This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Dimerization of genomic RNA as exemplified by HIV has been shown to be an important event in the life cycle of retroviruses. Studies have indicated that interfering with this dimerization process impairs the ability of the virus to replicate. Therefore much interest exist in understanding the mechanism with the goal of designing anti-dimerization drugs that will ultimately interfere with replication. Dimerization is initiated in the 5'UTR end of the HIV genome. This site is aptly named the dimerization initiation site (DIS). Dimerization involves two steps: first, two DISs from separate copies of the genome associate via their loop regions to form what is known as a loop-loop kissing complex (KC). Second, the kissing complex is then converted to an extended duplex (ED), (see Figure 1). Two distinct models have been proposed to describe the KC => ED conversion. The first involve melting of the helices in both DIS followed by re-annealing to the strand of the other DIS to form the ED. The second involves the cleavage and then religation in the loop-loop region. Up to this point, most of the mechanistic studies that have been carried out have utilized one form of spectroscopy or another. They have revealed that conformational dynamics of the KC plays a key role in the conversion process. However, these methods all suffer from an inherent weakness in that they cannot give us exact atomistic details about the mechanism. Hence MD simulations can prove to be a valuable tool in this regard. As of the writing of this proposal, only a handful of simulations have been carried out on KC and ED. Clearly there is a need to carry out state of the art MD simulations of this dimerization. To determine the mechanism for the KC => ED conversion Biased Molecular Dynamics (BMD) will be used to derive an initial guess to the path between the two conformations, and then Conjugate Peak Refinement (CPR) will be utilized to determine the minimum energy path (MEP) for the conformational change. In agreement with available experiment data, preliminary data from implicit solvent simulations suggest that adenines in the loop-loop region of the KC play an important role in the occurrence of this change. There is now a need to carry out expensive MD simulations utilizing explicit solvent to further and more accurately characterized this KC => ED conversion.
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