2au4
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(New page: 200px<br /><applet load="2au4" size="350" color="white" frame="true" align="right" spinBox="true" caption="2au4" /> '''Class I GTP aptamer'''<br /> ==Overview== H...)
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Revision as of 16:09, 29 January 2008
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Class I GTP aptamer
Overview
Higher-affinity RNA aptamers to GTP are more informationally complex than, lower-affinity aptamers. Analog binding studies have shown that the, additional information needed to improve affinity does not specify more, interactions with the ligand. In light of those observations, we would, like to understand the structural characteristics that enable complex, aptamers to bind their ligands with higher affinity. Here we present the, solution structure of the 41-nt Class I GTP aptamer (K(d) = 75 nM) as, determined by NMR. The backbone of the aptamer forms a reverse-S that, shapes the binding pocket. The ligand nucleobase stacks between purine, platforms and makes hydrogen bonds with the edge of another base., Interestingly, the local modes of interaction for the Class I aptamer and, an RNA aptamer that binds ATP with a K(d) of 6 microM are very much alike., The aptamers exhibit nearly identical levels of binding specificity and, fraction of ligand sequestered from the solvent (81%-85%). However, the, GTP aptamer is more informationally complex (approximately 45 vs. 35 bits), and has a larger recognition bulge (15 vs. 12 nucleotides) with many more, stabilizing base-base interactions. Because the aptamers have similar, modes of ligand binding, we conclude that the stabilizing structural, elements in the Class I aptamer are responsible for much of the difference, in K(d). These results are consistent with the hypothesis that increasing, the number of intra-RNA interactions, rather than adding specific contacts, to the ligand, is the simplest way to improve binding affinity.
About this Structure
2AU4 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Solution structure of an informationally complex high-affinity RNA aptamer to GTP., Carothers JM, Davis JH, Chou JJ, Szostak JW, RNA. 2006 Apr;12(4):567-79. Epub 2006 Feb 28. PMID:16510427
Page seeded by OCA on Tue Jan 29 18:09:56 2008
Categories: Protein complex | Carothers, J.M. | Chou, J.J. | Davis, J.H. | Szostak, J.W. | GTP | Aptamer | Rna