Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein Export

@article{citeulike:3268720, abstract = {We are interested in the role of asymmetric phosphate neutralization in DNA bending induced by proteins. We describe an experimental estimate of the actual electrostatic contribution of asymmetric phosphate neutralization to the bending of DNA by the Escherichia coli catabolite activator protein (CAP), a prototypical DNA-bending protein. Following assignment of putative electrostatic interactions between CAP and DNA phosphates based on X-ray crystal structures, appropriate phosphates in the CAP half-site DNA were chemically neutralized by methylphosphonate substitution. DNA shape was then evaluated using a semi-synthetic DNA electrophoretic phasing assay. Our results confirm that the unmodified CAP DNA half-site sequence is intrinsically curved by 26{degrees} in the direction enhanced in the complex with protein. In the absence of protein, neutralization of five appropriate phosphates increases DNA curvature to 32{degrees} ([\~{}]23\% increase), in the predicted direction. Shifting the placement of the neutralized phosphates changes the DNA shape, suggesting that sequence-directed DNA curvature can be modified by the asymmetry of phosphate neutralization. We suggest that asymmetric phosphate neutralization contributes favorably to DNA bending by CAP, but cannot account for the full DNA deformation. 10.1093/nar/30.9.1879}, author = {Hardwidge, Philip R. and Zimmerman, Jeff M. and Maher}, citeulike-article-id = {3268720}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/30.9.1879}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/30/9/1879}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/11972323}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=11972323}, day = {1}, doi = {10.1093/nar/30.9.1879}, journal = {Nucl. Acids Res.}, keywords = {cap, cap\_dna, dna, protein}, month = {May}, number = {9}, pages = {1879--1885}, posted-at = {2008-09-15 11:00:24}, priority = {2}, title = {Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein}, url = {http://dx.doi.org/10.1093/nar/30.9.1879}, volume = {30}, year = {2002} }

TY - JOUR ID - citeulike:3268720 L3 - citeulike-article-id:3268720 N2 - We are interested in the role of asymmetric phosphate neutralization in DNA bending induced by proteins. We describe an experimental estimate of the actual electrostatic contribution of asymmetric phosphate neutralization to the bending of DNA by the Escherichia coli catabolite activator protein (CAP), a prototypical DNA-bending protein. Following assignment of putative electrostatic interactions between CAP and DNA phosphates based on X-ray crystal structures, appropriate phosphates in the CAP half-site DNA were chemically neutralized by methylphosphonate substitution. DNA shape was then evaluated using a semi-synthetic DNA electrophoretic phasing assay. Our results confirm that the unmodified CAP DNA half-site sequence is intrinsically curved by 26{degrees} in the direction enhanced in the complex with protein. In the absence of protein, neutralization of five appropriate phosphates increases DNA curvature to 32{degrees} ([~]23% increase), in the predicted direction. Shifting the placement of the neutralized phosphates changes the DNA shape, suggesting that sequence-directed DNA curvature can be modified by the asymmetry of phosphate neutralization. We suggest that asymmetric phosphate neutralization contributes favorably to DNA bending by CAP, but cannot account for the full DNA deformation. 10.1093/nar/30.9.1879 IS - 9 JF - Nucl. Acids Res. EP - 1885 TI - Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein VL - 30 SP - 1879 KW - cap KW - cap_dna KW - dna KW - protein AU - Hardwidge, Philip AU - Zimmerman, Jeff AU - Maher PY - 2002/05/01/ UR - http://dx.doi.org/10.1093/nar/30.9.1879 ER -