Abstract

Conformational dynamics plays an essential role in the functions of many HIV-1 viral regulatory RNA elements. Our long term goal is to elucidate the molecular basis for functional dynamics in these RNAs as a prerequisite for rationally designing anti-HIV therapeutics targeting RNA. The main hypothesis in this proposal is that conformational dynamics plays an essential role in adpative recognition underlying the function of the transactivation response element (TAR) and structural isomerization underlying the function of the dimerization initiation site (DIS). This hypothesis is supported by the following observations, (i) TAR can promiscuously bind unrelated compounds by undergoing distinct structural changes, (ii) Compounds that diminish TAR's conformational flexibility inhibit its function, (iii) The DIS can spontanously undergo large secondary structural transitions needed for its function, (iv) Structural dynamics in DIS has been directly correlated with the rate at which it undergoes these transitions. The overall objective of this proposal is to develop NMR methods for elucidating the role of conformational flexibility in the functions of TAR and DIS and to apply this understanding in the rational design of anti-HIV therapeutics targeting TAR and DIS.
The specific aims are to: 1. Develop and apply NMR methods to elucidate the role of conformational dynamics in TAR adaptive recognition. Results will be used to examine if TAR can dynamically access protein bound states. 2. Elucidate the role of structural dynamics in the DIS structural isomerization. Results will be used to examine if DIS can access conformations uniquely poised for structural isomerization dynamically. 3. Elucidate the role of RNA flexibility in aminoglycoside recognition. Results will be used to examine the hypothesis that electrostatic interactions play a primary role in arresting RNA global motions and that different aminoglycosides can bind different conformational manifestations of the same RNA target. ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI066975-02
Application #
7081252
Study Section
AIDS Molecular and Cellular Biology Study Section (AMCB)
Program Officer
Miller, Roger H
Project Start
2005-07-01
Project End
2010-03-31
Budget Start
2006-04-01
Budget End
2007-03-31
Support Year
2
Fiscal Year
2006
Total Cost
$254,717
Indirect Cost

  Institution

Name
University of Michigan Ann Arbor
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
073133571
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109

  Publications

Shi, Honglue; Clay, Mary C; Rangadurai, Atul et al. (2018) Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. J Biomol NMR 70:229-244
Ganser, Laura R; Lee, Janghyun; Rangadurai, Atul et al. (2018) High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nat Struct Mol Biol 25:425-434
Andra?oj?, Witold; Ravera, Enrico; Salmon, Loïc et al. (2016) Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Phys Chem Chem Phys 18:5743-52
Salmon, Loïc; Giamba?u, George M; Nikolova, Evgenia N et al. (2015) Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 137:12954-65
Yang, Shan; Al-Hashimi, Hashim M (2015) Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs. J Phys Chem B 119:9614-26
Xue, Yi; Kellogg, Dawn; Kimsey, Isaac J et al. (2015) Characterizing RNA Excited States Using NMR Relaxation Dispersion. Methods Enzymol 558:39-73
Frank, Aaron T; Zhang, Qi; Al-Hashimi, Hashim M et al. (2015) Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J 108:2876-85
Bothe, Jameson R; Stein, Zachary W; Al-Hashimi, Hashim M (2014) Evaluating the uncertainty in exchange parameters determined from off-resonance R1? relaxation dispersion for systems in fast exchange. J Magn Reson 244:18-29
Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441-66
Dickson, Alex; Mustoe, Anthony M; Salmon, Loïc et al. (2014) Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res 42:12126-37

Showing the most recent 10 out of 45 publications