DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.

ABSTRACT: DNA molecules are highly charged semi-flexible polymers that are involved in a wide variety of dynamical processes such as transcription and replication. Characterizing the binding landscapes around DNA molecules is essential to understanding the energetics and kinetics of various biological processes. We present a curvilinear coordinate system that fully takes into account the helical symmetry of a DNA segment. The latter naturally allows to characterize the spatial organization and motions of ligands tracking the minor or major grooves, in a motion reminiscent of sliding. Using this approach, we performed umbrella sampling (US) molecular dynamics (MD) simulations to calculate the three-dimensional potentials of mean force (3D-PMFs) for a Na+ cation and for methyl guanidinium, an arginine

SUBMITTER: Echeverria I 

PROVIDER: S-EPMC4326129 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature