Structural characterization of the complex of the Rev response element RNA with a selected peptide.
BACKGROUND
The RSG-1.2 peptide was selected for specific binding to the Rev response element RNA, as the natural Rev peptide does. The RSG-1.2 sequence has features incompatible with the helical structure of the bound Rev peptide, indicating that it must bind in a different conformation.


RESULTS
The binding of the RSG-1.2 peptide to the Rev response element RNA was characterized using multinuclear, multidimensional NMR. The RSG-1.2 peptide is shown to bind with the N-terminal segment of the peptide along the major groove in an extended conformation and turn preceding a C-terminal helical segment, which crosses the RNA groove in the region widened by the presence of purine-purine base pairs. These features make the details of the bound state rather different than that of the Rev peptide which targets the same RNA sequence binding as a single helix along the groove axis.


CONCLUSIONS
These studies further demonstrate the versatility of arginine-rich peptides in recognition of specific RNA elements and the lack of conserved structural features in the bound state.
Zhang
Q
Q
Department of Chemistry MC-1460, University of California, and Physical Biosciences, Lawrence Berkeley National Laboratory, CA 94720, USA.
Harada
K
K
Cho
H S
HS
Frankel
A D
AD
Wemmer
D E
DE
D001120:Arginine / Q000737:chemistry*; D001665:Binding Sites / Q000502:physiology; D015752:Genes, env / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry*; D011687:Purines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry* / Q000235:genetics
D010455:Peptides; D011687:Purines; D012313:RNA; D001120:Arginine