title: Distinct Dynamic Modes Enable the Engagement of Dissimilar Ligands in a Promiscuous Atypical RNA Recognition Motif.
abstract: Conformational dynamics play a critical role in ligand binding, often conferring divergent activities and specificities even in species with highly similar ground-state structures. Here, we employ time-resolved electrospray ionization hydrogen-deuterium exchange (TRESI-HDX) to characterize the changes in dynamics that accompany oligonucleotide binding in the atypical RNA recognition motif (RRM2) in the C-terminal domain (CTD) of human La protein. Using this approach, which is uniquely capable of probing changes in the structure and dynamics of weakly ordered regions of proteins, we reveal that binding of RRM2 to a model 23-mer single-stranded RNA and binding of RRM2 to structured IRES domain IV of the hepatitis C viral (HCV) RNA are driven by fundamentally different dynamic processes. In particular, binding of the single-stranded RNA induces helical "unwinding" in a region of the CTD previously hypothesized to play an important role in La and La-related protein-associated RNA remodeling, while the same region becomes less dynamic upon engagement with the double-stranded HCV RNA. Binding of double-stranded RNA also involves less penetration into the RRM2 binding pocket and more engagement with the unstructured C-terminus of the La CTD. The complementarity between TRESI-HDX and Δδ nuclear magnetic resonance measurements for ligand binding analysis is also explored.
authors.affiliation: Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada.|Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Kerene A
authors.initials: KA
authors.lastname: Brown
authors.affiliation: Department of Biology, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Samel
authors.initials: S
authors.lastname: Sharifi
authors.affiliation: Department of Biology, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Rawaa
authors.initials: R
authors.lastname: Hussain
authors.affiliation: Department of Biology, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Logan
authors.initials: L
authors.lastname: Donaldson
authors.affiliation: Department of Biology, York University , Toronto, ON M3J 1P3, Canada.|Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Bayfield
authors.affiliation: Department of Chemistry, York University , Toronto, ON M3J 1P3, Canada.|Centre for Research in Mass Spectrometry, York University , Toronto, ON M3J 1P3, Canada.|Centre for Research in Biomolecular Interactions, York University , Toronto, ON M3J 1P3, Canada.
authors.forename: Derek J
authors.identifier: http://orcid.org/0000-0002-7012-6085
authors.initials: DJ
authors.lastname: Wilson
mesh_terms: D001324:Autoantigens / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D041961:Deuterium Exchange Measurement / Q000379:methods; D006526:Hepatitis C / Q000235:genetics; D006801:Humans; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D013058:Mass Spectrometry / Q000379:methods; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D011131:Polyribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D000072417:Protein Domains; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000071377:RNA Recognition Motif; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000097585:SS-B Antigen
chemical_list: D001324:Autoantigens; D008024:Ligands; D011131:Polyribonucleotides; D012313:RNA; D012330:RNA, Double-Stranded; D012367:RNA, Viral; D012261:Ribonucleoproteins; D000097585:SS-B Antigen