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Ensemble Allosteric Model for the Modified Wobble Hypothesis
A.K. Sarkar, J. Sarzynska,
Published in American Chemical Society
PMID: 32701298
Volume: 11
Issue: 15
Pages: 6337 - 6343
The residue 2-Thiouridine (s2U) provides a remarkable example for the "modified wobble"hypothesis, which postulates that some post-Transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χIDRP force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in Gs2UUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-To-order transition. The conformational redistribution and the slowing down of the transition between the clusters within the population in the presence of s2U suggest ensemble allostery to be a key mechanism that may play a general role in the functioning of the wobble modifications of tRNAs. Copyright © 2020 American Chemical Society.
About the journal
JournalData powered by TypesetJournal of Physical Chemistry Letters
PublisherData powered by TypesetAmerican Chemical Society