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Science 13 September 1996:
Vol. 273. no. 5281, pp. 1547 - 1551
DOI: 10.1126/science.273.5281.1547
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Reports

alpha Helix-RNA Major Groove Recognition in an HIV-1 Rev Peptide-RRE RNA Complex

John L. Battiste, Hongyuan Mao, N. Sambasiva Rao, Ruoying Tan, D. R. Muhandiram, Lewis E. Kay, Alan D. Frankel, James R. Williamson *

The solution structure of a human immunodeficiency virus type-1 (HIV-1) Rev peptide bound to stem-loop IIB of the Rev response element (RRE) RNA was solved by nuclear magnetic resonance spectroscopy. The Rev peptide has an alpha -helical conformation and binds in the major groove of the RNA near a purine-rich internal loop. Several arginine side chains make base-specific contacts, and an asparagine residue contacts a G·A base pair. The phosphate backbone adjacent to a G·G base pair adopts an unusual structure that allows the peptide to access a widened major groove. The structure formed by the two purine-purine base pairs of the RRE creates a distinctive binding pocket that the peptide can use for specific recognition.

J. L. Battiste, H. Mao, J. R. Williamson, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
N. S. Rao, D. R. Muhandiram, L. E. Kay, Protein Engineering Centers of Excellence and Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
R. Tan and A. D. Frankel, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
*   To whom correspondence should be addressed.


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