@article{milton_draughn_bobay_stowe_olson_feldmann_thompson_myers_santoro_kearns_et al._2020, title={The Solution Structures and Interaction of SinR and SinI: Elucidating the Mechanism of Action of the Master Regulator Switch for Biofilm Formation in Bacillus subtilis}, volume={432}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2019.08.019}, abstractNote={Bacteria have developed numerous protection strategies to ensure survival in harsh environments, with perhaps the most robust method being the formation of a protective biofilm. In biofilms, bacterial cells are embedded within a matrix that is composed of a complex mixture of polysaccharides, proteins, and DNA. The gram-positive bacterium Bacillus subtilis has become a model organism for studying regulatory networks directing biofilm formation. The phenotypic transition from a planktonic to biofilm state is regulated by the activity of the transcriptional repressor, SinR, and its inactivation by its primary antagonist, SinI. In this work, we present the first full-length structural model of tetrameric SinR using a hybrid approach combining high-resolution solution nuclear magnetic resonance (NMR), chemical cross-linking, mass spectrometry, and molecular docking. We also present the solution NMR structure of the antagonist SinI dimer and probe the mechanism behind the SinR-SinI interaction using a combination of biochemical and biophysical techniques. As a result of these findings, we propose that SinI utilizes a residue replacement mechanism to block SinR multimerization, resulting in diminished DNA binding and concomitant decreased repressor activity. Finally, we provide an evidence-based mechanism that confirms how disruption of the SinR tetramer by SinI regulates gene expression.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Milton, Morgan E. and Draughn, G. Logan and Bobay, Benjamin G. and Stowe, Sean D. and Olson, Andrew L. and Feldmann, Erik A. and Thompson, Richele J. and Myers, Katherine H. and Santoro, Michael T. and Kearns, Daniel B. and et al.}, year={2020}, month={Jan}, pages={343–357} }
 @article{bordelon_bobay_murphy_reese_shanahan_odeh_broussard_kormos_menegatti_2019, title={Translating antibody-binding peptides into peptoid ligands with improved affinity and stability}, volume={1602}, ISSN={["1873-3778"]}, DOI={10.1016/j.chroma.2019.05.047}, abstractNote={A great number of protein-binding peptides are known and utilized as drugs, diagnostic reagents, and affinity ligands. Recently, however, peptide mimetics have been proposed as valuable alternative to peptides by virtue of their excellent biorecognition activity and higher biochemical stability. This poses the need to develop a strategy for translating known protein-binding peptides into peptoid analogues with comparable or better affinity. This work proposes a route for translation utilizing the IgG-binding peptide HWRGWV as reference sequence. An ensemble of peptoid analogues of HWRGWV were produced by adjusting the number and sequence arrangement of residues containing functional groups that resemble both natural and non-natural amino acids. The variants were initially screened via IgG binding tests in non-competitive mode to select candidate ligands. A set of selected peptoids were studied in silico by docking onto putative binding sites identified on the crystal structures of human IgG1, IgG2, IgG3, and IgG4 subclasses, returning values of predicted binding energy that aligned well with the binding data. Selected peptoids PL-16 and PL-22 were further characterized by binding isotherm analysis to determine maximum capacity (Qmax ˜ 48–57 mg of IgG per mL of adsorbent) and binding strength on solid phase (KD ˜ 5.4–7.8 10−7 M). Adsorbents PL-16-Workbeads and PL-22-Workbeads were used for purifying human IgG from a cell culture supernatant added with bovine serum, affording high values of IgG recovery (up to 85%) and purity (up to 98%) under optimized binding and elution conditions. Both peptoid ligands also proved to be stable against proteolytic enzymes and strong alkaline agents. Collectively, these studies form a method guiding the design of peptoid variants of cognate peptide ligands, and help addressing the challenges that, despite the structural similarity, the peptide-to-peptoid translation presents.}, journal={JOURNAL OF CHROMATOGRAPHY A}, author={Bordelon, Tee and Bobay, Benjamin and Murphy, Andrew and Reese, Hannah and Shanahan, Calvin and Odeh, Fuad and Broussard, Amanda and Kormos, Chad and Menegatti, Stefano}, year={2019}, month={Sep}, pages={284–299} }
 @article{kish_sachi_naik_roach_bobay_blackburn_menegatti_carbonell_2017, title={Design, selection, and development of cyclic peptide ligands for human erythropoietin}, volume={1500}, ISSN={["1873-3778"]}, DOI={10.1016/j.chroma.2017.04.019}, abstractNote={This work presents the selection and characterization of erythropoietin (EPO)-binding cyclic peptide ligands. The sequences were selected by screening a focused library of cyclic depsipeptides cyclo[(Nα-Ac)Dap(A)-X1-X6-AE], whose structure and amino acid compositions were tailored to mimic the EPO receptor. The sequences identified through library screening were synthesized on chromatographic resin and characterized via binding-and-elution studies against EPO to select a pool of candidate ligands. Sequences with higher hydrophobicity consistently showed stronger binding to EPO, with the exception of FSLLSH, which was noted for its lower hydrophobicity and high EPO binding. Mutagenesis studies performed on FSLLSH with natural and non-natural amino acid substitutions led to the identification of critical EPO-binding determinants, and the discovery of new peptide ligands. In particular, histidine-scanning mutagenesis performed on three lead sequences yielded the discovery of variants whose EPO-binding is more pH-sensitive, which facilitates EPO recovery. Selected ligands were studied to correlate the elution yield to the salinity of the binding buffer and the elution pH. Elution yields were consistently higher when EPO binding was performed at low ionic strength. The crystal structures of lead cyclic peptides were docked in silico against EPO to estimate the binding affinity in solution. Isotherm adsorption studies performed on FSLLSH indicated that the cyclic version of the ligand (KD = 0.46 μM) has a higher affinity for EPO than its corresponding linear variant (KD = 1.44 μM). Collectively, these studies set the stage for use of the cyclic peptide ligands as EPO purification and detection tools.}, journal={JOURNAL OF CHROMATOGRAPHY A}, author={Kish, William S. and Sachi, Hiroyuki and Naik, Amith D. and Roach, Matthew K. and Bobay, Benjamin G. and Blackburn, Robert K. and Menegatti, Stefano and Carbonell, Ruben G.}, year={2017}, month={Jun}, pages={105–120} }
 @article{milton_allen_feldmann_bobay_jung_stephens_melander_theisen_zeng_thompson_et al._2017, title={Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds}, volume={106}, ISSN={["1365-2958"]}, DOI={10.1111/mmi.13759}, abstractNote={Summary}, number={2}, journal={MOLECULAR MICROBIOLOGY}, author={Milton, Morgan E. and Allen, C. Leigh and Feldmann, Erik A. and Bobay, Benjamin G. and Jung, David K. and Stephens, Matthew D. and Melander, Roberta J. and Theisen, Kelly E. and Zeng, Daina and Thompson, Richele J. and et al.}, year={2017}, month={Oct}, pages={223–235} }
 @article{moore_bobay_mertens_jaykus_2016, title={Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to That of Receptors and Discriminates Particle Functionality}, volume={1}, ISSN={["2379-5042"]}, DOI={10.1128/msphere.00298-16}, abstractNote={Human noroviruses impose a considerable health burden globally. However, study of their inactivation is still challenging with currently reported cell culture models, as discrimination of infectious viral particles is still difficult. Traditionally, the ability of particles to bind putative carbohydrate receptors is conducted as a proxy for infectivity, but these receptors are inconsistent, expensive, and hard to purify/modify. We report a hitherto unexplored property of a different type of ligand, a nucleic acid aptamer, to mimic receptor binding behavior and assess capsid functionality for a selected strain of norovirus. These emerging ligands are cheaper, more stable, and easily synthesized/modified. The previously unutilized characteristic reported here demonstrates the fundamental potential of aptamers to serve as valuable, accessible tools for any microorganism that is difficult to cultivate/study. Therefore, this novel concept suggests a new use for aptamers that is of great value to the microbiological community—specifically that involving fastidious microbes.}, number={6}, journal={MSPHERE}, author={Moore, Matthew D. and Bobay, Benjamin G. and Mertens, Brittany and Jaykus, Lee-Ann}, year={2016} }
 @article{harris_bobay_sarachan_sims_bilbille_deutsch_iwata-reuyl_agris_2015, title={NMR-based structural analysis of threonylcarbamoyl-AMP synthase and Its substrate interactions}, volume={290}, number={33}, journal={Journal of Biological Chemistry}, author={Harris, K. A. and Bobay, B. G. and Sarachan, K. L. and Sims, A. F. and Bilbille, Y. and Deutsch, C. and Iwata-Reuyl, D. and Agris, P. F.}, year={2015}, pages={20032–20043} }
 @article{tucker_bobay_banse_olson_soderblom_moseley_thompson_varney_losick_cavanagh_2014, title={A DNA Mimic: The Structure and Mechanism of Action for the Anti-Repressor Protein AbbA}, volume={426}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2014.02.010}, abstractNote={Bacteria respond to adverse environmental conditions by switching on the expression of large numbers of genes that enable them to adapt to unfavorable circumstances. In Bacillus subtilis, many adaptive genes are under the negative control of the global transition state regulator, the repressor protein AbrB. Stressful conditions lead to the de-repression of genes under AbrB control. Contributing to this de-repression is AbbA, an anti-repressor that binds to and blocks AbrB from binding to DNA. Here, we have determined the NMR structure of the functional AbbA dimer, confirmed that it binds to the N-terminal DNA-binding domain of AbrB, and have provided an initial description for the interaction using computational docking procedures. Interestingly, we show that AbbA has structural and surface characteristics that closely mimic the DNA phosphate backbone, enabling it to readily carry out its physiological function.}, number={9}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Tucker, Ashley T. and Bobay, Benjamin G. and Banse, Allison V. and Olson, Andrew L. and Soderblom, Erik J. and Moseley, M. Arthur and Thompson, Richele J. and Varney, Kristen M. and Losick, Richard and Cavanagh, John}, year={2014}, month={May}, pages={1911–1924} }
 @article{bobay_thompson_milton_cavanagh_2014, title={Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum}, volume={8}, ISSN={["1874-270X"]}, DOI={10.1007/s12104-013-9478-2}, abstractNote={Vibrio anguillarum is a biofilm forming Gram-negative bacterium that survives prolonged periods in seawater and causes vibriosis in marine life. A quorum-sensing signal transduction pathway initiates biofilm formation in response to environmental stresses. The phosphotransferase protein VanU is the focal point of the quorum-sensing pathway and facilitates the regulation between independent phosphorelay systems that activate or repress biofilm formation. Here we report the 1H, 13C, and 15N backbone and side chain resonance assignments and secondary structure prediction for VanU from V. anguillarum.}, number={1}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Bobay, Benjamin G. and Thompson, Richele J. and Milton, Debra L. and Cavanagh, John}, year={2014}, month={Apr}, pages={177–179} }
 @article{olson_tucker_bobay_soderblom_moseley_thompson_cavanagh_2014, title={Structure and DNA-Binding Traits of the Transition State Regulator AbrB}, volume={22}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2014.08.018}, abstractNote={The AbrB protein from Bacillus subtilis is a DNA-binding global regulator controlling the onset of a vast array of protective functions under stressful conditions. Such functions include biofilm formation, antibiotic production, competence development, extracellular enzyme production, motility, and sporulation. AbrB orthologs are known in a variety of prokaryotic organisms, most notably in all infectious strains of Clostridia, Listeria, and Bacilli. Despite its central role in bacterial response and defense, its structure has been elusive because of its highly dynamic character. Orienting its N- and C-terminal domains with respect to one another has been especially problematic. Here, we have generated a structure of full-length, tetrameric AbrB using nuclear magnetic resonance, chemical crosslinking, and mass spectrometry. We note that AbrB possesses a strip of positive electrostatic potential encompassing its DNA-binding region and that its C-terminal domain aids in DNA binding.}, number={11}, journal={STRUCTURE}, author={Olson, Andrew L. and Tucker, Ashley T. and Bobay, Benjamin G. and Soderblom, Erik J. and Moseley, M. Arthur and Thompson, Richele J. and Cavanagh, John}, year={2014}, month={Nov}, pages={1650–1656} }
 @article{olson_bobay_melander_cavanagh_2012, title={H-1, C-13, and N-15 resonance assignments and secondary structure prediction of the full-length transition state regulator AbrB from Bacillus anthracis}, volume={6}, ISSN={["1874-2718"]}, DOI={10.1007/s12104-011-9333-2}, abstractNote={The AbrB protein is a transcription factor that regulates the expression of numerous essential genes during the cells transition phase state. AbrB from Bacillus anthracis is, nototriously, the principal protein responsible for anthrax toxin gene expression and is highly homologous to the much-studied AbrB protein from Bacillus subtilis having 85% sequence identity and the ability to regulate the same target promoters. Here we report backbone and sidechain resonance assignments and secondary structure prediction for the full-length AbrB protein from B. anthracis.}, number={1}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Olson, Andrew L. and Bobay, Benjamin G. and Melander, Christian and Cavanagh, John}, year={2012}, month={Apr}, pages={95–98} }
 @article{thompson_bobay_stowe_olson_peng_su_actis_melander_cavanagh_2012, title={Identification of BfmR, a Response Regulator Involved in Biofilm Development, as a Target for a 2-Aminoimidazole-Based Antibiofilm Agent}, volume={51}, ISSN={["0006-2960"]}, DOI={10.1021/bi3015289}, abstractNote={2-Aminoimidazoles (2AIs) have been documented to disrupt bacterial protection mechanisms, including biofilm formation and genetically encoded antibiotic resistance traits. Using Acinetobacter baumannii, we provide initial insight into the mechanism of action of a 2AI-based antibiofilm agent. Confocal microscopy confirmed that the 2AI is cell permeable, while pull-down assays identified BfmR, a response regulator that is the master controller of biofilm formation, as a target for this compound. Binding assays demonstrated specificity of the 2AI for response regulators, while computational docking provided models for 2AI-BfmR interactions. The 2AI compound studied here represents a unique small molecule scaffold that targets bacterial response regulators.}, number={49}, journal={BIOCHEMISTRY}, author={Thompson, Richele J. and Bobay, Benjamin G. and Stowe, Sean D. and Olson, Andrew L. and Peng, Lingling and Su, Zhaoming and Actis, Luis A. and Melander, Christian and Cavanagh, John}, year={2012}, month={Dec}, pages={9776–9778} }
 @article{bobay_stewart_tucker_thompson_varney_cavanagh_2012, title={Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3}, volume={586}, ISSN={["0014-5793"]}, DOI={10.1016/j.febslet.2012.08.032}, abstractNote={Calbindin‐D28K and Caspase‐3 bind by isothermal titration calorimetry (View interaction)}, number={20}, journal={FEBS LETTERS}, author={Bobay, Benjamin G. and Stewart, Amanda L. and Tucker, Ashley T. and Thompson, Richele J. and Varney, Kristen M. and Cavanagh, John}, year={2012}, month={Oct}, pages={3582–3589} }
 @article{yang_gurgel_williams_bobay_cavanagh_muddiman_carbonell_2010, title={Binding site on human immunoglobulin G for the affinity ligand HWRGWV}, volume={23}, number={3}, journal={Journal of Molecular Recognition}, author={Yang, H. O. and Gurgel, P. V. and Williams, D. K. and Bobay, B. G. and Cavanagh, J. and Muddiman, D. C. and Carbonell, R. G.}, year={2010}, pages={271–282} }
 @article{bobay_thompson_hoch_cavanagh_2010, title={Long range dynamic effects of point-mutations trap a response regulator in an active conformation}, volume={584}, ISSN={["0014-5793"]}, DOI={10.1016/j.febslet.2010.08.051}, abstractNote={When a point‐mutation in a protein elicits a functional change, it is most common to assign this change to local structural perturbations. Here we show that point‐mutations, distant from an essential highly dynamic kinase recognition loop in the response regulator Spo0F, lock this loop in an active conformation. This ‘conformational trapping’ results in functionally hyperactive Spo0F. Consequently, point‐mutations are seen to affect functionally critical motions both close to and far from the mutational site.}, number={19}, journal={FEBS LETTERS}, author={Bobay, Benjamin G. and Thompson, Richele J. and Hoch, James A. and Cavanagh, John}, year={2010}, month={Oct}, pages={4203–4207} }
 @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} }
 @article{szurmant_bobay_white_sullivan_thompson_hwa_hoch_cavanagh_2008, title={Co-Evolving Motions at Protein−Protein Interfaces of Two-Component Signaling Systems Identified by Covariance Analysis†}, volume={47}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi8009604}, DOI={10.1021/bi8009604}, abstractNote={Short-lived protein interactions determine signal transduction specificity among genetically amplified, structurally identical two-component signaling systems. Interacting protein pairs evolve recognition precision by varying residues at specific positions in the interaction surface consistent with constraints of charge, size, and chemical properties. Such positions can be detected by covariance analyses of two-component protein databases. Here, covariance is shown to identify a cluster of co-evolving dynamic residues in two-component proteins. NMR dynamics and structural studies of both wild-type and mutant proteins in this cluster suggest that motions serve to precisely arrange the site of phosphoryl transfer within the complex.}, number={30}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Szurmant, Hendrik and Bobay, Benjamin G. and White, Robert A. and Sullivan, Daniel M. and Thompson, Richele J. and Hwa, Terence and Hoch, James A. and Cavanagh, John}, year={2008}, month={Jul}, pages={7782–7784} }
 @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{burns_bobay_basso_cavanagh_melander_2008, title={Targeting RNA with cysteine-constrained peptides}, volume={18}, ISSN={["0960-894X"]}, DOI={10.1016/j.bmcl.2007.11.096}, abstractNote={A combined approach for targeting RNA with novel, biologically active ligands has been developed using a cyclic peptide library and in silico modeling. This approach has successfully identified novel cyclic peptide constructs that can target bTAR RNA. Subsequently, RNA/peptide interactions were effectively modeled using the HADDOCK docking program.}, number={2}, journal={BIOORGANIC & MEDICINAL CHEMISTRY LETTERS}, author={Burns, Virginia A. and Bobay, Benjamin G. and Basso, Anne and Cavanagh, John and Melander, Christian}, year={2008}, month={Jan}, pages={565–567} }
 @article{strauch_bobay_cavanagh_yao_wilson_le breton_2007, title={Abh and AbrB control of Bacillus subtilis antimicrobial gene expression}, volume={189}, ISSN={["1098-5530"]}, DOI={10.1128/JB.01081-07}, abstractNote={ABSTRACT}, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Strauch, Mark A. and Bobay, Benjamin G. and Cavanagh, John and Yao, Fude and Wilson, Angelo and Le Breton, Yoann}, year={2007}, month={Nov}, pages={7720–7732} }
 @article{kordys_bobay_thompson_venters_cavanagh_2007, title={Peptide binding proclivities of calcium loaded calbindin-D28k}, volume={581}, ISSN={["0014-5793"]}, DOI={10.1016/j.febslet.2007.09.004}, abstractNote={Calbindin‐D28k is known to function as a calcium‐buffering protein in the cell. Moreover, recent evidence shows that it also plays a role as a sensor. Using circular dichroism and NMR, we show that calbindin‐D28k undergoes significant conformational changes upon binding calcium, whereas only minor changes occur when binding target peptides in its Ca2+‐loaded state. NMR experiments also identify residues that undergo chemical shift changes as a result of peptide binding. The subsequent use of computational protein–protein docking protocols produce a model describing the interaction interface between calbindin‐D28k and its target peptides.}, number={24}, journal={FEBS LETTERS}, author={Kordys, David R. and Bobay, Benjamin G. and Thompson, Richele J. and Venters, Ronald A. and Cavanagh, John}, year={2007}, month={Oct}, pages={4778–4782} }
 @article{mclaughlin_bobaya_regel_thompson_hoch_cavanagh_2007, title={Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition}, volume={581}, ISSN={["0014-5793"]}, DOI={10.1016/j.febslet.2007.02.061}, abstractNote={Several alanine mutations in the response regulator Spo0F induce hypersporulation in Bacillus subtilis. L66A, I90A and H101A mutants are purported to be involved in contacts stabilizing the orientation of the α4‐helix and hence the β4–α4 kinase recognition loop. Y13A is thought to affect the orientation of the α1‐helix and consequently phosphatase action. Using comparative NMR chemical shift analyses for these mutants, we have confirmed these suppositions and isolated residues in Spo0F critical in sensor kinases discrimination. In addition, we discuss how buried residues and intra‐protein communication networks contribute to precise molecular recognition by ensuring that the correct surface is presented.}, number={7}, journal={FEBS LETTERS}, author={McLaughlin, Patrick D. and Bobaya, Benjamm G. and Regel, Erin J. and Thompson, Richele J. and Hoch, James A. and Cavanagh, John}, year={2007}, month={Apr}, pages={1425–1429} }
 @article{soderblom_bobay_cavanagh_goshe_2007, title={Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents}, volume={21}, ISSN={["0951-4198"]}, DOI={10.1002/rcm.3213}, abstractNote={Abstract}, number={21}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Soderblom, Erik J. and Bobay, Benjamin G. and Cavanagh, John and Goshe, Michael B.}, year={2007}, pages={3395–3408} }
 @article{bobay_mueller_thompson_murzin_venters_strauch_cavanagh_2006, title={NMR structure of AbhN and comparison with AbrBN - First insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins}, volume={281}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M601963200}, abstractNote={Understanding the molecular mechanisms of transition state regulator proteins is critical, since they play a pivotal role in the ability of bacteria to cope with changing environments. Although much effort has focused on their genetic characterization, little is known about their structural and functional conservation. Here we present the high resolution NMR solution structure of the N-terminal domain of the Bacillus subtilis transition state regulator Abh (AbhN), only the second such structure to date. We then compare AbhN to the N-terminal DNA-binding domain of B. subtilis AbrB (AbrBN). This is the first such comparison between two AbrB-like transition state regulators. AbhN and AbrBN are very similar, suggesting a common structural basis for their DNA binding. However, we also note subtle variances between the AbhN and AbrBN structures, which may play important roles in DNA target specificity. The results of accompanying in vitro DNA-binding studies serve to highlight binding differences between the two proteins.}, number={30}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Bobay, Benjamin G. and Mueller, Geoffrey A. and Thompson, Richele J. and Murzin, Alexey G. and Venters, Ronald A. and Strauch, Mark A. and Cavanagh, John}, year={2006}, month={Jul}, pages={21399–21409} }
 @article{bobay_andreeva_mueller_cavanagh_murzin_2005, title={Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins}, volume={579}, ISSN={["1873-3468"]}, DOI={10.1016/j.febslet.2005.09.045}, abstractNote={New relationships found in the process of updating the structural classification of proteins (SCOP) database resulted in the revision of the structure of the N‐terminal, DNA‐binding domain of the transition state regulator AbrB. The dimeric AbrB domain shares a common fold with the addiction antidote MazE and the subunit of uncharacterized protein MraZ implicated in cell division and cell envelope formation. It has a detectable sequence similarity to both MazE and MraZ thus providing an evolutionary link between the two proteins. The putative DNA‐binding site of AbrB is found on the same face as the DNA‐binding site of MazE and appears similar, both in structure and sequence, to the exposed conserved region of MraZ. This strongly suggests that MraZ also binds DNA and allows for a consensus model of DNA recognition by the members of this novel protein superfamily.}, number={25}, journal={FEBS LETTERS}, author={Bobay, BG and Andreeva, A and Mueller, GA and Cavanagh, J and Murzin, AG}, year={2005}, month={Oct}, pages={5669–5674} }
 @article{bobay_benson_naylor_feeney_clark_goshe_strauch_thompson_cavanagh_2004, title={Evaluation of the DNA Binding Tendencies of the Transition State Regulator AbrB†}, volume={43}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi048399h}, DOI={10.1021/bi048399h}, abstractNote={Global transition state regulator proteins represent one of the most diverse classes of prokaryotic transcription factors. One such transition state regulator, AbrB from Bacillus subtilis, is known to bind more than 60 gene targets yet displays specificity within this target set by binding each promoter with a different affinity. Microelectrospray ionization mass spectrometry (microESI-MS), circular dichroism, fluorescence, UV spectroscopy, and molecular modeling were used to elucidate differences among AbrB, DNA, and AbrB-DNA complexes. MicroESI-MS analysis of AbrB confirmed its stable macromolecular state as being tetrameric and verified the same stoichiometric state in complex with DNA targets. MicroESI-MS, circular dichroism, and fluorescence provided relative binding affinities for AbrB-DNA interactions in a qualitative manner. UV spectroscopy was used in a quantitative manner to determine solution phase dissociation constants for AbrB-DNA complexes. General DNA structural parameters for all known natural AbrB binding sequences were also studied and significant similarities in topological constraints (stretch, opening, and propeller twist) were observed. It is likely that these parameters contribute to the differential binding proclivities of AbrB. In addition to providing an improved understanding of transition state regulator-DNA binding properties and structural tendencies of target promoters, this comprehensive and corroborative spectroscopic study endorses the use of microESI-MS for rapidly ascertaining qualitative binding trends in noncovalent systems in a high-throughput manner.}, number={51}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Bobay, Benjamin G. and Benson, Linda and Naylor, Stephen and Feeney, Brett and Clark, A. Clay and Goshe, Michael B. and Strauch, Mark A. and Thompson, Richele and Cavanagh, John}, year={2004}, month={Dec}, pages={16106–16118} }
 @article{benson_vaughn_strauch_bobay_thompson_naylor_cavanagh_2002, title={Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry}, volume={306}, ISSN={["1096-0309"]}, DOI={10.1006/abio.2002.5704}, abstractNote={The Bacillus subtilis global transition-state regulator AbrB specifically recognizes over 60 different DNA regulatory regions of genes expressed during cellular response to suboptimal environments. Most interestingly the DNA regions recognized by AbrB share no obvious consensus base sequence. To more clearly understand the functional aspects of AbrB activity, microelectrospray ionization mass spectrometry has been employed to resolve the macromolecular assembly of unbound and DNA-bound AbrB. Analysis of the N-terminal DNA binding domain of AbrB (AbrBN53, residues 1-53) demonstrates that AbrBN53 is a stable dimer, showing no apparent exchange with a monomeric form as a function of pH, ionic strength, solvent, or protein concentration. AbrBN53 demonstrates a capacity for DNA binding, underscoring the role of the N-terminal domain in both DNA recognition and dimerization. Full-length AbrB is shown to exist as a homotetramer. An investigation of the binding of AbrBN53 and AbrB to the natural DNA target element sinIR shows that AbrBN53 binds as a dimer and AbrB binds as a tetramer. This study represents the first detailed characterization of the stoichiometry of a transition-state regulator binding to one of its target promoters.}, number={2}, journal={ANALYTICAL BIOCHEMISTRY}, author={Benson, LM and Vaughn, JL and Strauch, MA and Bobay, BG and Thompson, R and Naylor, S and Cavanagh, J}, year={2002}, month={Jul}, pages={222–227} }
 @article{cavanagh_thompson_bobay_benson_naylor_2002, title={Stoichiometries of protein - Protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry}, volume={41}, ISSN={["0006-2960"]}, DOI={10.1021/bi0202225}, abstractNote={We have developed on-line pseudo cell-size exclusion chromatography-mass spectrometry (PsC-SEC-MS) for the rapid, real time analyses of noncovalently bound protein complexes. The methodology can be used to determine constituent components of such complexes, as well as exact stoichiometries. Furthermore, it enables the efficient determination of gross conformational changes upon complexation. The power of the new approach is demonstrated in the analysis of the global transition-state regulator AbrB and its complex with a target DNA sequence from the promoter sinIR. Using PsC-SEC-MS, we confirm that AbrB is assembled as a homotetramer and not as a homohexamer as previously suggested. Additionally, we show that AbrB binds to the sinIR DNA target element as a homotetramer, affording a 4:1 protein:DNA stoichiometry. Finally, we demonstrate that when the complex binds to sinIR, the hydrodynamic volume (size) of the complex is notably reduced compared to that of the apoprotein, indicating a protein conformational change.}, number={25}, journal={BIOCHEMISTRY}, author={Cavanagh, J and Thompson, R and Bobay, B and Benson, LM and Naylor, S}, year={2002}, month={Jun}, pages={7859–7865} }