In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins |
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| Authors: | Nancy D’ Arminio,Deborah Giordano,Bernardina Scafuri,Carmen Biancaniello,Mauro Petrillo,Angelo Facchiano,Anna Marabotti |
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| Affiliation: | 1.Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (N.D.); (B.S.);2.National Research Council, Institute of Food Science, 83100 Avellino, Italy;3.Department of Electrical Engineering and Information Technology, University of Naples “Federico II”, 80128 Naples, Italy;4.Seidor Italy SRL, 21029 Milan, Italy; |
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| Abstract: | The SARS-CoV-2 variant Omicron is characterized, among others, by more than 30 amino acid changes occurring on the spike glycoprotein with respect to the original SARS-CoV-2 spike protein. We report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human antibodies, obtained by modeling them into selected publicly available resolved 3D structures of spike–antibody complexes and investigating the effects of these mutations at structural level. We predict that the interactions of Omicron spike with human antibodies can be either negatively or positively affected by amino acid changes, with a predicted total loss of interactions only in a few complexes. Moreover, our analysis applied also to the spike-ACE2 interaction predicts that these amino acid changes may increase Omicron transmissibility. Our approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology and represents a model to be adopted also in the case of other variants. |
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| Keywords: | protein variants, spike, SARS-CoV-2, antibodies, protein– protein interactions |
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