Abstract
Many proteins bend DNA significantly upon binding. To simulate this bending within the time scales accessible to molecular dynamics, we used adaptive umbrella sampling on the roll angles. We studied the inherent flexibility of bare DNA by simulating dodecamers with varying sequences and made comparisons to the worm-like chain model. Simulations of bare DNA were also performed to assess the co-operativity of the bending of adjacent roll angles. A study of DNA bending by the archaeal DNA packaging protein Sac7d will be presented as well.
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