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A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings

Borkar, Aditi N.; De Simone, Alfonso; Montalvao, Rinaldo W.; Vendruscolo, Michele

Authors

Dr ADITI BORKAR Aditi.Borkar@nottingham.ac.uk
ASSISTANT PROFESSOR IN MOLECULARBIOCHEMISTRY & BIOPHYSICS

Alfonso De Simone

Rinaldo W. Montalvao

Michele Vendruscolo



Abstract

We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.

Citation

Borkar, A. N., De Simone, A., Montalvao, R. W., & Vendruscolo, M. (2013). A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings. Journal of Chemical Physics, 138(21), Article 215103. https://doi.org/10.1063/1.4804301

Journal Article Type Article
Acceptance Date Apr 24, 2013
Online Publication Date Jun 7, 2013
Publication Date Jun 7, 2013
Deposit Date Sep 8, 2022
Journal The Journal of Chemical Physics
Print ISSN 0021-9606
Electronic ISSN 1089-7690
Publisher American Institute of Physics
Peer Reviewed Peer Reviewed
Volume 138
Issue 21
Article Number 215103
DOI https://doi.org/10.1063/1.4804301
Public URL https://nottingham-repository.worktribe.com/output/3291388
Publisher URL https://aip.scitation.org/doi/full/10.1063/1.4804301