Journal
BIOPHYSICAL JOURNAL
Volume 113, Issue 2, Pages 313-320Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2017.06.008
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Funding
- National Institutes of Health [R01-GM098102]
- Blue Waters sustained-petascale computing project [NSF OCI 07-25070, PRAC OCI-1515572]
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [1515572] Funding Source: National Science Foundation
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Though the structure of the substrate stem loop I (SLI)-stem loop V (SLV) kissing loop junction of the Varkud Satellite ribozyme has been experimentally characterized, the dynamics of this Mg2+ -dependent loop-loop interaction have been elusive. Specifically, each hairpin loop contains a U-turn motif, but only SLV shows a conformational shift triggered by Mg2+ ion association. Here, we use molecular dynamics simulations to analyze the binding and dynamics of this kissing loop junction. We show that SLV acts as a scaffold, providing stability to the junction. Mg2+ ions associate with SLV when it is part of the junction in a manner similar to when it is unbound, but there is no specificity in Mg2+ binding for the SLI loop. This suggests that the entropic penalty of ordering the larger SLI is too high, allowing SLV to act as a scaffold for multiple substrate loop sequences.
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