Paper Citing NAMD - Abstract
Barr, Daniel; van der Vaart, Arjan
The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:2070-2077, 2012
We performed molecular dynamics simulations of the lac repressor headpiece-O1 operator complex for natural, over and underbent DNA to assess the factors that determine the natural DNA bending angle. At the natural angle, the specific and nonspecific contacts between the protein and DNA are optimized. Protein-DNA contacts show different angle dependences in the right and left sites, with the left site generally getting weaker and the right site getting stronger as the bending angle increases. Two entropic factors were identified as well: at the natural bending angle, water release and the quasiharmonic protein configurational entropy are maximized. The gain in protein configurational entropy might stem from an entropy-entropy compensation mechanism, in which a reduction in protein fluctuations is offset by a loss in correlations between the right and left sites.
