The MutS DNA mismatch recognition protein was studied by using a combination of molecular dynamics simulations and normal mode analysis. Both methods revealed uniquely different structural conformations that were collectively used to characterize a new functional cycle for mismatch recognition. The DNA dynamics from the MutS simulations were also assessed. The G·T mismatch contained within the DNA was found to be relatively stable, whereas the 5' adjacent base next to the mispaired thymine was highly dynamic. In one simulation, the 5' adjacent base opened up via the major groove and stayed flipped-out for the entire duration of the 200 ns simulation. The energetics of base-flipping in the MutS-DNA system were examined and the relevance and importance of these observations were discussed.The development of a new path-based restraint is presented and applied to study DNA translocation in the Hin recombinase test system. Using multiple path-base restraints, the DNA was successfully translocated by one full base pair in both the forward and backward directions. The method for calculating the corresponding free energy profile along a single DNA translocation reaction coordinate was also reformulated and explained.
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