Genetic diversity and structural characterization of spike glycoprotein of newly emerged SARS-CoV-2

<p>A new beta Coronavirus (SARS-CoV-2) infection was first identified in the Wuhan City, China in December 2019 and after that it had spread rapidly throughout the globe and subsequently WHO have announced it as a pandemic. So, SARS-CoV-2 has now become a global threat to human civilization. Recent studies showed that the proteomic data of SARS-CoV-2 is closely related with other beta Coronavirus. The phylogenetic tree revealed the closeness of recently reported SAR-CoV2 with SARS-CoV by using MEGA 7 along with the suitable protocol of Neighbor joining algorithm. The spike glycoprotein plays the most important role during the onset of infection. Several mutations have been reported across the globe in the S Proteins. In this research, molecular docking between the SARS-CoV-2 spike glycoprotein and ACE2 protein was carried out in PatchDock web servers. WEBnm@ calculated the molecular simulation using Normal Mode Analysis (NMA) along with lowest deformation energy value which signifies the domain motions. Also during multiple sequence analysis, variations were observed within the Spike protein reported globally. 3- Dimensional structure of protein molecules were designed using homology modeling and the structure were validated through Q mean score and Ramachandran plot. All of the designed sequences were having around 91% of the amino acid in the favored region of Ramachandran plot. In order to check the binding affinity difference between the mutated and non-mutated strains, the generated models were docked with human ACE2 molecules. The non mutated strains have given the similar ACE value. However, there were variations in ACE value of the mutated strains. This observation provides evidence of Phylogenetic diversity and evolution.</p><p>
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