title: Modelling the three-dimensional structure of the right-terminal domain of pospiviroids.
abstract: Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain.
authors.affiliation: Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany. steger@biophys.uni-duesseldorf.de.
authors.forename: Gerhard
authors.identifier: http://orcid.org/0000-0001-6992-1236
authors.initials: G
authors.lastname: Steger
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D000072417:Protein Domains; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry*; D014772:Viroids / Q000378:metabolism*
chemical_list: D006657:Histones; D012367:RNA, Viral; D014764:Viral Proteins