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

ABSTRACT: 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.

SUBMITTER: Philipp M

PROVIDER: S-EPMC8239525 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The SARS coronavirus (SARS-CoV) replicase gene encodes 16 nonstructural proteins (nsps) with multiple enzymatic activities. Several of these enzymes are common components of replication complexes of other plus-strand RNA viruses, such as picornavirus 3C-like protease, papain-like protease, RNA-dependent RNA polymerase, RNA helicase, and ribose 2′-O-methyltransferase activities, while others such as exoribonuclease, endoribonuclease, and adenosine diphosphate-ribose 1″-phosphatase activities, are rarely or not conserved in viruses outside the order Nidovirales. The latter enzymes are believed to be involved in unique metabolic pathways used by coronaviruses to (1) replicate and transcribe their extremely large RNA genomes, and (2) interfere with cellular functions and antiviral host responses. Since the global outbreak of SARS in 2003, major efforts have been made to elucidate the structures of the protein components of the SARS-CoV replication/transcription complex. Thus, in less than 5 years, the structures of as many as 16 SARS-CoV proteins or functional domains have been determined. Remarkably, eight of these 16 structures had novel folds, illustrating the uniqueness of the coronavirus replicative machinery. Furthermore, several new protein functions and potential drug targets have been identified in these studies. Current structural studies mainly focus on the few remaining proteins for which no structural information is available and larger protein complexes comprised of different nsps. The studies aim at obtaining detailed information on the functions and macromolecular assembly of the coronavirus replication/transcription machinery which, over a long period of time, may be used to develop selective antiviral drugs. This chapter reviews structural information on the SARS-CoV macro domain (ADRP) as well as nsps 7, 8, 9, and 15 and summarizes our current knowledge of active-site residues and intermolecular interactions of these proteins.

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

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