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Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography
Published on: April 19, 2016
Modelling the three-dimensional structure of the right-terminal domain of pospiviroids
1Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany. steger@biophys.uni-duesseldorf.de.
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.
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