@article{hobbs_bobay_thompson_perego_cavanagh_2010, title={NMR Solution Structure and DNA-binding Model of the DNA-binding Domain of Competence Protein A}, volume={398}, ISSN={["0022-2836"]}, DOI={10.1016/j.jmb.2010.03.003}, abstractNote={Competence protein A (ComA) is a response regulator protein involved in the development of genetic competence in the Gram-positive spore-forming bacterium Bacillus subtilis, as well as the regulation of the production of degradative enzymes and antibiotic synthesis. ComA belongs to the NarL family of proteins, which are characterized by a C-terminal transcriptional activator domain that consists of a bundle of four helices, where the second and third helices (alpha 8 and alpha 9) form a helix-turn-helix DNA-binding domain. Using NMR spectroscopy, the high-resolution 3D solution structure of the C-terminal DNA-binding domain of ComA (ComAC) has been determined. In addition, surface plasmon resonance and NMR protein-DNA titration experiments allowed for the analysis of the interaction of ComAC with its target DNA sequences. Combining the solution structure and biochemical data, a model of ComAC bound to the ComA recognition sequences on the srfA promoter has been developed. The model shows that for DNA binding, ComA uses the conserved helix-turn-helix motif present in other NarL family members. However, the model reveals also that ComA might use a slightly different part of the helix-turn-helix motif and there appears to be some associated domain re-orientation. These observations suggest a basis for DNA binding specificity within the NarL family.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Hobbs, Carey A. and Bobay, Benjamin G. and Thompson, Richele J. and Perego, Marta and Cavanagh, John}, year={2010}, month={Apr}, pages={248–263} }
 @article{hobbs_deterding_perera_bobay_thompson_darden_cavanagh_tomer_2009, title={Structural Characterization of the Conformational Change in Calbindin-D-28k upon Calcium Binding Using Differential Surface Modification Analyzed by Mass Spectrometry}, volume={48}, ISSN={["0006-2960"]}, DOI={10.1021/bi900350q}, abstractNote={Calbindin-D28k is a calcium binding protein with six EF hand domains. Calbindin-D28k is unique in that it functions as both a calcium buffer and a sensor protein. It is found in many tissues, including brain, pancreas, kidney, and intestine, playing important roles in each. Calbindin-D28k is known to bind four calcium ions and upon calcium binding undergoes a conformational change. The structure of apo calbindin-D28k is in an ordered state, transitioning into a disordered state as calcium is bound. Once fully loaded with four calcium ions, it again takes on an ordered state. The solution structure of disulfide-reduced holo-calbindin-D28k has been determined by NMR, while the structure of apo calbindin-D28k has yet to be determined. Differential surface modification of lysine and histidine residues analyzed by mass spectrometry has been used in this study to identify, for the first time, the specific regions of calbindin-D28k undergoing conformational changes between the holo and apo states. Using differential surface modification in combination with mass spectrometry, EF hands 1 and 4 as well as the linkers before EF hand 1 and the linkers between EF hands 4 and 5 and EF hands 5 and 6 were identified as regions of conformational change between apo and holo calbindin-D28k. Under the experimental conditions employed, EF hands 2 and 6, which are known not to bind calcium, were unaffected in either form. EF hand 2 is highly accessible; however, EF hand 6 was determined not to be surface accessible in either form. Previous research has identified a disulfide bond between cysteines 94 and 100 in the holo state. Until now, it was unknown whether this bond also exists in the apo form. Our data confirm the presence of the disulfide bond between cysteines 94 and 100 in the holo form and indicate that there is predominantly no disulfide bond between these residues in the apoprotein.}, number={36}, journal={BIOCHEMISTRY}, author={Hobbs, Carey A. and Deterding, Leesa J. and Perera, Lalith and Bobay, Benjamin G. and Thompson, Richele J. and Darden, Thomas A. and Cavanagh, John and Tomer, Kenneth B.}, year={2009}, month={Sep}, pages={8603–8614} }