Usage
  • 123 views
  • 242 downloads

Force spectroscopy of the frameshift signal from West Nile virus reveals multiple folding pathways and structural heterogeneity

  • Author / Creator
    Halma, Matthew
  • Programmed ribosomal frameshifting (PRF) represents an important mechanism for translational genetic recoding, especially in viruses. The components of a PRF stimulator have been well characterized, though accounting for the variation in the frameshift stimulating efficiency has thus far been elusive. Frameshift efficiencies at known PRF sites vary from a few percent to 70-80%, and several studies have been undertaken to determine what distinguishes a high efficiency PRF site from a low efficiency PRF site via structural characterization of the stimulatory structure. Observations suggest that conformational plasticity, the ability of a certain sequence to adopt multiple conformations, is correlated with frameshift efficiency. We examine a very high efficiency (70%) PRF stimulatory structure responsible for the NS1′ frameshift in West Nile virus (WNV) to determine its characteristics. We find a high degree of structural plasticity and heterogeneity; the PRF signal exhibits multiple different starting states and unfolds via two main pathways. Furthermore, we characterize the structures involved in these pathways, and find that they correspond to predicted structures using bioinformatic predictions and SHAPE analysis. Moreover, we suggest a new operational metric of conformational plasticity, one that obviates two existing problems with the previous method for defining conformational plasticity, namely the requirement to specify a native state, and the insensitivity to multiple conformations. Additionally, we extend this definition to be force dependent, and find that the value of this conformational plasticity metric in the force range of ribosomal stalling correlates highly with frameshifting efficiency. These results may elucidate the process of frameshifting by illustrating the relationship between conformational plasticity within a specific force range and frameshift efficiency. In addition, the characterization of a high efficiency frameshift signal allows for a better understanding of the structural dynamics underlying frameshifting.

  • Subjects / Keywords
  • Graduation date
    Spring 2019
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/r3-epe8-0p53
  • License
    Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.