DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures.

ABSTRACT: Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To investigate the role of electrostatics in helical deformation, we quantified the relationship between protein cationic residue density (Cpc) and DNA phosphate crowding (Cpp). The correlation between Cpc and Cpp was then calculated for a subset of 58 high resolution protein-DNA crystal structures. Those structures containing strong Cpc/Cpp correlation (>±0.25) were likely to contain DNA helical curvature. Further, the correlation factor sign predicted the direction of helical

SUBMITTER: Grant BN 

PROVIDER: S-EPMC3753625 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature