Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.

ABSTRACT:

Background

Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied extensively, very little is known how cellular crowding affects the conformational sampling of nucleic acids.

Results

The effect of protein crowding on the conformational preferences of DNA (deoxyribonucleic acid) is described from fully atomistic molecular dynamics simulations of systems containing a DNA dodecamer surrounded by protein crowders. From the simulations, it was found that DNA structures prefer to stay in B-like conformations in the presence of the crowders. The preference for B-like conformations results from non-specific interactions of crowder pr

SUBMITTER: Yildirim A 

PROVIDER: S-EPMC6286541 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature