Functional dynamics in HIV-1 regulatory RNA elements

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DESCRIPTION (provided by applicant): Conformational dynamics plays an essential role in the functions of many HIV-1 viral regulatory RNA elements. Our long term goal is to elucidate the molecular basis for functional dynamics in these RNAs as a prerequisite for rationally designing anti-HIV therapeutics targeting RNA. The main hypothesis in this proposal is that conformational dynamics plays an essential role in adpative recognition underlying the function of the transactivation response element (TAR) and structural isomerization underlying the function of the dimerization initiation site (DIS). This hypothesis is supported by the following observations, (i) TAR can promiscuously bind unrelated compounds by undergoing distinct structural changes, (ii) Compounds that diminish TAR's conformational flexibility inhibit its function, (iii) The DIS can spontanously undergo large secondary structural transitions needed for its function, (iv) Structural dynamics in DIS has been directly correlated with the rate at which it undergoes these transitions. The overall objective of this proposal is to develop NMR methods for elucidating the role of conformational flexibility in the functions of TAR and DIS and to apply this understanding in the rational design of anti-HIV therapeutics targeting TAR and DIS. The specific aims are to: 1. Develop and apply NMR methods to elucidate the role of conformational dynamics in TAR adaptive recognition. Results will be used to examine if TAR can dynamically access protein bound states. 2. Elucidate the role of structural dynamics in the DIS structural isomerization. Results will be used to examine if DIS can access conformations uniquely poised for structural isomerization dynamically. 3. Elucidate the role of RNA flexibility in aminoglycoside recognition. Results will be used to examine the hypothesis that electrostatic interactions play a primary role in arresting RNA global motions and that different aminoglycosides can bind different conformational manifestations of the same RNA target.