smutations. The free energy landscapes (FELs) suggested that mutations induce more energetic states in NRAS than the GDP-bound WT NRAS and lead to high disorder in the switch domains. The FELs also indicated that the different numbers of sodium ions entering the GDP binding regions compensate for the changes in electrostatic environments caused by mutations, especially for G13D. The GDP-residue interactions revealed that the disorder in the switch domains was attributable to the unstable hydrogen bonds between GDP and two residues, V29 and D30. This work is expected to provide information on the energetic basis and dynamics of conformational changes in switch domains that can aid in deeply understanding the target roles of NRAS in anticancer treatment.
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