Article pubs.acs.org/JPCB
Unveiling Inherent Degeneracies in Determining PopulationWeighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs Shan Yang† and Hashim M. Al-Hashimi*,‡ †
Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, United States Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27705, United States
‡
S Supporting Information *
ABSTRACT: A growing number of studies employ time-averaged experimental data to determine dynamic ensembles of biomolecules. While it is well-known that different ensembles can satisfy experimental data to within error, the extent and nature of these degeneracies, and their impact on the accuracy of the ensemble determination remains poorly understood. Here, we use simulations and a recently introduced metric for assessing ensemble similarity to explore degeneracies in determining ensembles using NMR residual dipolar couplings (RDCs) with specific application to A-form helices in RNA. Various target ensembles were constructed representing different domain−domain orientational distributions that are confined to a topologically restricted (
