Saray Shai; Kelly M. Thayer; Michael P. Weir
The ribosome is a biological machine which translates mRNA into protein, at the rate of one amino acid from a decoded codon every tenth of a second. Computational chemists have developed a technique called Molecular Dynamics (MD), which allows molecular behaviour to be explicitly modeled and calculated on the nanosecond timescale using computers.
For my thesis, I used the AMBER MD framework to model the ribosome’s catalytically active core, to evaluate the feasibility of potential mRNA-rRNA interaction during ribosomal translocation. In this thesis, I give an overview on how modern MD programs calculate molecular behaviour in an efficient manner, and MD's application to our ribosomal model system of interest.
Additionally, I give an overview of how statistical biasing techniques like UMBRELLA Sampling, WHAM, and Partial Nudged Elastic Band are used to generalize conclusions from nanosecond-level calculations to second-level biological processes, again with applications to the ribosome.
Williams, Elliot J., "Molecular Dynamics and Computational Analysis of Potential 18S rRNA-mRNA Interactions During Ribosomal Translocation" (2019). Masters Theses. 231.
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