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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.

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) 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.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Al-Hashimi HM,Gosser Y,Gorin A,Hu W,Majumdar A,Patel DJ

doi

10.1006/jmbi.2001.5235

keywords:

subject

Has Abstract

pub_date

2002-01-11 00:00:00

pages

95-102

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022283602952356

journal_volume

315

pub_type

杂志文章

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