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

Publication ,  Journal Article
Al-Hashimi, HM; Gosser, Y; Gorin, A; Hu, W; Majumdar, A; Patel, DJ
Published in: J Mol Biol
January 11, 2002

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) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. 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.

Duke Scholars

Published In

J Mol Biol

DOI

ISSN

0022-2836

Publication Date

January 11, 2002

Volume

315

Issue

2

Start / End Page

95 / 102

Location

Netherlands

Related Subject Headings

  • tat Gene Products, Human Immunodeficiency Virus
  • Static Electricity
  • RNA-Binding Proteins
  • RNA, Viral
  • Protein Binding
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Motion
  • Models, Molecular
  • HIV-1
 

Citation

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Al-Hashimi, H. M., Gosser, Y., Gorin, A., Hu, W., Majumdar, A., & Patel, D. J. (2002). Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol, 315(2), 95–102. https://doi.org/10.1006/jmbi.2001.5235
Al-Hashimi, Hashim M., Yuying Gosser, Andrey Gorin, Weidong Hu, Ananya Majumdar, and Dinshaw J. Patel. “Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.J Mol Biol 315, no. 2 (January 11, 2002): 95–102. https://doi.org/10.1006/jmbi.2001.5235.
Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol. 2002 Jan 11;315(2):95–102.
Al-Hashimi, Hashim M., et al. “Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.J Mol Biol, vol. 315, no. 2, Jan. 2002, pp. 95–102. Pubmed, doi:10.1006/jmbi.2001.5235.
Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol. 2002 Jan 11;315(2):95–102.
Journal cover image

Published In

J Mol Biol

DOI

ISSN

0022-2836

Publication Date

January 11, 2002

Volume

315

Issue

2

Start / End Page

95 / 102

Location

Netherlands

Related Subject Headings

  • tat Gene Products, Human Immunodeficiency Virus
  • Static Electricity
  • RNA-Binding Proteins
  • RNA, Viral
  • Protein Binding
  • Nucleic Acid Conformation
  • Nuclear Magnetic Resonance, Biomolecular
  • Motion
  • Models, Molecular
  • HIV-1