ArticleBiophysics and physicobiology2024
Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor.
Article in Biophysics and physicobiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- An integrated subtractive genomics and immunoinformatics approach for designing a universal multi-epitope vaccine againstFrontiers in bioinformatics · 2026Article
- Identification of novel DYRK1A inhibitors as treatment options for alzheimer's disease through comprehensive in silico approaches.Scientific reports · 2025Article
- Coordinated subdomain movements of MlaC regulate ligand binding and transport.Computational and structural biotechnology journal · 2025Article
- Structure-threshold relationship in food aroma molecules: Insights from S-curve method, molecular docking, and dynamics simulations.Current research in food science · 2025Article
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2 authors.
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Abstract
Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlphaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the α-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 → Phe182 → (Leu259 or Tyr260) → Tyr291 induced by the ligand binding with a time scale of 4-6 ns.
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