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Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site

Chia-Chieh Chu, Raphael Plangger, Christoph Kreutz, Hashim M. Al-Hashimi
doi: https://doi.org/10.1101/498907
Chia-Chieh Chu
Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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Raphael Plangger
Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
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Christoph Kreutz
Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
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Hashim M. Al-Hashimi
Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USADepartment of Chemistry, Duke University, Durham, NC 27708, USA
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  • For correspondence: hashim.al.hashimi@duke.edu
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ABSTRACT

The HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native ‘excited state’ (ES) conformations that have a combined population of ~20%. The ESs disrupt the Rev binding site by changing local secondary structure and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 18, 2018.
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Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site
Chia-Chieh Chu, Raphael Plangger, Christoph Kreutz, Hashim M. Al-Hashimi
bioRxiv 498907; doi: https://doi.org/10.1101/498907
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Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev binding site
Chia-Chieh Chu, Raphael Plangger, Christoph Kreutz, Hashim M. Al-Hashimi
bioRxiv 498907; doi: https://doi.org/10.1101/498907

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