The specific objectives of this project are to design and experimentally verify an RNA-protein binding interaction with high affinity and high specificity. Such a complex would be a useful biotechnological tool, with applications for in vitro and in vivo systems. We have explored a strategy of covalent dimerization of the peptide and the RNA, and chosen a structurally characterized relative of HIV as the monomer unit of the design. The NMR structure of the monomer BIV Tat peptide-BIV TAR RNA reveals a beta-hairpin peptide structure and an RNA structure consisting of a hairpin with two bulges. Previously, I examined three relative orientations of the half-sites in an unrefined manner, by simple overlapping of bases using two copies of the NMR average structure. The goals of this modeling were to determine which orientation of the half-sites positioned the termini of the peptides closest to one another, and to approximate the optimal length of the linker between the two peptides. I will be using the Computer Graphics Laboratory facilities to make energy-minimized models that necessitate using individual NMR structures. I am planning on creating the following models: 1) at least one BIV TAR dimer RNA structure and 2) several peptide linker sequences. These types of models should help us rationalize some of the experimental binding data obtained from gel shift (in vitro) and CAT assays (in vivo).
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