title: In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.
abstract: ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since structural models from experiments are still lacking, computational methods can be challenged to generate such models. In this study, a 'sequential approach' for the assembly is proposed in which the individual TMDs are assembled one by one. This protocol is compared with a concerted protocol in which all TMDs are assembled simultaneously. The role of the loops between the TMDs during assembly of the monomers into a bundle is investigated. Molecular dynamics simulations for 20 ns are performed as a short equilibration to assess the bundle stability in a lipid environment. The results suggest that bundles are likely with the second TMD facing the putative pore. All the putative bundles show water molecules trapped within the lumen of the pore with only occasional events of complete crossing.
authors.affiliation: Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Hsu
authors.forename: Wolfgang B
authors.initials: WB
authors.lastname: Fischer
mesh_terms: D000818:Animals; D006801:Humans; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D055503:Protein Multimerization; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry*; D015678:Viral Structural Proteins / Q000737:chemistry*; D000086082:Viroporin Proteins
chemical_list: D015678:Viral Structural Proteins; C515313:ORF3A protein, SARS coronavirus; D000086082:Viroporin Proteins