Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings Journal Article


Authors: Al-Hashimi, H. M.; Gosser, Y.; Gorin, A.; Hu, W.; Majumdar, A.; Patel, D. J.
Article Title: Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
Abstract: Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(±4)°, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44° and 54°. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture. © 2002 Academic Press.
Keywords: protein conformation; protein binding; rna-binding proteins; virus rna; transactivator protein; models, molecular; human immunodeficiency virus; nucleic acid conformation; protein secondary structure; motion; dna responsive element; dynamics; protein tertiary structure; nuclear magnetic resonance; rna, viral; human immunodeficiency virus 1; hiv-1; nuclear magnetic resonance, biomolecular; hiv long terminal repeat; electrostatics; tat protein; priority journal; article; rna recognition; collective motions; induced-fit interactions; tertiary structure capture; gene products, tat
Journal Title: Journal of Molecular Biology
Volume: 315
Issue: 2
ISSN: 0022-2836
Publisher: Academic Press Inc., Elsevier Science  
Date Published: 2002-01-11
Start Page: 95
End Page: 102
Language: English
DOI: 10.1006/jmbi.2001.5235
PUBMED: 11779230
PROVIDER: scopus
DOI/URL:
Notes: Export Date: 14 November 2014 -- Source: Scopus
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MSK Authors
  1. Yuying Gosser
    7 Gosser
  2. Weidong Hu
    16 Hu
  3. Andrey A Gorin
    25 Gorin
  4. Dinshaw J Patel
    392 Patel