Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations

An RNA kissing loop from the Moloney murine leukemia virus (MMLV) exhibits unusual mechanical stability despite having only two intermolecular base pairs. Mutations at this junction have been shown to destabilize genome dimerization, with concomitant reductions in viral packaging efficiency and infectivity. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an 11-bp RNA hairpin [Li PTX, Bustamante C, Tinoco I (2006) Proc Natl Acad Sci USA 103:15847-15852]. Using nonequilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV dimerization initiation site kissing loop. Two hundred and eight dissociation events were simulated (approximately 16 mu s total simulation time) under conditions of constant applied external force, which we use to construct a Markov state model for kissing-loop dissociation. We find that the complex undergoes a conformational rearrangement, which allows for equal distribution of the applied force among all of the intermolecular hydrogen bonds, which is intrinsically more stable than the sequential unzipping of an ordinary hairpin. Stacking interactions with adjacent, unpaired loop adenines further stabilize the complex by increasing the repair rate of partially broken H-bonds. These stacking interactions are prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site.