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Structural modeling of Omicron spike protein and its complex with human ACE-2 receptor: Molecular basis for high transmissibility of the virus.
Koley, Tirthankar; Kumar, Manoj; Goswami, Arunima; Ethayathulla, Abdul S; Hariprasad, Gururao.
  • Koley T; Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
  • Kumar M; Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
  • Goswami A; Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
  • Ethayathulla AS; Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
  • Hariprasad G; Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India. Electronic address: dr.hariprasadg@gmail.com.
Biochem Biophys Res Commun ; 592: 51-53, 2022 02 12.
Article in English | MEDLINE | ID: covidwho-1611626
ABSTRACT
Omicron is a new variant of SARS-CoV-2, which is currently infecting people around the world. Spike glycoprotein, an important molecule in pathogenesis of infection has been modeled and the interaction of its Receptor Binding Domain with human ACE-receptor has been analysed by simulation studies. Structural analysis of Omicron spike glycoprotein shows the 30 mutations to be distributed over all domains of the trimeric protein, wherein the mutant residues are seen to be participating in higher number of intra-molecular interactions including two salt bridges emanating from mutant residues thereby stabilizing their conformation, as compared to wild type. Complex of Receptor Binding Domain (RBD) with human ACE-2 receptor shows seven mutations at interacting interface comprising of two ionic interactions, eight hydrogen bonds and seven Van der Waals interactions. The number and quality of these interactions along with other binding biophysical parameters suggests more potency of RBD domain to the receptor as compared to the wild type counterpart. Results of this study explains the high transmissibility of Omicron variant of SARS-CoV-2 that is currently observed across the world.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / Angiotensin-Converting Enzyme 2 / SARS-CoV-2 / COVID-19 Topics: Variants Limits: Humans Language: English Journal: Biochem Biophys Res Commun Year: 2022 Document Type: Article Affiliation country: J.bbrc.2021.12.082

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Spike Glycoprotein, Coronavirus / Angiotensin-Converting Enzyme 2 / SARS-CoV-2 / COVID-19 Topics: Variants Limits: Humans Language: English Journal: Biochem Biophys Res Commun Year: 2022 Document Type: Article Affiliation country: J.bbrc.2021.12.082