McCarthy, Erika: Evolution of SARS CoV-2 Proteins in 3D During the COVID-19 Pandemic: Nsp3e NAB domain

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Title: Evolution of SARS CoV-2 Proteins in 3D During the COVID-19 Pandemic: Nsp3e NAB domain

Name: Erika McCarthy

Home Institute: Stevens Institute of Technology

Programs: RISE program, Protein Data Bank

Other contributors: Lindsey Whitmore, Sophia Staggers, Elliott M. Dolan, Changpeng Lu, Vidur Sarma, Zhuofan Shen, Lingjun Xie, Joseph L. Lubin, Christine Zardecki, Sagar D. Khare, Stephen K. Burley

Abstract: “As part of a virtual summer research experience with the RCSB PDB, we studied how SARS-CoV-2 proteins protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools, including Clustal Omega (www.ebi.ac.uk/Tools/msa/clustalo/) for sequence alignments and phylogenetic trees; Mol* (molstar.org) for 3D molecular visualization; and Foldit (fold.it) for structural/energetic effects of sequence mutations.

Nonstructural protein 3 (NSP3) is a 15 domain protein of SARS CoV-2. The nucleic acid binding (NAB) domain is highly conserved from the SARS CoV virus, with expectedly similar ssRNA binding and dsDNA unwinding capabilities. A SARS CoV-2 homolog of the SARS CoV NAB domain was constructed to analyze the effects of reported mutations on the structure and function of the protein. Positively charged surface residues are essential for NAB function, which is supported by the properties of frequently occurring mutations.
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Biography: I am a chemistry major with a minor in pure and applied Mathematics at Stevens Institute of Technology. I am also a goal keeper for the soccer team and a chemistry tutor. I am from Vermont, but I love living in Hoboken and being close to NYC!