Conformational Pathway for the Kissing Complex→Extended Dimer Transition of the SL1 Stem-Loop from Genomic HIV-1 RNA as Monitored by Targeted Molecular Dynamics Techniques

HIV-1 retroviral genomic RNA dimerization is initiated by loop-loop interactions between the SL1 stem-loops of two identical RNA molecules. The SL1–SL1 unstable resulting kissing complex (KC) then refolds irreversibly into a more stable complex called extended dimer (ED). Although the structures of both types of complex have been determined, very little is known about the conformational pathway corresponding to the transition, owing to the difficulty of observing experimentally intermediate conformations. In this study, we applied targeted molecular dynamics simulation techniques (TMD) to the phosphorus atoms for monitoring this pathway for the backbone, and a two-step strategy was adopted. In a first step, called TMD−1, the dimer structure was constrained to progressively move away from KC without indicating the direction, until the RMSD from KC reaches 36 Å. A total of 20 TMD−1 simulations were performed under different initial conditions and different simulation parameters. For RMSD ranging between 0 and 22 Å, the whole set of TMD−1 simulations follows a similar pathway, then divergences are observed. None of the simulations leads to the ED structure. At RMSD=22 Å, the dimers look like two parallel Us, still linked by the initial loop-loop interaction, but the strands of the stems (the arms of the Us) are positioned in such a manner that they can form intramolecular as well as intermolecular Watson–Crick base-pairs. This family of structure is called UU. In a second step (TMD simulations), 18 structures were picked up along the pathways generated with TMD−1 and were constrained to move toward ED by decreasing progressively their RMSD from ED. We found that only structures from the UU family are able to easily reach ED-like conformations of the backbones without exhibiting a large constraint energy.