Microsecond-Scale MD Simulations of HIV‑1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

We report an extensive set of explicit
solvent molecular dynamics
(MD) simulations (∼25 μs of accumulated simulation time)
of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization
site. Despite many structural investigations by X-ray, NMR, and MD
techniques, the position of the bulged purines of the kissing complex
has not been unambiguously resolved. The X-ray structures consistently
show bulged-out positions of the unpaired bases, while several NMR
studies show bulged-in conformations. The NMR studies are, however,
mutually inconsistent regarding the exact orientations of the bases.
The earlier simulation studies predicted the bulged-out conformation;
however, this finding could have been biased by the short simulation
time scales. Our microsecond-long simulations reveal that all unpaired
bases of the kissing-loop complex stay preferably in the interior
of the kissing-loop complex. The MD results are discussed in the context
of the available experimental data and we suggest that both conformations
are biochemically relevant. We also show that MD provides a quite
satisfactory description of this RNA system, contrasting recent reports
of unsatisfactory performance of the RNA force fields for smaller
systems such as tetranucleotides and tetraloops. We explain this by
the fact that the kissing complex is primarily stabilized by an extensive
network of Watson–Crick interactions which are rather well
described by the force fields. We tested several different sets of
water/ion parameters but they all lead to consistent results. However,
we demonstrate that a recently suggested modification of van der Waals
interactions of the Cornell et al. force field deteriorates the description
of the kissing complex by the loss of key stacking interactions stabilizing
the interhelical junction and excessive hydrogen-bonding interactions.