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This paper identifies a tripeptide from a combinatorial library composed of D- and L-amino acids that binds to HIV-1 TAR and inhibits transcriptional activation. This tripeptide appears to lock TAR into a different conformation from the Tat-bound conformation, providing an example of how an inhibitor might take advantage of RNA flexibility and stabilize a conformation that cannot be bound by its protein target
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This paper presents the structure of the human T-cell leukemia virus type I (HTLV-I) Rex peptide bound to an RNA aptamer. The RNA adopts a very interesting architecture that includes a series of three base triples and an unpaired base that stacks over the peptide to help stabilize its extended conformation. The structure adds considerable diversity to the repertoire of peptide-RNA complexes
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Jiang F., Gorin A., Hu W., Majumdar A., Baskerville S., Xu W., Ellington A., Patel D.J. Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples. Structure. 7:1999;1461-1472. This paper presents the structure of the human T-cell leukemia virus type I (HTLV-I) Rex peptide bound to an RNA aptamer. The RNA adopts a very interesting architecture that includes a series of three base triples and an unpaired base that stacks over the peptide to help stabilize its extended conformation. The structure adds considerable diversity to the repertoire of peptide-RNA complexes.
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A striking demonstration that a single peptide can adopt different conformations when bound to two different RNA aptamers. Instead of binding as an α helix (as previously observed [39,43]), the Rev peptide is anchored in the RNA loop via an interesting set of stacking interactions and the remainder of the RNA creates a binding pocket in the major groove that holds the rest of the peptide in an extended conformation
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Ye X., Gorin A., Frederick R., Hu W., Majumdar A., Xu W., McLendon G., Ellington A., Patel D.J. RNA architecture dictates the conformations of a bound peptide. Chem Biol. 6:1999;657-669. A striking demonstration that a single peptide can adopt different conformations when bound to two different RNA aptamers. Instead of binding as an α helix (as previously observed [39,43]), the Rev peptide is anchored in the RNA loop via an interesting set of stacking interactions and the remainder of the RNA creates a binding pocket in the major groove that holds the rest of the peptide in an extended conformation.
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McColl D.J., Honchell C.D., Frankel A.D. Structure-based design of an RNA-binding zinc finger. Proc Natl Acad Sci USA. 96:1999;9521-9526. Using existing structural information, a specific RRE-binding zinc finger was created by placing the Rev α helix into the framework of a zinc finger from the Zif268 DNA-binding protein. This study demonstrates that a relatively unstructured RNA-binding peptide can be prestabilized prior to binding.
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