@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{milton_minrovic_harris_kang_jung_lewis_thompson_melander_zeng_melander_et al._2018, title={Re-sensitizing Multidrug Resistant Bacteria to Antibiotics by Targeting Bacterial Response Regulators: Characterization and Comparison of Interactions between 2-Aminoimidazoles and the Response Regulators BfmR from Acinetobacter baumannii and QseB from Francisella spp.}, volume={5}, ISSN={["2296-889X"]}, DOI={10.3389/fmolb.2018.00015}, abstractNote={2-aminoimidazole (2-AI) compounds inhibit the formation of bacterial biofilms, disperse preformed biofilms, and re-sensitize multidrug resistant bacteria to antibiotics. 2-AIs have previously been shown to interact with bacterial response regulators, but the mechanism of interaction is still unknown. Response regulators are one part of two-component systems (TCS). TCSs allow cells to respond to changes in their environment, and are used to trigger quorum sensing, virulence factors, and antibiotic resistance. Drugs that target the TCS signaling process can inhibit pathogenic behavior, making this a potent new therapeutic approach that has not yet been fully exploited. We previously laid the groundwork for the interaction of the Acinetobacter baumannii response regulator BfmR with an early 2-AI derivative. Here, we further investigate the response regulator/2-AI interaction and look at a wider library of 2-AI compounds. By combining molecular modeling with biochemical and cellular studies, we expand on a potential mechanism for interaction between response regulators and 2-AIs. We also establish that Francisella tularensis/novicida, encoding for only three known response regulators, can be a model system to study the interaction between 2-AIs and response regulators. We show that knowledge gained from studying Francisella can be applied to the more complex A. baumannii system, which contains over 50 response regulators. Understanding the impact of 2-AIs on response regulators and their mechanism of interaction will lead to the development of more potent compounds that will serve as adjuvant therapies to broad-range antibiotics.}, journal={FRONTIERS IN MOLECULAR BIOSCIENCES}, author={Milton, Morgan E. and Minrovic, Bradley M. and Harris, Danni L. and Kang, Brian and Jung, David and Lewis, Caleb P. and Thompson, Richele J. and Melander, Roberta J. and Zeng, Daina and Melander, Christian and et al.}, year={2018}, month={Feb} }
 @article{draughn_milton_feldmann_bobay_roth_olson_thompson_actis_davies_cavanagh_2018, title={The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism}, volume={430}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/J.JMB.2018.02.002}, DOI={10.1016/J.JMB.2018.02.002}, abstractNote={The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global health care. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling. We also show that BfmR binds the previously proposed bfmRS promoter sequence with moderate affinity. While BfmR shares many traits with other OmpR/PhoB family response regulators, some unusual properties were observed. Most importantly, we observe that when phosphorylated, BfmR binds this promoter sequence with a lower affinity than when not phosphorylated. All other OmpR/PhoB family members studied to date show an increase in DNA-binding affinity upon phosphorylation. Understanding the structural and biochemical mechanisms of BfmR will aid in the development of new antimicrobial therapies.}, number={6}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Draughn, G. Logan and Milton, Morgan E. and Feldmann, Erik A. and Bobay, Benjamin G. and Roth, Braden M. and Olson, Andrew L. and Thompson, Richele J. and Actis, Luis A. and Davies, Christopher and Cavanagh, John}, year={2018}, month={Mar}, pages={806–821} }
 @article{draughn_allen_routh_stone_kirker_boegli_schuchman_linder_baynes_james_et al._2017, title={Evaluation of a 2-aminoimidazole variant as adjuvant treatment for dermal bacterial infections}, volume={11}, journal={Drug Design Development and Therapy}, author={Draughn, G. L. and Allen, C. L. and Routh, P. A. and Stone, M. R. and Kirker, K. R. and Boegli, A. and Schuchman, R. M. and Linder, K. E. and Baynes, R. E. and James, G. and et al.}, year={2017}, pages={153–162} }
 @article{stephens_hubble_ernst_hoek_melander_cavanagh_melander_2016, title={Potentiation of Francisella resistance to conventional antibiotics through small molecule adjuvants}, volume={7}, ISSN={["2040-2511"]}, DOI={10.1039/c5md00353a}, abstractNote={A screen of 20 compounds identified small molecule adjuvants capable of potentiating antibiotic activity against Francisella philomiragia.}, number={1}, journal={MEDCHEMCOMM}, author={Stephens, Matthew D. and Hubble, Veroncia B. and Ernst, Robert K. and Hoek, Monique L. and Melander, Roberta J. and Cavanagh, John and Melander, Christian}, year={2016}, pages={128–131} }
 @article{wahome_beauchesne_pedone_cavanagh_melander_zimba_moeller_2015, title={Augmenting anti-cancer natural products with a small molecule adjuvant}, volume={13}, number={1}, journal={Marine Drugs}, author={Wahome, P. G. and Beauchesne, K. R. and Pedone, A. C. and Cavanagh, J. and Melander, C. and Zimba, P. and Moeller, P. D. R.}, year={2015}, pages={65–75} }
 @article{stowe_thompson_peng_su_blackledge_draughn_coe_johannes_lapham_mackenzie_et al._2015, title={Membrane-Permeabilizing Activity of Reverse-Amide 2-Aminoimidazole Antibiofilm Agents Against Acinetobacter baumannii}, volume={12}, ISSN={["1875-5704"]}, DOI={10.2174/1567201811666140924125740}, abstractNote={Acinetobacter baumannii has quickly become one of the most insidious and prevalent nosocomial infections. Recently, the reverse-amide class of 2-aminoimidazole compounds (RA-2AI) was found both to prevent A. baumannii biofilm formation and also to disperse preexisting formations, putatively through interactions with cytosolic response regulators. Here we focus on how this class of antibiofilm agent traverses cellular membranes. Following the discovery of dosage-dependent growth rate changes, the cellular effects of RA-2AI were investigated using a combination of molecular assays and microscopic techniques. It was found that RA-2AI exposure has measureable effects on the bacterial membranes, resulting in a period of increased permeability and visible structural aberrations. Based on these results, we propose a model that describes how the structure of RA-2AI allows it to insert itself into and disrupt the fluidity of the membrane, creating an opportunity for increased molecular permeability.}, number={2}, journal={CURRENT DRUG DELIVERY}, author={Stowe, Sean D. and Thompson, Richele J. and Peng, Lingling and Su, Zhaoming and Blackledge, Meghan S. and Draughn, G. Logan and Coe, William H. and Johannes, Eva and Lapham, Valerie K. and Mackenzie, John and et al.}, year={2015}, pages={223–230} }
 @article{feldmann_cavanagh_2015, title={Teaching old drugs new tricks: Addressing resistance in Francisella}, volume={6}, ISSN={["2150-5608"]}, DOI={10.1080/21505594.2015.1053689}, abstractNote={Francisella tularensis is a Gram-negative bacterial pathogen and causative agent of the disease tularemia, also known as “rabbit fever.” The Centers for Disease Control and Prevention (CDC) lists the virulent form of F. tularensis as a Tier 1 pathogen based on its ease in aerosolizing and the lethal damage an inhaled infection can cause in humans. Because of its high pathogenicity and aerosolization ease, F. tularensis is classified as a Category A select agent and represents a significant potential threat as a biological weapon. Especially concerning is the emergence of multi-drug resistant (MDR) Francisella strains adding to the already dire public health and safety concerns. Discovery of therapeutic strategies that avoid conferring resistance is crucial for any long-term solution to address the problem of MDR bacteria and enhances the motivation for Francisella research. Francisella novicida is a useful model strain for studying virulence, biofilm formation, and drug resistance in the far more virulent strain, F. tularensis. Unlike other bacteria, F. novicida relies on only two intact 2-component systems (TCSs) and two orphaned members for its virulence and resistive strategies, making any of these select members particularly attractive drug targets. Francisella, like all bacteria, utilize TCS signaling pathways to respond to environmental stimuli through concerted communication between a histidine sensor kinase and a response regulator target. If the TCS signaling components malfunction, bacterial defense mechanisms are compromised, rendering them susceptible to environmental stress. When TCS functionality is specifically targeted, using small molecule drugs or biologics for example, even MDR bacteria can once again show vulnerability to the same antibiotics to which they had previously acquired resistance. Similar to F. novicida, F. tularensis encodes orphaned TCS components but the identity and number of these differ depending on the substrain. For example, the highly virulent strain F. tularensis Schu S4 encodes QseC, PmrA/QseB, KdpD, and FTT1543 (the conserved homolog of FTN1452 in F. novicida) all as orphans (QseC and KdpD are sensor kinases; PmrA/QseB and FTT1543 are response regulators). TCS signal transduction pathways generally make attractive targets for the development of anti-infective therapeutics since so many cellular processes rely on the downstream activities from both sensor kinases and response regulators. The accelerated work over the last 20 years is indicative of their potential for use as therapeutics and has been reviewed elsewhere. Recently, efforts have been made to target response regulator proteins in a variety of systems to thwart bacterial resistance and the onset of virulence. For example, PmrA/QseB is the lone response regulator orphan in F. novicida and is an important regulator of biofilm formation across the Francisella genus. PmrA/QseB has been shown to be required for virulence and proper expression of Francisella pathogenicity island (FPI) virulence factors, many of which themselves are also required for virulence and infectivity. PmrA/QseB upregulates the transcription of FPI genes, most notably the levels of intracellular growth locus C (iglC). The activation of PmrA/QseB is mediated by phosphorylation from an upstream sensor kinase, the identity of which is still unclear, but this action could be accomplished by KdpD or even multiple kinases. A proposed model suggests that Francisella sensor kinases may not necessarily discriminate for a single response regulator partner, but rather phosphorylate their targets more “promiscuously”. Regardless, PmrA/ QseB appears to form a complex with another virulence factor, MglA, a regulator of IglC. MglA has subsequently been suggested to form a complex with yet another virulence factor, SspA. Furthermore, transcription of FPI appears to be controlled by the phosphorylation/activation of PmrA/QseB which then recruits MglA-SspA together with RNA-polymerase to bind target gene promoters and upregulate the virulence pathway. However, it has historically been the sensor kinases, not the response regulators, that have attracted the most attention for therapeutic intervention. QseC from Francisella is a sensor kinase found in many bacteria including other biothreat pathogens like MDR Salmonella, Coxiella brunettii, and enterohemorrhagic E. coli (EHEC). The operon for QseC in F. novicida does not encode a paired response regulator, unlike KdpD (paired response regulator is KdpE) and FTN1453 (paired response regulator is FTN1452), and is thus considered orphaned. However despite this, QseC has been shown together with PmrA/QseB to regulate biofilm development in F. novicida and is required for virulence. QseC in Francisella is homologous to QseC in E. coli,}, number={5}, journal={VIRULENCE}, author={Feldmann, Erik A. and Cavanagh, John}, year={2015}, month={Jul}, pages={414–416} }
 @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{olson_thompson_melander_cavanagh_2014, title={Chemical shift assignments and secondary structure prediction of the C-terminal domain of the response regulator BfmR from Acinetobacter baumannii}, volume={8}, ISSN={["1874-270X"]}, DOI={10.1007/s12104-012-9454-2}, abstractNote={Acinetobacter baumannii is a Gram-negative pathogen responsible for severe nocosomial infections by forming biofilms in healthcare environments. The two-domain response regulator BfmR has been shown to be the master controller for biofilm formation. Inactivation of BfmR resulted in an abolition of pili production and consequently biofilm creation. Here we report backbone and sidechain resonance assignments and secondary structure prediction for the C-terminal domain of BfmR (residues 130–238) from A. baumannii.}, number={1}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Olson, Andrew L. and Thompson, Richele J. and Melander, Christian and Cavanagh, John}, year={2014}, month={Apr}, pages={67–70} }
 @article{stowe_olson_losick_cavanagh_2014, title={Chemical shift assignments and secondary structure prediction of the master biofilm regulator, SinR, from Bacillus subtilis}, volume={8}, ISSN={["1874-270X"]}, DOI={10.1007/s12104-013-9473-7}, abstractNote={Bacillus subtilis is a soil-dwelling Gram-positive bacterial species that has been extensively studied as a model of biofilm formation and stress-induced cellular differentiation. The tetrameric protein, SinR, has been identified as a master regulator for biofilm formation and linked to the regulation of the early transition states during cellular stress response, such as motility and biofilm-linked biosynthetic genes. SinR is a 111-residue protein that is active as a dimer of dimers, composed of two distinct domains, a DNA-binding helix-turn-helix N-terminus domain and a C-terminal multimerization domain. In order for biofilm formation to proceed, the antagonist, SinI, must inactivate SinR. This interaction results in a dramatic structural rearrangement of both proteins. Here we report the full-length backbone and side chain chemical shift values in addition to the experimentally derived secondary structure predictions as the first step towards directly studying the complex interaction dynamics between SinR and SinI.}, number={1}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Stowe, Sean D. and Olson, Andrew L. and Losick, Richard and Cavanagh, John}, year={2014}, month={Apr}, pages={155–158} }
 @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{brackett_melander_an_krishnamurthy_thompson_cavanagh_melander_2014, title={Small-Molecule Suppression of beta-Lactam Resistance in Multidrug-Resistant Gram-Negative Pathogens}, volume={57}, ISSN={["1520-4804"]}, DOI={10.1021/jm501050e}, abstractNote={Recent efforts toward combating antibiotic resistance in bacteria have focused on Gram-positive bacteria; however, multidrug-resistant Gram-negative bacteria pose a significant risk to public health. An orthogonal approach to the development of new antibiotics is to develop adjuvant compounds that enhance the susceptibility of drug-resistant strains of bacteria to currently approved antibiotics. This paper describes the synthesis and biological activity of a library of aryl amide 2-aminoimidazoles based on a lead structure from an initial screen. A small molecule was identified from this library that is capable of lowering the minimum inhibitory concentration of β-lactam antibiotics by up to 64-fold.}, number={17}, journal={JOURNAL OF MEDICINAL CHEMISTRY}, author={Brackett, Christopher M. and Melander, Roberta J. and An, Il Hwan and Krishnamurthy, Aparna and Thompson, Richele J. and Cavanagh, John and Melander, Christian}, year={2014}, month={Sep}, pages={7450–7458} }
 @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_liu_tucker_goshe_cavanagh_2013, title={Chemical crosslinking and LC/MS analysis to determine protein domain orientation: Application to AbrB}, volume={431}, ISSN={["1090-2104"]}, DOI={10.1016/j.bbrc.2012.12.124}, abstractNote={To fully understand the modes of action of multi-protein complexes, it is essential to determine their overall global architecture and the specific relationships between domains and subunits. The transcription factor AbrB is a functional homotetramer consisting of two domains per monomer. Obtaining the high-resolution structure of tetrameric AbrB has been extremely challenging due to the independent character of these domains. To facilitate the structure determination process, we solved the NMR structures of both domains independently and utilized gas-phase cleavable chemical crosslinking and LC/MS(n) analysis to correctly position the domains within the full tetrameric AbrB protein structure.}, number={2}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, author={Olson, Andrew L. and Liu, Fan and Tucker, Ashley T. and Goshe, Michael B. and Cavanagh, John}, year={2013}, month={Feb}, pages={253–257} }
 @article{stowe_tucker_thompson_piper_richards_rogers_mathies_melander_cavanagh_2012, title={Evaluation of the toxicity of 2-aminoimidazole antibiofilm agents using both cellular and model organism systems}, volume={35}, ISSN={["1525-6014"]}, DOI={10.3109/01480545.2011.614620}, abstractNote={Biofilm formation is a ubiquitous bacterial defense mechanism and has been shown to be a primary element in the antibiotic resistance of many human diseases, especially in the case of nosocomial infections. Recently, we have developed several compound libraries that are extremely effective at both dispersing preexisting biofilms and also inhibiting their initial formation. In addition to their antibiofilm properties, some of these molecules are able to resensitize resistant bacterial strains to previously ineffective antibiotics and are being assessed as adjuvants. In this study, we evaluated the toxic effects of three of our most effective 2-aminoimidazole compounds (dihydrosventrin, RA, and SPAR) using a rapid pipeline that combines a series of assays. A methylthiazolyldiphenyl-tetrazolium assay, using the HaCaT keratinocyte cell line was used to determine epidermal irritants and was combined with Caenorhabditis elegans fecundity assays that demonstrated the effects of environmental exposure to various concentrations of these molecules. In each case, the assays showed that the compounds did not exhibit toxicity until they reached well above their current biofilm dispersion/inhibition concentrations. The most effective antibiofilm compound also had significant effects when used in conjunction with several standard antibiotics against resistant bacteria. Consequently, it was further investigated using the C. elegans assay in combination with different antibiotics and was found to maintain the same low level of toxicity as when acting alone, bolstering its candidacy for further testing as an adjuvant.}, number={3}, journal={DRUG AND CHEMICAL TOXICOLOGY}, author={Stowe, Sean D. and Tucker, Ashley T. and Thompson, Richele and Piper, Amanda and Richards, Justin J. and Rogers, Steven A. and Mathies, Laura D. and Melander, Christian and Cavanagh, John}, year={2012}, month={Jul}, pages={310–315} }
 @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} }
 @misc{stowe_richards_tucker_thompson_melander_cavanagh_2011, title={Anti-biofilm compounds derived from marine sponges}, volume={9}, number={10}, journal={Marine Drugs}, author={Stowe, S. D. and Richards, J. J. and Tucker, A. T. and Thompson, R. and Melander, C. and Cavanagh, J.}, year={2011}, pages={2010–2035} }
 @article{bunders_cavanagh_melander_2011, title={Flustramine inspired synthesis and biological evaluation of pyrroloindoline triazole amides as novel inhibitors of bacterial biofilms}, volume={9}, ISSN={["1477-0539"]}, DOI={10.1039/c1ob05605k}, abstractNote={Anti-biofilm agents have been developed based upon the flustramine family of alkaloids isolated from Flustra foliacea. A Garg interrupted Fischer indolization reaction was employed to access a core pyrroloindoline scaffold that was subsequently employed to create a pyrroloindoline triazole amide library. Screening for the ability to modulate biofilm formation against strains of Gram-positive and Gram-negative bacteria identified several compounds with low micromolar, non-toxic IC(50) values.}, number={15}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Bunders, Cynthia and Cavanagh, John and Melander, Christian}, year={2011}, pages={5476–5481} }
 @article{bunders_minvielle_worthington_ortiz_cavanagh_melander_2011, title={Intercepting Bacterial Indole Signaling with Flustramine Derivatives}, volume={133}, ISSN={["1520-5126"]}, DOI={10.1021/ja209836z}, abstractNote={Indole signaling is one of the putative universal signaling networks in bacteria. We have investigated the use of desformylflustrabromine (dFBr) derivatives for the inhibition of biofilm formation through modulation of the indole-signaling network in Escherichia coli and Staphylococcus aureus . We have found dFBr derivatives that are 10-1000 times more active than indole itself, demonstrating that the flustramine family of indolic natural products represent a privileged scaffold for the design of molecules to control pathogenic bacterial behavior.}, number={50}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Bunders, Cynthia A. and Minvielle, Marine J. and Worthington, Roberta J. and Ortiz, Minoshka and Cavanagh, John and Melander, Christian}, year={2011}, month={Dec}, pages={20160–20163} }
 @article{refaei_combs_kojetin_cavanagh_caperelli_rance_sapitro_tsang_2011, title={Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy}, volume={49}, ISSN={["1573-5001"]}, DOI={10.1007/s10858-010-9464-2}, abstractNote={NMR spectroscopy has distinct advantages for providing insight into protein structures, but faces significant resolution challenges as protein size increases. To alleviate such resonance overlap issues, the ability to produce segmentally labeled proteins is beneficial. Here we show that the S. aureus transpeptidase sortase A can be used to catalyze the ligation of two separately expressed domains of the same protein, MecA (B. subtilis). The yield of purified, segmentally labeled MecA protein conjugate is ~40%. The resultant HSQC spectrum obtained from this domain-labeled conjugate demonstrates successful application of sortase A for segmental labeling of multi-domain proteins for solution NMR study.}, number={1}, journal={JOURNAL OF BIOMOLECULAR NMR}, author={Refaei, Mary Anne and Combs, Al and Kojetin, Douglas J. and Cavanagh, John and Caperelli, Carol and Rance, Mark and Sapitro, Jennifer and Tsang, Pearl}, year={2011}, month={Jan}, pages={3–7} }
 @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{rogers_huigens_cavanagh_melander_2010, title={Synergistic Effects between Conventional Antibiotics and 2-Aminoimidazole-Derived Antibiofilm Agents}, volume={54}, ISSN={["0066-4804"]}, DOI={10.1128/aac.01418-09}, abstractNote={ABSTRACT}, number={5}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Rogers, Steven A. and Huigens, Robert W., III and Cavanagh, John and Melander, Christian}, year={2010}, month={May}, pages={2112–2118} }
 @article{richards_reyes_stowe_tucker_ballard_mathies_cavanagh_melander_2009, title={Amide Isosteres of Oroidin: Assessment of Antibiofilm Activity and C. elegans Toxicity}, volume={52}, ISSN={["1520-4804"]}, DOI={10.1021/jm900378s}, abstractNote={The synthesis and antibiofilm activities of sulfonamide, urea, and thiourea oroidin analogues are described. The most active derivative was able to selectively inhibit P. aeruginosa biofilm development and is also shown to be nontoxic upward of 1 mM to the development of C. elegans in comparison to other similar isosteric analogues and the natural product oroidin.}, number={15}, journal={JOURNAL OF MEDICINAL CHEMISTRY}, author={Richards, Justin J. and Reyes, Samuel and Stowe, Sean D. and Tucker, Ashley T. and Ballard, T. Eric and Mathies, Laura D. and Cavanagh, John and Melander, Christian}, year={2009}, month={Aug}, pages={4582–4585} }
 @article{yang_gurgel_williams_bobay_cavanagh_muddiman_carbonell_2009, title={Binding site on human immunoglobulin G for the affinity ligand HWRGWV}, ISSN={0952-3499 1099-1352}, url={http://dx.doi.org/10.1002/jmr.967}, DOI={10.1002/jmr.967}, abstractNote={Abstract}, journal={Journal of Molecular Recognition}, publisher={Wiley}, author={Yang, Haiou and Gurgel, Patrick V. and Williams, D. Keith, Jr and Bobay, Benjamin G. and Cavanagh, John and Muddiman, David C. and Carbonell, Ruben G.}, year={2009}, pages={n/a-n/a} }
 @article{melander_moeller_ballard_richards_huigens_cavanagh_2009, title={Evaluation of dihydrooroidin as an antifouling additive in marine paint}, volume={63}, ISSN={["0964-8305"]}, DOI={10.1016/j.ibiod.2008.08.009}, abstractNote={Methods used to deter biofouling of underwater structures and marine vessels present a serious environmental issue and are both problematic and costly for government and commercial marine vessels worldwide. Current antifouling methods include compounds that are toxic to aquatic wildlife and marine ecosystems. Dihydrooroidin (DHO) was shown to completely inhibit Halomonas pacifica biofilms at 100 μM in a static biofilm inhibition assay giving precedence for the inhibition of other marine biofilm-forming organisms. Herein we present DHO as an effective paint-based, non-cytotoxic, antifouling agent against marine biofouling processes in a marine mesocosm.}, number={4}, journal={INTERNATIONAL BIODETERIORATION & BIODEGRADATION}, author={Melander, Christian and Moeller, Peter D. R. and Ballard, T. Eric and Richards, Justin J. and Huigens, Robert W., III and Cavanagh, John}, year={2009}, month={Jun}, pages={529–532} }
 @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{kojetin_mclaughlin_thompson_dubnau_prepiak_rance_cavanagh_2009, title={Structural and Motional Contributions of the Bacillus subtilis ClpC N-Domain to Adaptor Protein Interactions}, volume={387}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2009.01.046}, abstractNote={The AAA + (ATPases associated with a variety of cellular activities) superfamily protein ClpC is a key regulator of cell development in Bacillus subtilis. As part of a large oligomeric complex, ClpC controls an array of cellular processes by recognizing, unfolding, and providing misfolded and aggregated proteins as substrates for the ClpP peptidase. ClpC is unique compared to other HSP100/Clp proteins, as it requires an adaptor protein for all fundamental activities. The NMR solution structure of the N-terminal repeat domain of ClpC (N-ClpCR) comprises two structural repeats of a four-helix motif. NMR experiments used to map the MecA adaptor protein interaction surface of N-ClpCR reveal that regions involved in the interaction possess conformational flexibility and conformational exchange on the microsecond-to-millisecond timescale. The electrostatic surface of N-ClpCR differs substantially from the N-domain of Escherichia coli ClpA and ClpB, suggesting that the electrostatic surface characteristics of HSP100/Clp N-domains may play a role in adaptor protein and substrate interaction specificity, and perhaps contribute to the unique adaptor protein requirement of ClpC.}, number={3}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Kojetin, Douglas J. and McLaughlin, Patrick D. and Thompson, Richele J. and Dubnau, David and Prepiak, Peter and Rance, Mark and Cavanagh, John}, year={2009}, month={Apr}, pages={639–652} }
 @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{huigens_ma_gambino_moeller_basso_cavanagh_wozniak_melander_2008, title={Control of bacterial biofilms with marine alkaloid derivatives}, volume={4}, ISSN={["1742-2051"]}, DOI={10.1039/b719989a}, abstractNote={Bacterial biofilms are defined as a community of surface-attached bacteria that are protected by an extracellular matrix of biomolecules. We have recently reported the synthesis of a small molecule, denoted TAGE, based on the natural product bromoageliferin and demonstrated that TAGE has anti-biofilm activity against Pseudomonas aeruginosa. Herein we demonstrate that TAGE: (1) does not have selective toxicity against cells within the biofilm state, (2) will inhibit biofilm development under flow conditions, indicating that the CV staining protocol correlates with the ability to be active under biomimetic conditions, and (3) will disperse preformed P. aeruginosa biofilms. We also present preliminary toxicity work that indicates that TAGE is devoid of cytotoxicity in rat and mice cell lines. Advanced derivatives of TAGE have generated compounds shown to be exceedingly effective as biofilm inhibitors against the gamma-proteobacteria in this study (P. aeruginosa strains PAO1, PA14, PDO300, and Acinetobacter baumannii). TAGE derivatives also possessed anti-biofilm activity against the beta-proteobacterium Bordetella bronchiseptica (Rb50) and the Gram-positive bacterium Staphylococcus aureus;TAGE derivatives inhibited the formation of biofilms, however, some of this activity is attributed to microbicidal activity. The TAGE derivatives presented in this study, however, do not disperse pre-formed biofilms with the same efficiency as TAGE.}, number={6}, journal={MOLECULAR BIOSYSTEMS}, author={Huigens, Robert W., III and Ma, Luyan and Gambino, Christopher and Moeller, Peter D. R. and Basso, Anne and Cavanagh, John and Wozniak, Daniel J. and Melander, Christian}, year={2008}, pages={614–621} }
 @article{richards_huigens iii_ballard_basso_cavanagh_melander_2008, title={Inhibition and dispersion of proteobacterial biofilms}, ISSN={1359-7345 1364-548X}, url={http://dx.doi.org/10.1039/b719802g}, DOI={10.1039/b719802g}, abstractNote={A small molecule derived from a marine natural product with the ability to inhibit biofilm formation and also disperse established proteobacterial biofilms is presented.}, number={14}, journal={Chemical Communications}, publisher={Royal Society of Chemistry (RSC)}, author={Richards, Justin J. and Huigens III, Robert W. and Ballard, T. Eric and Basso, Anne and Cavanagh, John and Melander, Christian}, year={2008}, pages={1698} }
 @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={<h2>Summary</h2> 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 <i>Bacillus subtilis</i> 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 AbrBN<sup>55</sup> and its cognate promoter, <i>abrB8</i>. 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{kojetin_mclaughlin_thompson_venters_rance_cavanagh_2007, title={NMR assignment of the N-terminal repeat domain of Bacillus subtilis ClpC}, volume={1}, ISSN={["1874-2718"]}, DOI={10.1007/s12104-007-9046-8}, abstractNote={The HSP100/AAA+ superfamily protein ClpC is a key regulator of cell development in Bacillus subtilis. We present here the backbone and side-chain assignments of the N-terminal repeat domain (residues 1-145) of ClpC from Bacillus subtilis.}, number={2}, journal={BIOMOLECULAR NMR ASSIGNMENTS}, author={Kojetin, Douglas J. and McLaughlin, Patrick D. and Thompson, Richele J. and Venters, Ronald A. and Rance, Mark and Cavanagh, John}, year={2007}, month={Dec}, pages={163–165} }
 @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{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} }
 @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{kojetin_venters_kordys_thompson_kumar_cavanagh_2006, title={Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D-28K}, volume={13}, DOI={10.1038/nsmb1112d}, number={7}, journal={Nature Structural & Molecular Biology}, author={Kojetin, D. J. and Venters, R. A. and Kordys, D. R. and Thompson, R. J. and Kumar, R. and Cavanagh, J.}, year={2006}, pages={641–647} }
 @article{kojetin_venters_kordys_thompson_kumar_cavanagh_2006, title={Structure, binding interface and hydrophobic transitions of Ca2+-loaded calbindin-D28K}, volume={13}, ISSN={1545-9993 1545-9985}, url={http://dx.doi.org/10.1038/nsmb1112}, DOI={10.1038/nsmb1112}, abstractNote={Calbindin-D(28K) is a Ca2+-binding protein, performing roles as both a calcium buffer and calcium sensor. The NMR solution structure of Ca2+-loaded calbindin-D(28K) reveals a single, globular fold consisting of six distinct EF-hand subdomains, which coordinate Ca2+ in loops on EF1, EF3, EF4 and EF5. Target peptides from Ran-binding protein M and myo-inositol monophosphatase, along with a new target from procaspase-3, are shown to interact with the protein on a surface comprised of alpha5 (EF3), alpha8 (EF4) and the EF2-EF3 and EF4-EF5 loops. Fluorescence experiments reveal that calbindin-D(28K) adopts discrete hydrophobic states as it binds Ca2+. The structure, binding interface and hydrophobic characteristics of Ca2+-loaded calbindin-D(28K) provide the first detailed insights into how this essential protein may function. This structure is one of the largest high-resolution NMR structures and the largest monomeric EF-hand protein to be solved to date.}, number={7}, journal={Nature Structural & Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Kojetin, Douglas J and Venters, Ronald A and Kordys, David R and Thompson, Richele J and Kumar, Rajiv and Cavanagh, John}, year={2006}, month={Jun}, pages={641–647} }
 @article{venters_coggins_kojetin_cavanagh_zhou_2005, title={(4,2)D projection-reconstruction experiments for protein backbone assignment: Application to human carbonic anhydrase II and calbindin D-28K}, volume={127}, ISSN={["0002-7863"]}, DOI={10.1021/ja0509580}, abstractNote={Projection-reconstruction NMR experiments have been shown to significantly reduce the acquisition time required to obtain protein backbone assignment data. To date, this concept has only been applied to smaller (15)N/(13)C-labeled proteins. Here, we show that projection-reconstruction NMR techniques can be extended to larger protonated and perdeuterated proteins. We present a suite of (4,2)D triple-resonance experiments for protein backbone assignment and a Hybrid Backprojection/Lower-Value algorithm for reconstructing data with relatively weak signal-to-noise ratios. In addition, we propose a sampling theorem and discuss its implication on the choice of projection angles. We demonstrate the efficacy of this approach using the 29 kDa protein, human carbonic anhydrase II and the 30 kDa protein, calbindin D(28K).}, number={24}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Venters, RA and Coggins, BE and Kojetin, D and Cavanagh, J and Zhou, P}, year={2005}, month={Jun}, pages={8785–8795} }
 @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{ulrich_kojetin_bassler_cavanagh_loria_2005, title={Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing}, volume={347}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2005.01.039}, abstractNote={The marine bacterium Vibrio harveyi controls its bioluminescence by a process known as quorum sensing. In this process, autoinducer molecules are detected by membrane-bound sensor kinase/response regulator proteins (LuxN and LuxQ) that relay a signal via a series of protein phosphorylation reactions to another response regulator protein, LuxO. Phosphorylated LuxO indirectly represses the expression of the proteins responsible for bioluminescence. Integral to this quorum sensing process is the function of the phosphotransferase protein, LuxU. LuxU acts to shuttle the phosphate from the membrane-bound proteins, LuxN and LuxQ, to LuxO. LuxU is a 114 amino acid residue monomeric protein. Solution NMR was used to determine the three-dimensional structure of LuxU. LuxU contains a four-helix bundle topology with the active-site histidine residue (His58) located on α-helix C and exposed to solution. The active site represents a cluster of positively charged residues located on an otherwise hydrophobic protein face. NMR spin-relaxation experiments identify a collection of flexible residues localized on the same region of LuxU as His58. The studies described here represent the first structural characterization of an isolated, monomeric bacterial phosphotransferase protein.}, number={2}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Ulrich, DL and Kojetin, D and Bassler, BL and Cavanagh, J and Loria, JP}, year={2005}, month={Mar}, pages={297–307} }
 @article{kojetin_thompson_benson_naylor_waterman_davies_opperman_stephenson_hoch_cavanagh_2005, title={Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for In vitro metalloregulation in the initiation of sporulation}, volume={18}, ISSN={["1572-8773"]}, DOI={10.1007/s10534-005-4303-8}, abstractNote={The presence of a divalent metal ion in a negatively charged aspartic acid pocket is essential for phosphorylation of response regulator proteins. Here, we present metal binding studies of the Bacillus subtilis response regulator Spo0F using NMR and microESI-MS. NMR studies show that the divalent metals Ca(2+), Mg(2+) and Mn(2+) primarily bind, as expected, in the Asp pocket phosphorylation site. However, identical studies with Cu(2+) show distinct binding effects in three specific locations: (i) the Asp pocket, (ii) a grouping of charged residues at a site opposite of the Asp pocket, and (iii) on the beta 4-alpha 4 loop and the beta 5/alpha 5 interface, particularly around and including H101. microESI-MS studies stoichiometrically confirm the NMR studies and demonstrate that most divalent metal ions bind to Spo0F primarily in a 1:1 ratio. Again, in the case of Cu(2+), multiple metal-bound species are observed. Subsequent experiments reveal that Mg(2+) supports phosphotransfer between KinA and Spo0F, while Cu(2+) fails to support KinA phosphotransfer. Additionally, the presence of Cu(2+) at non-lethal concentrations in sporulation media for B. subtilis and the related organism Pasteuria penetrans was found to inhibit spore formation while continuing to permit vegetative growth. Depending on the type of divalent metal ion present, in vitro phosphorylation of Spo0F by its cognate kinase KinA can be inhibited.}, number={5}, journal={BIOMETALS}, author={Kojetin, DJ and Thompson, RJ and Benson, LM and Naylor, S and Waterman, J and Davies, KG and Opperman, CH and Stephenson, K and Hoch, JA and Cavanagh, J}, year={2005}, month={Oct}, pages={449–466} }
 @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{ulrich_thompson_bassler_cavanagh_loria_2004, title={H-1, N-15, and C-13 chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU}, volume={29}, ISSN={["1573-5001"]}, DOI={10.1023/B:JNMR.0000034349.22942.e1}, number={4}, journal={JOURNAL OF BIOMOLECULAR NMR}, author={Ulrich, DL and Thompson, R and Bassler, B and Cavanagh, J and Loria, JP}, year={2004}, month={Aug}, pages={551–552} }
 @article{naylor_cavanagh_2004, title={Status of systems biology - does it have a future?}, volume={2}, ISSN={1741-8364}, url={http://dx.doi.org/10.1016/S1741-8364(04)02421-7}, DOI={10.1016/S1741-8364(04)02421-7}, number={5}, journal={Drug Discovery Today: BIOSILICO}, publisher={Elsevier BV}, author={Naylor, Stephen and Cavanagh, John}, year={2004}, month={Sep}, pages={171–174} }
 @article{kojetin_thompson_cavanagh_2004, title={Sub-classification of response regulators using the surface characteristics of their receiver domains (FEBS 27785) (vol 554, pg 231, 2003)}, volume={560}, ISSN={["1873-3468"]}, DOI={10.1016/s0014-5793(04)00063-8}, number={1-3}, journal={FEBS LETTERS}, author={Kojetin, DJ and Thompson, RJ and Cavanagh, J}, year={2004}, month={Feb}, pages={227–228} }
 @article{lutz_frank_craig_thompson_venters_kojetin_cavanagh_kumar_2003, title={Calbindin D-28K interacts with Ran-binding protein M: identification of interacting domains by NMR spectroscopy}, volume={303}, ISSN={["0006-291X"]}, DOI={10.1016/S0006-291X(03)00499-6}, abstractNote={Calbindin D28K is an EF-hand containing protein that plays a vital role in neurological function. We now show that calcium-loaded calbindin D28K interacts with Ran-binding protein M, a protein known to play a role in microtubule function. Using NMR methods, we show that a peptide, LASIKNR, derived from Ran-binding protein M, interacts with several regions of the calcium-loaded protein including the amino terminus and two other regions that exhibit conformational exchange on the NMR timescale. We suggest that the interaction between calbindin D28K and Ran-binding protein M may be important in calbindin D28K function.}, number={4}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, author={Lutz, W and Frank, EM and Craig, TA and Thompson, R and Venters, RA and Kojetin, D and Cavanagh, J and Kumar, R}, year={2003}, month={Apr}, pages={1186–1192} }
 @article{cavanagh_benson_thompson_naylor_2003, title={In-line desalting mass spectrometry for the study of noncovalent biological complexes}, volume={75}, ISSN={["1520-6882"]}, DOI={10.1021/ac030182q}, abstractNote={Electrospray ionization-mass spectrometry is becoming widely used as a high-throughput method for the study of biomolecular interactions. It allows for the analysis of complexes from heterogeneous mixtures with high sensitivity and selectivity. In many cases, biomolecules and their complexes must be stored in nonvolatile salt buffers and other solubilizing agents, such as organics or detergents, to maintain stability and integrity. To ensure an efficient electrospray process, desalting and exchanging the biomolecular solutions into a volatile buffer is imperative. Current off-line or on-line methods to accomplish this are time-consuming, frequently disrupt noncovalent interactions, and can result in considerable sample loss. Here we describe a simple, general, and highly efficient, rapid in-line desalting approach using a small gel cartridge to assist in the mass spectrometric analysis of biomolecules and their complexes. Though the method has broad applicability, we focus our analysis on proteins and demonstrate its usefulness by examining protein-metal, protein-protein, protein-DNA, and protein-RNA interactions. The method is shown to provide rapid direct analysis of analyte solutions containing salts, glycerol, organics, and involatile buffers without deleterious effects.}, number={14}, journal={ANALYTICAL CHEMISTRY}, author={Cavanagh, J and Benson, LM and Thompson, R and Naylor, S}, year={2003}, month={Jul}, pages={3281–3286} }
 @article{benson_kumar_cavanagh_naylor_2003, title={Protein-metal ion interactions, stoichiometries and relative affinities determined by on-line size exclusion gel filtration mass spectrometry}, volume={17}, ISSN={["0951-4198"]}, DOI={10.1002/rcm.903}, abstractNote={Abstract}, number={4}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Benson, LM and Kumar, R and Cavanagh, J and Naylor, S}, year={2003}, pages={267–271} }
 @article{kojetin_thompson_cavanagh_2003, title={Sub-classification of response regulators using the surface characteristics of their receiver domains}, volume={554}, ISSN={["0014-5793"]}, DOI={10.1016/S0014-5793(03)01167-0}, abstractNote={The omnipresent bacterial switch known as a two‐component system is comprised of a response regulator and a sensor kinase with which it interacts. Sensor kinases have been classified and further sub‐classified into groups based on their sequence similarity, loop lengths and domain organization. Response regulators have been classified predominantly by the identity and function of their output domains. Here, comparative based homology modeling of the receiver domains of the OmpR sub‐family of response regulators in Bacillus subtilis and Escherichia coli suggests further sub‐classification is possible. A color‐coded scale is used to show trends in surface hydrophobicity. For the OmpR receiver domains modeled these trends allow further sub‐classification. The specific surface regions used for this sub‐classification procedure correlate with clusters of residues that are important for interaction with cognate four helix bundle HisKA/Hpt domains.}, number={3}, journal={FEBS LETTERS}, author={Kojetin, DJ and Thompson, RJ and Cavanagh, J}, year={2003}, month={Nov}, pages={231–236} }
 @article{venters_benson_craig_paul_kordys_thompson_naylor_kumar_cavanagh_2003, title={The effects of Ca2+ binding on the conformation of calbindin D-28K: A nuclear magnetic resonance and microelectrospray mass spectrometry study}, volume={317}, ISSN={["0003-2697"]}, DOI={10.1016/S0003-2697(03)00084-8}, abstractNote={Calbindin D(28K) is a six-EF-hand calcium-binding protein found in the brain, peripheral nervous system, kidney, and intestine. There is a paucity of information on the effects of calcium binding on calbindin D(28K) structure. To further examine the mechanism and structural consequences of calcium binding to calbindin D(28K) we performed detailed complementary heteronuclear NMR and microelectrospray mass spectrometry investigations of the calcium-induced conformational changes of calbindin D(28K). The combined use of these two powerful analytical techniques clearly and very rapidly demonstrates the following: (i). apo-calbindin D(28K) has an ordered structure which changes to a notably different ordered conformation upon Ca(2+) loading, (ii). calcium binding is a sequential process and not a simultaneous event, and (iii). EF-hands 1, 3, 4, and 5 take up Ca(2+), whereas EF-hands 2 and 6 do not. Our results support the opinion that calbindin D(28K) has characteristics of both a calcium sensor and a buffer.}, number={1}, journal={ANALYTICAL BIOCHEMISTRY}, author={Venters, RA and Benson, LM and Craig, TA and Paul, KH and Kordys, DR and Thompson, R and Naylor, S and Kumar, R and Cavanagh, J}, year={2003}, month={Jun}, pages={59–66} }
 @article{helton_kojetin_cavanagh_horne_2002, title={Alternative splicing of a beta(4) subunit proline-rich motif regulates voltage-dependent gating and toxin block of Ca(v)2.1 Ca2+ channels}, volume={22}, DOI={10.1523/jneurosci.22-21-09331.2002}, abstractNote={Ca2+ channel β subunits modify α1 subunit gating properties through direct interactions with intracellular linker domains. In a previous report (Helton and Horne, 2002), we showed that alternative splicing of the β4 subunit had α1 subunit subtype-specific effects on Ca2+ channel activation and fast inactivation. We extend these findings in the present report to include effects on slow inactivation and block by the peptide toxin ω-conotoxin (CTx)-MVIIC. N-terminal deletion and site-directed mutagenesis experiments revealed that the effects of alternative splicing on toxin block and all aspects of gating could be attributed to a proline-rich motif found within N-terminal β4b amino acids 10–20. Interestingly, this motif is conserved within the third postsynaptic density-95 (PSD-95)/Discs large/zona occludens-1 domain of the distantly related membrane-associated guanylate kinase homolog, PSD-95. Sequence identity of ∼30% made possible the building of β4a and β4bthree-dimensional structural models using PSD-95 as the target sequence. The models (1) reveal that alternative splicing of the β4 N terminus results in dramatic differences in surface charge distribution and (2) localize the proline-rich motif of β4b to an extended arm structure that flanks what would be the equivalent of a highly modified PSD-95 carboxylate binding loop. Northern blot analysis revealed a markedly different pattern of distribution for β4a versus β4bin the human CNS. Whereas β4a is distributed throughout evolutionarily older regions of the CNS, β4b is concentrated heavily in the forebrain. These results raise interesting questions about the functional role that alternative splicing of the β4 subunit has played in the evolution of complex neural networks.}, number={21}, journal={Journal of Neuroscience}, author={Helton, T. D. and Kojetin, D. J. and Cavanagh, J. and Horne, W. A.}, year={2002}, pages={9331–9339} }
 @article{venters_thompson_cavanagh_2002, title={Current approaches for the study of large proteins by NMR}, volume={602}, ISSN={["1872-8014"]}, DOI={10.1016/s0022-2860(01)00690-1}, abstractNote={An overview of current methods employed for characterizing larger (>25 kDa) proteins by NMR is presented. These techniques include: the attenuation of T2 relaxation effects by offsetting dipole–dipole and chemical shift anisotropy relaxation mechanisms (TROSY); the extraction of residual dipolar couplings from partially oriented molecules; the elimination of relaxation pathways by incorporating deuterium nuclei into protein samples; the easing of resonance overlap by isotopically labeling only specific protein segments; and the decrease of rotational correlation times by dissolving proteins in low viscosity solvents.}, journal={JOURNAL OF MOLECULAR STRUCTURE}, author={Venters, RA and Thompson, R and Cavanagh, J}, year={2002}, month={Jan}, pages={275–292} }
 @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} }
 @article{sehgal_tompson_cavanagh_kelly_2002, title={Structural and catalytic response to temperature and cosolvents of carboxylesterase EST1 from the extremely thermoacidophilic archaeon Sulfolobus solfataricus P1}, volume={80}, ISSN={["0006-3592"]}, DOI={10.1002/bit.10433}, abstractNote={Abstract}, number={7}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Sehgal, AC and Tompson, R and Cavanagh, J and Kelly, RM}, year={2002}, month={Dec}, pages={784–793} }
 @article{cavanagh_venters_2001, title={Protein dynamic studies move to a new time slot}, volume={8}, ISSN={["1072-8368"]}, DOI={10.1038/nsb1101-912}, number={11}, journal={NATURE STRUCTURAL BIOLOGY}, author={Cavanagh, J and Venters, RA}, year={2001}, month={Nov}, pages={912–914} }
 @article{vaughn_feher_bracken_cavanagh_2001, title={The DNA-binding domain in the Bacillus subtilis transition-state regulator AbrB employs significant motion for promiscuous DNA recognition}, volume={305}, ISSN={["0022-2836"]}, DOI={10.1006/jmbi.2000.4305}, abstractNote={AbrB is a Bacillus subtilis protein responsible for regulating a diverse array of unrelated genes during periods of sub-optimal growth conditions. DNA binding by AbrB is unique in that sequence recognition is specific, yet no obvious consensus sequence of bound promoter regions is apparent. The N-terminal domain is a recently characterized representative of a novel class of DNA-binding proteins that possess a looped-hinge helix DNA-binding topology. Although the structural characterization of this DNA-binding topology contributed to an understanding of the architectural basis for recognition of DNA target sequences, specific mechanisms responsible for promiscuity in DNA sequence recognition still were not apparent. Analysis of (15)N backbone relaxation parameters shows that dynamic motion of regions directly linked to DNA binding show concerted motion on the microsecond-millisecond timescale. Furthermore, dynamic motion of the hinge region suggests that the DNA-binding region is capable of conformational orientations that allow it to accommodate DNA sequence variability in the cognate binding sites.}, number={3}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Vaughn, JL and Feher, VA and Bracken, C and Cavanagh, J}, year={2001}, month={Jan}, pages={429–439} }
 @article{vaughn_feher_naylor_strauch_cavanagh_2000, title={Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator AbrB}, volume={7}, number={12}, journal={Nature Structural Biology}, author={Vaughn, J. L. and Feher, V. and Naylor, S. and Strauch, M. A. and Cavanagh, J.}, year={2000}, pages={1139–1146} }
 @article{feher_zapf_hoch_whiteley_cavanagh_w._1995, title={Functional implications of the structure of the bacterial response regulator Spo0F}, volume={Suppl. 21B}, journal={Journal of Cellular Biochemistry}, author={Feher, V. A. and Zapf, J. and Hoch, J. A. and Whiteley, J. M. and Cavanagh, J. and W., Dahlquist F.}, year={1995}, pages={25} }
 @article{solution structure of the bacillus subtilis glucose permease iia domain and its interaction with another phosphocarrier protein hpr. j_1993, volume={Suppl. 17C}, journal={Journal of Cellular Biochemistry}, year={1993}, pages={271} }