title: Long-Range Communication between Different Functional Sites in the Picornaviral 3C Protein.
abstract: The 3C protein is a master regulator of the picornaviral infection cycle, responsible for both cleaving viral and host proteins, and interacting with genomic RNA replication elements. Here we use nuclear magnetic resonance spectroscopy and molecular dynamics simulations to show that 3C is conformationally dynamic across multiple timescales. Binding of peptide and RNA lead to structural dynamics changes at both the protease active site and the RNA-binding site, consistent with these sites being dynamically coupled. Indeed, binding of RNA influences protease activity, and likewise, interactions at the active site affect RNA binding. We propose that RNA and peptide binding re-shapes the conformational energy landscape of 3C to regulate subsequent functions, including formation of complexes with other viral proteins. The observed channeling of the 3C energy landscape may be important for regulation of the viral infection cycle.
authors.affiliation: Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Yan M
authors.initials: YM
authors.lastname: Chan
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Ibrahim M
authors.initials: IM
authors.lastname: Moustafa
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Jamie J
authors.initials: JJ
authors.lastname: Arnold
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Craig E
authors.initials: CE
authors.lastname: Cameron
authors.affiliation: Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address: ddb12@psu.edu.
authors.forename: David D
authors.initials: DD
authors.lastname: Boehr
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D003546:Cysteine Endopeptidases / Q000737:chemistry* / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000378:metabolism*; D010849:Picornaviridae / Q000737:chemistry / Q000201:enzymology*; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D010455:Peptides; D014764:Viral Proteins; D012313:RNA; D003546:Cysteine Endopeptidases