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Structure Refinement of the Spike Protein of SARS-COV-2

Structure Refinement of the Spike Protein of SARS-COV-2

Ching Wai Yum

Wai-Yim Ching is a Professor in the Dept. of Physics and Astronomy at the U. of Missouri-Kansas City.

Investigator: Wai-Yim Ching
Affiliation: University of Missouri-Kansas City

Award from the COVID-19 HPC Consortium

The current COVID-19 pandemic is a severe threat in human health leading to social, and economic disruption in the entire world. The spike (S) glycoprotein of SARS-COV-2 is considered to be a key target for vaccine development since it makes first contact to ACE2 acceptor in human protein. The structure of the spike protein was recently determined by cryo-EM techniques with a resolution of 3.5 Å. It contains three chains and each chain consists of four structural domains: receptor binding domain (RBD), n-terminal domain (NTD), subdomain 1 and 2 (SD1-SD2) and S2. This project will refine the structures of these domains to much higher accuracy using large scale ab initio simulations and investigate their atomic scale interaction and intra molecular binding mechanism. They will also present electronic structure calculations with detailed intra and intermolecular interactions of the spike protein in the pre- and post-fusion configuration which are difficult to determine experimentally. In addition, they are studying the further interaction between the spike protein and ACE2 to shed some light on the genetic modification due to mutation and thereby provide useful insights for various vaccine development and drug design.

Publications: Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding, Adhikari, Puja and Li, Neng and Shin, Matthew and Steinmetz, Nicole F. and Twarock, Reidun and Podgornik, Rudolf and Ching, Wai-Yim. Phys. Chem. Chem. Phys., 2020, DOI: 10.1039/D0CP03145C


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