@article{sullivan_bobay_kojetin_thompson_rance_strauch_cavanagh_2008, title={Insights into the Nature of DNA Binding of AbrB-like Transcription Factors}, volume={16}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2008.08.014}, abstractNote={Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these “transition-state regulator” proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators: AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel-shift assays, and mutagenic and NMR studies to generate a structural model of the complex between AbrBN55 and its cognate promoter, abrB8. These investigations have enabled us to generate a model for the specific nature of the transition-state regulator-DNA interaction, a structure that has remained elusive thus far.}, number={11}, journal={STRUCTURE}, author={Sullivan, Daniel M. and Bobay, Benjamin G. and Kojetin, Douglas J. and Thompson, Richele J. and Rance, Mark and Strauch, Mark A. and Cavanagh, John}, year={2008}, month={Nov}, pages={1702–1713} }
 @article{sharp_sullivan_cavanagh_tomer_2006, title={Measurement of multisite oxidation kinetics reveals an active site conformational change in Spo0F as a result of protein oxidation}, volume={45}, ISSN={["0006-2960"]}, DOI={10.1021/bi060470r}, abstractNote={When most proteins undergo oxidative damage, they yield a variety of products containing oxidative damage at a large number of sites, most of which are modified substoichiometrically. The resulting complex mixture of products is not amenable to high-resolution structural analyses. The previous methods of structural analysis have relied upon either very generalized structural analyses such as circular dichroism or the creation of a battery of mutants to try to isolate single-residue damage effects. We present a methodology using mass spectrometry to measure the kinetics of oxidation at many sites simultaneously. Previous studies have shown that these kinetics are determined by the chemical nature of the damage site and by the accessibility of that site to the radical. By measuring deviations in the rate of oxidation from the expected pseudo-zero-order kinetics, we can detect and characterize local structural changes due to the oxidative damage. We demonstrate the application of this new technique to the Spo0F protein, a regulator of sporulation in Bacillus subtilis. Circular dichroism studies suggest a partial loss of helical structure of Spo0F as a result of oxidative damage. We report that oxidation causes a three-stage conformational change in Spo0F. Furthermore, we find the dramatic structural changes affect only the region surrounding the active site, while the remainder of the structure remains relatively unperturbed. Finally, we are able to determine that the specific oxidation event that triggers the conformational change at the active site of Spo0F occurs at Met81, a partially conserved methionine in the CheY superfamily.}, number={20}, journal={BIOCHEMISTRY}, author={Sharp, JS and Sullivan, DM and Cavanagh, J and Tomer, KB}, year={2006}, month={May}, pages={6260–6266} }