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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 curvature with positive (16 structures) and negative (seven structures) correlation containing concave (DNA curved toward protein) and convex (DNA curved away from protein) curvature, respectively. Protein-DNA complexes without significant Cpc/Cpp (36 structures) correlation (-0.25<0<0.25) tended to contain DNA without significant curvature. Interestingly, concave and convex complexes also include more arginine and lysine phosphate contacts, respectively, whereas linear complexes included essentially equivalent numbers of Lys/Arg phosphate contacts. Together, these findings suggest an important role for electrostatic interactions in protein-DNA complexes involving helical curvature.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Grant BN,Dourlain EM,Araneda JN,Throneberry ML,McFail-Isom LA

doi

10.1093/nar/gkt492

subject

Has Abstract

pub_date

2013-08-01 00:00:00

pages

7547-55

issue

15

eissn

0305-1048

issn

1362-4962

pii

gkt492

journal_volume

41

pub_type

杂志文章

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