title: Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?
abstract: The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. ria2@psu.edu.
authors.forename: Ibrahim M
authors.initials: IM
authors.lastname: Moustafa
authors.affiliation: Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, 1100 South Grand Ave, St Louis, MO 63104, USA. sdg0919@gmail.com.
authors.forename: David W
authors.initials: DW
authors.lastname: Gohara
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. akira.uc@gmail.com.
authors.forename: Akira
authors.initials: A
authors.lastname: Uchida
authors.affiliation: Huck Institutes of life sciences, The Pennsylvania State University, University Park, PA 16802, USA. nhy1@psu.edu.
authors.forename: Neela
authors.initials: N
authors.lastname: Yennawar
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. cec9@psu.edu.
authors.forename: Craig E
authors.initials: CE
authors.lastname: Cameron
mesh_terms: D000086042:3C Viral Proteases; D003546:Cysteine Endopeptidases / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017955:Poliovirus / Q000737:chemistry* / Q000502:physiology*; D011487:Protein Conformation; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000378:metabolism*; D053838:Scattering, Small Angle; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; C090443:polymerase 3Dpol, poliovirus; D012324:RNA-Dependent RNA Polymerase; D003546:Cysteine Endopeptidases; D000086042:3C Viral Proteases
keywords: 3CD; MD simulations; RNA virus; SAXS; conformational dynamics; poliovirus; polyprotein