D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1

The clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, contribution of the mutations in each of the viral genes towards the degree of severity needs a deeper understanding for designing a better therapeutic approach against COVID-19. Open Reading Frame-3a (ORF3a) protein has been found to be mutated at several positions. In this work, we have studied the effect of one of the most frequently occurring mutants, D155Y of ORF3a protein, found in Indian COVID-19 patients. Using computational simulations we demonstrated that the substitution at 155th changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein compared with the other substitutions found in Indian patients. Protein-protein docking using HADDOCK analysis revealed that substitution D155Y weakened the binding affinity of ORF3a with caveolin-1 compared with the other substitutions, suggesting its importance in the overall stability of ORF3a-caveolin-1 complex, which may modulate the virulence property of SARS-CoV-2. ### Competing Interest Statement The authors have declared no competing interest. * ARL6IP6 : ADP Ribosylation Factor Like GTPase 6 interacting protein 6 ASC : Apoptosis associated speck-like protein containing a caspase recruitment domain BLAST : Basic Local Alignment Search Tool CD4+ : Cluster of Differentiation 4+ CD8+ : Cluster of Differentiation 8+ COVID-19 : Coronavirus Disease 2019 Cryo-EM : Cryo Electron Microscope HMOX1 : Heme Oxygenase 1 IFN : Interferon MERS-CoV : Middle East respiratory syndrome coronavirus MMGBSA : Molecular mechanics with generalized Born and surface area solvation NCBI : National Centre for Biotechnology Information NF- κ B : Nuclear factor kappa light chain enhancer of activated B cells NLRP3 : Nucleotide-binding oligomerization domain,Leucine rich repeat and Pyrin domain containing ORF : Open Reading Frame PDB : Protein Data Bank PISA : Protein Interfaces Surfaces and Assemblies PROVEAN : Protein Variation Effect Analyzer RMSD : Root Mean Square Deviation SUN2 : SUN domain-containing protein 2 TRIM59 : Tripartite motif-containing protein 59.