Jump to main content
Jump to site search

Issue 8, 2016
Previous Article Next Article

Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

Author affiliations

Abstract

Detecting conformational heterogeneity in biological macromolecules is a key for the understanding of their biological function. We here provide a comparison between two independent approaches to assess conformational heterogeneity: molecular dynamics simulations, performed without inclusion of any experimental data, and maximum occurrence (MaxOcc) distribution over the topologically available conformational space. The latter only reflects the extent of the averaging and identifies regions which are most compliant with the experimentally measured NMR Residual Dipolar Couplings (RDCs). The analysis was performed for the HIV-1 TAR RNA, consisting of two helical domains connected by a flexible bulge junction, for which four sets of RDCs were available as well as an 8.2 μs all-atom molecular dynamics simulation. A sample and select approach was previously applied to extract from the molecular dynamics trajectory conformational ensembles in agreement with the four sets of RDCs. The MaxOcc analysis performed here identifies the most likely sampled region in the conformational space of the system which, strikingly, overlaps well with the structures independently sampled in the molecular dynamics calculations and even better with the RDC selected ensemble.

Graphical abstract: Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

Back to tab navigation

Supplementary files

Article information


Submitted
09 Jul 2015
Accepted
07 Sep 2015
First published
07 Sep 2015

Phys. Chem. Chem. Phys., 2016,18, 5743-5752
Article type
Paper
Author version available

Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

W. Andrałojć, E. Ravera, L. Salmon, G. Parigi, H. M. Al-Hashimi and C. Luchinat, Phys. Chem. Chem. Phys., 2016, 18, 5743
DOI: 10.1039/C5CP03993B

Social activity

Search articles by author

Spotlight

Advertisements