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Cited by 19Protein Structure and DynamicsReceptor Mechanisms and SignalingOlfactory and Sensory Function Studies

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Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor

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Okamoto, Chisato, Ando, Koji·2024·Biophysics and Physicobiology
DOI 10.2142/biophysico.bppb-v21.0007PMC PMC11128758

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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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Figures

Figure 1 A snapshot of the MD simulation showing the positions of the twelve key residues, Cys1063.33, Ser1133.40, Phe182, Phe2035.42, Asn2075.46, Glu2085.47, Leu2125.51, Phe2526.47, Ile2566.51, Leu2596.54, Tyr2606.55, and Tyr2917.53 (the superscripts denote Ballesteros-Weinstein numbers [20,21]), relative to the odorant ligand eugenol (EG).
Figure 1 A snapshot of the MD simulation showing the positions of the twelve key residues, Cys1063.33, Ser1133.40, Phe182, Phe2035.42, Asn2075.46, Glu2085.47, Leu2125.51, Phe2526.47, Ile2566.51, Leu2596.54, Tyr2606.55, and Tyr2917.53 (the superscripts denote Ballesteros-Weinstein numbers [20,21]), relative to the odorant ligand eugenol (EG).CC BY-NC-SA · PubMed Central
Figure 2 A snapshot of the MD simulation box.
Figure 2 A snapshot of the MD simulation box.CC BY-NC-SA · PubMed Central
Figure 3 Representative trajectories of the distance between the OH atom of eugenol and the O atoms of Ser113, Asn207, and Tyr260, starting from the docking configurations.
Figure 3 Representative trajectories of the distance between the OH atom of eugenol and the O atoms of Ser113, Asn207, and Tyr260, starting from the docking configurations.CC BY-NC-SA · PubMed Central
Figure 4 A snapshot of the hydrogen-bond structure between eugenol (EG) and Ser1133.40 and Glu1123.39.
Figure 4 A snapshot of the hydrogen-bond structure between eugenol (EG) and Ser1133.40 and Glu1123.39.CC BY-NC-SA · PubMed Central
Figure 5 Root-mean-square fluctuation (RMSF) of the Cα atoms of Olfr73 in the apo and holo forms and their difference (holo minus apo). The left panel shows all residues. TM1–TM7 denote the transmembrane α-helices. The vertical lines below the bar plot indicate the twelve key residues shown in the right panel.
Figure 5 Root-mean-square fluctuation (RMSF) of the Cα atoms of Olfr73 in the apo and holo forms and their difference (holo minus apo). The left panel shows all residues. TM1–TM7 denote the transmembrane α-helices. The vertical lines below the bar plot indicate the twelve key residues shown in the right panel.CC BY-NC-SA · PubMed Central
Figure 6 Dynamic cross-correlation map (DCCM) of the Cα atoms of Olfr73 in the apo and holo forms and their difference (holo minus apo).
Figure 6 Dynamic cross-correlation map (DCCM) of the Cα atoms of Olfr73 in the apo and holo forms and their difference (holo minus apo).CC BY-NC-SA · PubMed Central
Figure 7 Sections of the DCCMs in Figure 6 at Ser113 and difference of the DCCMs (holo minus apo) for the key residues.
Figure 7 Sections of the DCCMs in Figure 6 at Ser113 and difference of the DCCMs (holo minus apo) for the key residues.CC BY-NC-SA · PubMed Central
Figure 8 Time-dependent dynamic cross-correlation (TDDCC) of the apo and holo forms of Olfr73 between the key residues identified as being in the major correlation transfer pathway.
Figure 8 Time-dependent dynamic cross-correlation (TDDCC) of the apo and holo forms of Olfr73 between the key residues identified as being in the major correlation transfer pathway.CC BY-NC-SA · PubMed Central

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Metadata

Authors
Okamoto, C., & Ando, K.
Affiliations
Tokyo Woman's Christian University (JP)
Corresponding author
Ando, Koji
ORCID
Ando, Koji
Venue
Biophysics and Physicobiology
Publisher
Biophysical Society of Japan
Published
2024
Volume
21
Issue
1
Pages
n/a
ISSN
2189-4779 (ISSN-L)
DOI
10.2142/biophysico.bppb-v21.0007
PMC
PMC11128758
OpenAlex
W4390939122
Cited by
19
References
2
Citations by year
2026: 7 · 2025: 11 · 2024: 1
FWCI
2.59
Type
journal article
Language
en
Open access
Locations
  • Biophysics and Physicobiology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • arXiv (Cornell University)
Funders
Japan Society for the Promotion of Science (19K22173)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Life Sciences › Neuroscience › Sensory Systems › Olfactory and Sensory Function Studies
Keywords
eugenol, odorant binding, hydrogen bonding, structural fluctuations, ligand binding, RMSF

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