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- W1983626225 abstract "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 rates. Optical tweezers experiments have shown that it requires as much force to break the MMLV kissing-loop complex as is required to unfold an entire 11 base-pair RNA hairpin (Li PTX, Bustamante C, Tinoco I (2006) P.N.A.S. 103:15847). Using non-equilibrium all-atom molecular dynamics simulations, we have developed a detailed model for the kinetic intermediates of the force-induced dissociation of the MMLV kissing-loop. 208 dissociation events were simulated under constant applied external force, for a total of ∼16 μs simulation time. These events are combined to construct a Markov state model for kissing-loop dissociation, which is capable of predicting overall dissociation rates on timescales longer than were actually simulated. We find that the complex undergoes a conformational rearrangement which distributes the applied force in parallel among multiple intermolecular hydrogen-bonds, which is substantially more mechanically stable than the serial bond breaking observed in the force-unfolding of RNA hairpins. Stacking interactions with adjacent, unpaired adenine bases further stabilize the complex by increasing the repair rates for partially broken base-pairs. These stacking interactions are also prominently featured in the transition state, which requires additional coordinates orthogonal to the end-to-end extension to be uniquely identified. Our findings can be extended to explain the peculiar sequence-stability relationships of the 6 base-pair HIV-1 DIS kissing-loop." @default.
- W1983626225 created "2016-06-24" @default.
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- W1983626225 date "2012-01-01" @default.
- W1983626225 modified "2023-09-30" @default.
- W1983626225 title "Mechanism of Enhanced Mechanical Stability of Retroviral Kissing-Loops Elucidated by Non-Equilibrium Molecular Dynamics Simulations" @default.
- W1983626225 doi "https://doi.org/10.1016/j.bpj.2011.11.3508" @default.
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