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

Grant BN, Dourlain EM, Araneda JN, Throneberry ML, McFail-Isom LA - Nucleic Acids Res. (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Central Arkansas, Conway, AR 72035, USA.

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.

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Average calculated global curvature values. Structures classified as containing concave (black bar), linear (white bar) and convex (gray bar) helical curvature. Average of curvature obtained from Curves+ or primary citation (P < 0.001). Error bars represent the standard deviation of the averages.
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gkt492-F6: Average calculated global curvature values. Structures classified as containing concave (black bar), linear (white bar) and convex (gray bar) helical curvature. Average of curvature obtained from Curves+ or primary citation (P < 0.001). Error bars represent the standard deviation of the averages.

Mentions: The assigned helical curvature classification was confirmed from helical axis-bending values calculated using Curves+ and/or values reported in the structure’s primary citation. The average helical curvature for each bending category was calculated and is given in (Figure 6). The average global helical curvature for complexes classified as concave (38° ± 13°) or convex (42° ± 9°) was statistically greater (P < 0.001) than the average helical bend for complexes containing straight DNA (9°± 6°).Figure 6.


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

Grant BN, Dourlain EM, Araneda JN, Throneberry ML, McFail-Isom LA - Nucleic Acids Res. (2013)

Average calculated global curvature values. Structures classified as containing concave (black bar), linear (white bar) and convex (gray bar) helical curvature. Average of curvature obtained from Curves+ or primary citation (P < 0.001). Error bars represent the standard deviation of the averages.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753625&req=5

gkt492-F6: Average calculated global curvature values. Structures classified as containing concave (black bar), linear (white bar) and convex (gray bar) helical curvature. Average of curvature obtained from Curves+ or primary citation (P < 0.001). Error bars represent the standard deviation of the averages.
Mentions: The assigned helical curvature classification was confirmed from helical axis-bending values calculated using Curves+ and/or values reported in the structure’s primary citation. The average helical curvature for each bending category was calculated and is given in (Figure 6). The average global helical curvature for complexes classified as concave (38° ± 13°) or convex (42° ± 9°) was statistically greater (P < 0.001) than the average helical bend for complexes containing straight DNA (9°± 6°).Figure 6.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Central Arkansas, Conway, AR 72035, USA.

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.

Show MeSH
Related in: MedlinePlus