An investigation of NMR‐Derived Structures for the SARS Coronavirus E Channel Protein

Philipp, Manfred; Olumuyide, Ezekiel; Babalola, Blessing; Gonzalez, Janet

During the current Covid‐19 pandemic, college laboratories are shut down and undergraduate students who need research experience are having a hard time gaining those skills. Against this backdrop we developed a pilot project that would introduce students to internationally available online biochemical databases, open‐source modeling software and animation tools. The students received individual hands‐on training to generate data allowing them to engage in discovery and contextualize learning as they would in a face‐to face laboratory setting. We describe an investigation of NMR‐based structures of a SARS coronavirus E channel protein, structures found in the 5X29 pdb file deposited by Surya, Li, &, Torres, and described in (2018) Biochim. Biophys. Acta 1860: 1309‐1317. These small proteins form ion channels that are of interest because live attenuated vaccines target these channels promising prevention and treatment for coronavirus infections. The SARS coronavirus E channel protein, a right‐handed alpha‐helical bundle, is composed of 5 chains, A through E. Each chain has 16 NMR structures in the database. Incorporating computational and molecular visualization tools students generate data to observe, measure, and communicate the dihedral angle backbone movement of the whole pentamer, the separate chains, and individual amino acid residues on a bond‐by‐bond basis. All the open access software and programs used worked within a Windows/Mac environment except one program that used Linux command lines to create models from the PDB file. Afterwards these models were animated to demonstrate and analyze dihedral angle movement within structures. The students used this work to fulfill the laboratory component of their undergraduate independent study program at in the Biological Sciences and Chemistry Departments of Lehman College, a 4‐year college within the CUNY system.