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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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Visualizing the negative Cpp/Cpc correlation present in complexes with convex curvature. For the structure 1fdq, (a), (c), (e) and (g) display the protein (green ribbon) with cationic residues (magenta stick/spacefilled) for the whole structure (a) or those contributing to Cpc by falling within the specified cut off radius. The relative Cpc distribution for each corresponding cut off radius is presented in (d), (f) and (h). In these figures, the color of the POs (spacefilled) reflect the relative Cpc value with red representing the POs surrounded by the highest cationic side chain density (Cpc) value and blue the lowest. The phosphate crowding function (Cpp) values for the POs are displayed in (b) using the same spectrum with high phosphate crowding shown in red and low in blue.
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gkt492-F9: Visualizing the negative Cpp/Cpc correlation present in complexes with convex curvature. For the structure 1fdq, (a), (c), (e) and (g) display the protein (green ribbon) with cationic residues (magenta stick/spacefilled) for the whole structure (a) or those contributing to Cpc by falling within the specified cut off radius. The relative Cpc distribution for each corresponding cut off radius is presented in (d), (f) and (h). In these figures, the color of the POs (spacefilled) reflect the relative Cpc value with red representing the POs surrounded by the highest cationic side chain density (Cpc) value and blue the lowest. The phosphate crowding function (Cpp) values for the POs are displayed in (b) using the same spectrum with high phosphate crowding shown in red and low in blue.

Mentions: Visualization of the crowding function values reveal positioning of phosphate crowding, cationic side chain density and helical curvature consistent with subgroup assignment. The corresponding crowding function values were linked to each PO and visualized by spectrum-coding (blue—least, red—most) the crowding function data. One structure from each subgroup is presented in Figures 8, 9 and 10. For each structure, the first frame presents the protein/DNA complex with the protein backbone rendered in green ribbon and the cationic side chains in magenta sticks. The second frame presents the POs spectrum coded by phosphate crowding (Cpp) value. The Cpc data are presented for three cut off radii, each of which is paired with a rendering of the protein/DNA complex with the protein contacts within the specific cut off radius from the DNA shown with cationic side chains in magenta spheres representing the Van der Waals radii of the atoms.. The corresponding Cpp/Cpc correlation coefficient versus Cpc cut off radius graph for each structure is presented in Supplementary Figure S3.Figure 8.


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)

Visualizing the negative Cpp/Cpc correlation present in complexes with convex curvature. For the structure 1fdq, (a), (c), (e) and (g) display the protein (green ribbon) with cationic residues (magenta stick/spacefilled) for the whole structure (a) or those contributing to Cpc by falling within the specified cut off radius. The relative Cpc distribution for each corresponding cut off radius is presented in (d), (f) and (h). In these figures, the color of the POs (spacefilled) reflect the relative Cpc value with red representing the POs surrounded by the highest cationic side chain density (Cpc) value and blue the lowest. The phosphate crowding function (Cpp) values for the POs are displayed in (b) using the same spectrum with high phosphate crowding shown in red and low in blue.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt492-F9: Visualizing the negative Cpp/Cpc correlation present in complexes with convex curvature. For the structure 1fdq, (a), (c), (e) and (g) display the protein (green ribbon) with cationic residues (magenta stick/spacefilled) for the whole structure (a) or those contributing to Cpc by falling within the specified cut off radius. The relative Cpc distribution for each corresponding cut off radius is presented in (d), (f) and (h). In these figures, the color of the POs (spacefilled) reflect the relative Cpc value with red representing the POs surrounded by the highest cationic side chain density (Cpc) value and blue the lowest. The phosphate crowding function (Cpp) values for the POs are displayed in (b) using the same spectrum with high phosphate crowding shown in red and low in blue.
Mentions: Visualization of the crowding function values reveal positioning of phosphate crowding, cationic side chain density and helical curvature consistent with subgroup assignment. The corresponding crowding function values were linked to each PO and visualized by spectrum-coding (blue—least, red—most) the crowding function data. One structure from each subgroup is presented in Figures 8, 9 and 10. For each structure, the first frame presents the protein/DNA complex with the protein backbone rendered in green ribbon and the cationic side chains in magenta sticks. The second frame presents the POs spectrum coded by phosphate crowding (Cpp) value. The Cpc data are presented for three cut off radii, each of which is paired with a rendering of the protein/DNA complex with the protein contacts within the specific cut off radius from the DNA shown with cationic side chains in magenta spheres representing the Van der Waals radii of the atoms.. The corresponding Cpp/Cpc correlation coefficient versus Cpc cut off radius graph for each structure is presented in Supplementary Figure S3.Figure 8.

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