Benjamin Bobay
Research Associate, Senior
I am the Assistant Director of the Duke University NMR Center and a senior research associate in the Duke Radiology Department. I was originally trained as a structural biochemist with an emphasis on utilizing NMR and continue to use this technique daily helping collaborators characterize protein structures and small molecules through a diverse set of NMR experiments. Through the structural characterization of various proteins, from both planta and eukaryotes, I have developed a robust protocol of utilizing computational biology for describing binding events, mutations, post-translations modifications (PTMs), and/or general behavior within in silico
solution scenarios. I have utilized these techniques in collaborations ranging from plant pathologists at the Swammerdam Institute for Life Sciences department at the University of Amsterdam to biomedical engineers at North Carolina State University to professors in the Pediatrics department at Duke University. These studies have centered around the structural and functional consequences of PTMs (such as phosphorylation), mutation events, truncation of multi-domain proteins, dimer pulling experiments, to screening of large databases of ligands for potential binding events. Through this combination of NMR and computational biology I have amassed 50 peer-reviewed published articles and countless roles on scientific projects, as well as the development of several tutorials with regard to the creation of ligand databases and high-throughput screening of large databases utilizing several different molecular dynamic and computational docking programs.
Current Research Interests
I'm currently a Senior Research Associate at the Duke Magnetic Resonance Spectroscopy Center (DMRSC) and have over 20 years of experience in the characterization of protein structures and protein:small ligand interactions. The DMRSC provides access to high field NMR instrumentation, training in the use of NMR methods, and expert consultation on advanced NMR applications. The Center serves as a research resource and shared instrument facility for research programs at Duke and in the Southeastern region. My efforts are dedicated to the Chemistry Department and the maintenance, operation, training, etc. of the FFSC NMR facility as well as my own research interests. My interests lie with utilizing NMR, computational docking, and molecular dynamics simulations for characterization of bio-molecules and their interactions.
I am currently involved with one major research effort. I have an ongoing project with a multi-PI RO1 team aimed at developing anti-fungal inhibitors. We have made significant advances towards the goal of developing a fungal specific, non-immunosuppressive calcineurin inhibitors and have published five peer reviewed journal articles over the past few years.
My research interest focus on the determining structure to function activities of biomolecules (protein, DNA, RNA, carbohydrates, polymers, etc.) with ligands. Primarily my research is aimed at determining the structure, dynamics and function of important proteins and protein complexes using high-resolution Nuclear Magnetic Resonance Spectroscopy. My early work solely centered around the use of NMR experiments to characterize protein structures. Throughout my career I have continued my efforts in NMR and have added computational modeling, docking, and dynamic simulations with a heavy reliance on statistical analysis of those results. This unique combination has led to many peer reviewed manuscripts with significant results.
I am currently involved with one major research effort. I have an ongoing project with a multi-PI RO1 team aimed at developing anti-fungal inhibitors. We have made significant advances towards the goal of developing a fungal specific, non-immunosuppressive calcineurin inhibitors and have published five peer reviewed journal articles over the past few years.
My research interest focus on the determining structure to function activities of biomolecules (protein, DNA, RNA, carbohydrates, polymers, etc.) with ligands. Primarily my research is aimed at determining the structure, dynamics and function of important proteins and protein complexes using high-resolution Nuclear Magnetic Resonance Spectroscopy. My early work solely centered around the use of NMR experiments to characterize protein structures. Throughout my career I have continued my efforts in NMR and have added computational modeling, docking, and dynamic simulations with a heavy reliance on statistical analysis of those results. This unique combination has led to many peer reviewed manuscripts with significant results.
Current Appointments & Affiliations
- Research Associate, Senior, Radiology, Clinical Science Departments
Contact Information
- 308 Research Dr, Durham, NC 27710
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ben.bobay@duke.edu
+1 919 613 8884
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Duke NMR Center
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Google Scholar
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Linkedin
- Expertise
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Subject Headings
- Anti-fungal Drug Action Mechanisms
- Antifungal Agents
- Bacterial Proteins
- Biochemistry
- Biochemistry, molecular biology
- Chemistry
- Chemistry (general)
- Computational Biology
- Cyclic peptides
- DNA-Binding Proteins
- Ligand binding (Biochemistry)
- Microbial peptides
- Molecular Docking Simulation
- Molecular dynamics
- Nuclear magnetic resonance
- Nuclear magnetic resonance spectroscopy
- Peptides
- Plant Proteins
- Proteins
- RNA-protein interactions
- Recombinant Proteins
- Structure-activity relationships (Biochemistry)
- Research
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Selected Grants
- Structural Biological Development of Fungal-Specific Calcineurin Inhibitors awarded by National Institutes of Health 2014 - 2022
- Calcineurin regulatory network control of Aspergillus fumigatus hyphal septation awarded by Arkansas Children's Hospital Research Institute 2022
- Calcineurin regulatory network control of Aspergillus fumigatus hyphal septation awarded by National Institutes of Health 2021 - 2022
- Structural Biological Development of Fungal-Specific Calcineurin Inhibitors awarded by National Institutes of Health 2014 - 2019
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External Relationships
- Prometic
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Mukherjee, Rudra Palash, Geok-Yong Yow, Samuel Sarakbi, Stefano Menegatti, Patrick V. Gurgel, Ruben G. Carbonell, and Benjamin G. Bobay. “Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase.” Computational Biology and Chemistry 102 (February 2023): 107797. https://doi.org/10.1016/j.compbiolchem.2022.107797.Full Text
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Juvvadi, Praveen R., Benjamin G. Bobay, D Christopher Cole, Monaf Awwa, and William J. Steinbach. “Calcineurin Inhibitor CN585 Exhibits Off-Target Effects in the Human Fungal Pathogen Aspergillus fumigatus.” Journal of Fungi (Basel, Switzerland) 8, no. 12 (December 2022): 1281. https://doi.org/10.3390/jof8121281.Full Text
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Hoy, Michael J., Eunchong Park, Hyunji Lee, Won Young Lim, D Christopher Cole, Nicholas D. DeBouver, Benjamin G. Bobay, et al. “Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus.” Mbio 13, no. 3 (June 28, 2022): e0104922. https://doi.org/10.1128/mbio.01049-22.Full Text Link to Item
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Gobeil, Sophie M-C, Benjamin G. Bobay, Praveen R. Juvvadi, D Christopher Cole, Joseph Heitman, William J. Steinbach, Ronald A. Venters, and Leonard D. Spicer. “Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs.” Mbio 12, no. 6 (December 21, 2021): e0300021. https://doi.org/10.1128/mBio.03000-21.Full Text Link to Item
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Dahora, Lindsay C., Marije K. Verheul, Katherine L. Williams, Celina Jin, Lisa Stockdale, Guy Cavet, Eldar Giladi, et al. “Salmonella Typhi Vi capsule prime-boost vaccination induces convergent and functional antibody responses.” Sci Immunol 6, no. 64 (October 29, 2021): eabj1181. https://doi.org/10.1126/sciimmunol.abj1181.Full Text Link to Item
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Overdahl, Kirsten E., David Gooden, Benjamin Bobay, Gordon J. Getzinger, Heather M. Stapleton, and P Lee Ferguson. “Characterizing azobenzene disperse dyes in commercial mixtures and children's polyester clothing.” Environmental Pollution (Barking, Essex : 1987) 287 (October 2021): 117299. https://doi.org/10.1016/j.envpol.2021.117299.Full Text Open Access Copy
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Ascencio-Ibáñez, J Trinidad, and Benjamin G. Bobay. “Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep.” Biochemistry 60, no. 37 (September 2021): 2795–2809. https://doi.org/10.1021/acs.biochem.1c00408.Full Text
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Shwab, E Keats, Praveen R. Juvvadi, Greg Waitt, Shareef Shaheen, John Allen, Erik J. Soderblom, Benjamin G. Bobay, Yohannes G. Asfaw, M Arthur Moseley, and William J. Steinbach. “The Protein Kinase A-Dependent Phosphoproteome of the Human Pathogen Aspergillus fumigatus Reveals Diverse Virulence-Associated Kinase Targets.” Mbio 11, no. 6 (December 15, 2020). https://doi.org/10.1128/mBio.02880-20.Full Text Link to Item
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Brumos, Javier, Benjamin G. Bobay, Cierra A. Clark, Jose M. Alonso, and Anna N. Stepanova. “Structure-Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes.” Plant Physiology 183, no. 3 (July 2020): 1110–25. https://doi.org/10.1104/pp.20.00310.Full Text
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Juvvadi, Praveen R., Benjamin G. Bobay, Sophie M. C. Gobeil, D Christopher Cole, Ronald A. Venters, Joseph Heitman, Leonard D. Spicer, and William J. Steinbach. “FKBP12 dimerization mutations effect FK506 binding and differentially alter calcineurin inhibition in the human pathogen Aspergillus fumigatus.” Biochem Biophys Res Commun 526, no. 1 (May 21, 2020): 48–54. https://doi.org/10.1016/j.bbrc.2020.03.062.Full Text Link to Item
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Gobeil, Sophie M-C, Benjamin Bobay, Praveen Juvvadi, Christopher Cole, Joseph Heitman, William Steinbach, Ronald Venters, and Leonard Spicer. “Leveraging Fungal Calcineurin-Inhibitor Structures, Biophysics and Dynamics to Design Selective and Non-Immunosuppressive FK506 Analogs,” 2020. https://doi.org/10.1101/2020.04.14.039800.Full Text
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Milton, Morgan E., G Logan Draughn, Benjamin G. Bobay, Sean D. Stowe, Andrew L. Olson, Erik A. Feldmann, Richele J. Thompson, et al. “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.” Journal of Molecular Biology 432, no. 2 (January 2020): 343–57. https://doi.org/10.1016/j.jmb.2019.08.019.Full Text
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Juvvadi, Praveen R., David Fox, Benjamin G. Bobay, Michael J. Hoy, Sophie M. C. Gobeil, Ronald A. Venters, Zanetta Chang, et al. “Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents.” Nat Commun 10, no. 1 (September 19, 2019): 4275. https://doi.org/10.1038/s41467-019-12199-1.Full Text Link to Item
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Bordelon, Tee, Benjamin Bobay, Andrew Murphy, Hannah Reese, Calvin Shanahan, Fuad Odeh, Amanda Broussard, Chad Kormos, and Stefano Menegatti. “Translating antibody-binding peptides into peptoid ligands with improved affinity and stability.” Journal of Chromatography. A 1602 (September 2019): 284–99. https://doi.org/10.1016/j.chroma.2019.05.047.Full Text
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Maio, Francesca, Manuel Arroyo-Mateos, Benjamin G. Bobay, Eduardo R. Bejarano, Marcel Prins, and Harrold A. van den Burg. “A Lysine Residue Essential for Geminivirus Replication Also Controls Nuclear Localization of the Tomato Yellow Leaf Curl Virus Rep Protein.” Journal of Virology 93, no. 10 (May 2019): e01910–18. https://doi.org/10.1128/jvi.01910-18.Full Text
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Gobeil, Sophie M. C., Benjamin G. Bobay, Leonard D. Spicer, and Ronald A. Venters. “15N, 13C and 1H resonance assignments of FKBP12 proteins from the pathogenic fungi Mucor circinelloides and Aspergillus fumigatus.” Biomol Nmr Assign 13, no. 1 (April 2019): 207–12. https://doi.org/10.1007/s12104-019-09878-x.Full Text Link to Item
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Shen, Wei, Benjamin G. Bobay, Laura A. Greeley, Maria I. Reyes, Cyprian A. Rajabu, R Kevin Blackburn, Mary Beth Dallas, Michael B. Goshe, Jose T. Ascencio-Ibáñez, and Linda Hanley-Bowdoin. “Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection.” Plant Physiology 178, no. 1 (September 2018): 372–89. https://doi.org/10.1104/pp.18.00268.Full Text
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Draughn, G Logan, Morgan E. Milton, Erik A. Feldmann, Benjamin G. Bobay, Braden M. Roth, Andrew L. Olson, Richele J. Thompson, Luis A. Actis, Christopher Davies, and John Cavanagh. “The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism.” Journal of Molecular Biology 430, no. 6 (March 2018): 806–21. https://doi.org/10.1016/j.jmb.2018.02.002.Full Text
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Milton, Morgan E., C Leigh Allen, Erik A. Feldmann, Benjamin G. Bobay, David K. Jung, Matthew D. Stephens, Roberta J. Melander, et al. “Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds.” Molecular Microbiology 106, no. 2 (October 2017): 223–35. https://doi.org/10.1111/mmi.13759.Full Text
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Kish, William S., Hiroyuki Sachi, Amith D. Naik, Matthew K. Roach, Benjamin G. Bobay, Robert K. Blackburn, Stefano Menegatti, and Ruben G. Carbonell. “Design, selection, and development of cyclic peptide ligands for human erythropoietin.” Journal of Chromatography. A 1500 (June 2017): 105–20. https://doi.org/10.1016/j.chroma.2017.04.019.Full Text
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Whitham, Jason M., Mark J. Schulte, Benjamin G. Bobay, Jose M. Bruno-Barcena, Mari S. Chinn, Michael C. Flickinger, Joel J. Pawlak, and Amy M. Grunden. “Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain.” Applied Microbiology and Biotechnology 101, no. 4 (February 2017): 1615–30. https://doi.org/10.1007/s00253-016-7978-6.Full Text
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Olson, A. L., R. J. Thompson, J. Cavanagh, E. A. Feldmann, and B. G. Bobay. “The solution NMR structure of the C-terminal effector domain of BfmR from Acinetobacter baumannii,” January 18, 2017. https://doi.org/10.2210/pdb2naz/pdb.Full Text
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Moore, Matthew D., Benjamin G. Bobay, Brittany Mertens, and Lee-Ann Jaykus. “Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to That of Receptors and Discriminates Particle Functionality.” Msphere 1, no. 6 (November 2016): e00298–e00216. https://doi.org/10.1128/msphere.00298-16.Full Text
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Wojnilowicz, M., M. Tortora, B. G. Bobay, E. Santiso, M. Caruso, L. Micheli, M. Venanzi, S. Menegatti, and F. Cavalieri. “A combined approach for predicting the cytotoxic effect of drug-nanoaggregates.” Journal of Materials Chemistry. B 4, no. 40 (October 2016): 6516–23. https://doi.org/10.1039/c6tb02105k.Full Text
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Menegatti, Stefano, Benjamin G. Bobay, Kevin L. Ward, Tuhidul Islam, William S. Kish, Amith D. Naik, and Ruben G. Carbonell. “Design of protease-resistant peptide ligands for the purification of antibodies from human plasma.” Journal of Chromatography. A 1445 (May 2016): 93–104. https://doi.org/10.1016/j.chroma.2016.03.087.Full Text
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Harris, Kimberly A., Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, and Paul F. Agris. “NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.” The Journal of Biological Chemistry 290, no. 33 (August 2015): 20032–43. https://doi.org/10.1074/jbc.m114.631242.Full Text
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Harris, K. A., B. G. Bobay, K. L. Sarachan, A. F. Sims, Y. Bilbille, C. Deutsch, D. Iwata-Reuyl, and P. F. Agris. “Structure of the E. coli Threonylcarbamoyl-AMP Synthase TSAC,” June 17, 2015. https://doi.org/10.2210/pdb2mx1/pdb.Full Text
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Bobay, B. G., P. M. DiGennaro, and D. M. Bird. “Solution structure of the CLAVATA encoded peptide of Arabidopsis thaliana - AtCLE10,” January 14, 2015. https://doi.org/10.2210/pdb2mid/pdb.Full Text
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Bobay, B. G., P. M. DiGennaro, and D. M. Bird. “Solution structure of the CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4,” December 24, 2014. https://doi.org/10.2210/pdb2mif/pdb.Full Text
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Bobay, B. G., P. M. DiGennaro, and D. M. Bird. “Solution structure of the CLAVATA encoded peptide of Arabidopsis thaliana - AtCLE44,” December 24, 2014. https://doi.org/10.2210/pdb2mie/pdb.Full Text
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Bobay, B. G., P. M. DiGennaro, and D. M. Bird. “Solution structure of the CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE5,” December 24, 2014. https://doi.org/10.2210/pdb2mig/pdb.Full Text
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Bobay, B. G., P. M. Digennaro, and D. M. Bird. “Solution structure of the CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE6/7,” December 24, 2014. https://doi.org/10.2210/pdb2mih/pdb.Full Text
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Olson, Andrew L., Ashley T. Tucker, Benjamin G. Bobay, Erik J. Soderblom, M Arthur Moseley, Richele J. Thompson, and John Cavanagh. “Structure and DNA-binding traits of the transition state regulator AbrB.” Structure 22, no. 11 (November 4, 2014): 1650–56. https://doi.org/10.1016/j.str.2014.08.018.Full Text Link to Item
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Tóth, Eszter, Olivér Ozohanics, Balázs Bobály, Ágnes Gömöry, Anita Jekő, László Drahos, and Károly Vékey. “HPLC enrichment/isolation of proteins for post-translational modification studies from complex mixtures.” Journal of Pharmaceutical and Biomedical Analysis 98 (September 2014): 393–400. https://doi.org/10.1016/j.jpba.2014.06.025.Full Text
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Tucker, Ashley T., Benjamin G. Bobay, Allison V. Banse, Andrew L. Olson, Erik J. Soderblom, M Arthur Moseley, Richele J. Thompson, Kristen M. Varney, Richard Losick, and John Cavanagh. “A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA.” J Mol Biol 426, no. 9 (May 1, 2014): 1911–24. https://doi.org/10.1016/j.jmb.2014.02.010.Full Text Link to Item
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Bobay, Benjamin G., Richele J. Thompson, Debra L. Milton, and John Cavanagh. “Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum.” Biomolecular Nmr Assignments 8, no. 1 (April 2014): 177–79. https://doi.org/10.1007/s12104-013-9478-2.Full Text
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Bobay, B. G., P. DiGennaro, and D. M. Bird. “Solution structure of the C-terminally encoded peptide of the plant parasitic nematode Meloidogyne hapla - CEP11,” December 11, 2013. https://doi.org/10.2210/pdb2mfm/pdb.Full Text
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Bobay, B. G., P. DiGennaro, and D. M. Bird. “Solution structure of the C-terminally encoded peptide of the model plant host Medicago truncatula - CEP1,” December 11, 2013. https://doi.org/10.2210/pdb2mfo/pdb.Full Text
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Bobay, Benjamin G., Peter DiGennaro, Elizabeth Scholl, Nijat Imin, Michael A. Djordjevic, and David Mck Bird. “Solution NMR studies of the plant peptide hormone CEP inform function.” Febs Letters 587, no. 24 (December 2013): 3979–85. https://doi.org/10.1016/j.febslet.2013.10.033.Full Text
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Bobay, B. G., A. T. Tucker, R. Losick, and J. Cavanagh. “Structure of the biofilm matrix promoter AbbA from B. subtilis,” September 11, 2013. https://doi.org/10.2210/pdb2lzf/pdb.Full Text
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Harris, Kimberly A., Benjamin G. Bobay, Yann Bilbille, and Paul F. Agris. “27 Structural analyses by NMR reveal insights into the enzymatic mechanism of tRNA t6A modification biosynthesis.” Journal of Biomolecular Structure and Dynamics 31, no. sup1 (January 2013): 17–17. https://doi.org/10.1080/07391102.2013.786459.Full Text
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Thompson, Richele J., Benjamin G. Bobay, Sean D. Stowe, Andrew L. Olson, Lingling Peng, Zhaoming Su, Luis A. Actis, Christian Melander, and John Cavanagh. “Identification of BfmR, a response regulator involved in biofilm development, as a target for a 2-Aminoimidazole-based antibiofilm agent.” Biochemistry 51, no. 49 (December 2012): 9776–78. https://doi.org/10.1021/bi3015289.Full Text
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Bobay, Benjamin G., Amanda L. Stewart, Ashley T. Tucker, Richele J. Thompson, Kristen M. Varney, and John Cavanagh. “Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3.” Febs Letters 586, no. 20 (October 2012): 3582–89. https://doi.org/10.1016/j.febslet.2012.08.032.Full Text
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Olson, Andrew L., Benjamin G. Bobay, Christian Melander, and John Cavanagh. “¹H, ¹³C, and ¹⁵N resonance assignments and secondary structure prediction of the full-length transition state regulator AbrB from Bacillus anthracis.” Biomolecular Nmr Assignments 6, no. 1 (April 2012): 95–98. https://doi.org/10.1007/s12104-011-9333-2.Full Text
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Bobay, Benjamin G., James A. Hoch, and John Cavanagh. “Dynamics and activation in response regulators: the β4-α4 loop.” Biomolecular Concepts 3, no. 2 (February 2012): 175–82. https://doi.org/10.1515/bmc-2011-0063.Full Text
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Bobay, Benjamin G., Richele J. Thompson, James A. Hoch, and John Cavanagh. “Long range dynamic effects of point-mutations trap a response regulator in an active conformation.” Febs Letters 584, no. 19 (October 2010): 4203–7. https://doi.org/10.1016/j.febslet.2010.08.051.Full Text
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Yang, Haiou, Patrick V. Gurgel, D Keith Williams, Benjamin G. Bobay, John Cavanagh, David C. Muddiman, and Ruben G. Carbonell. “Binding site on human immunoglobulin G for the affinity ligand HWRGWV.” Journal of Molecular Recognition : Jmr 23, no. 3 (May 2010): 271–82. https://doi.org/10.1002/jmr.967.Full Text
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Hobbs, C. A., B. G. Bobay, R. J. Thompson, M. Perego, and J. Cavanagh. “NMR solution structure of the DNA binding domain of Competence protein A,” April 7, 2010. https://doi.org/10.2210/pdb2krf/pdb.Full Text
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Hobbs, Carey A., Benjamin G. Bobay, Richele J. Thompson, Marta Perego, and John Cavanagh. “NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A.” Journal of Molecular Biology 398, no. 2 (April 2010): 248–63. https://doi.org/10.1016/j.jmb.2010.03.003.Full Text
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Davis, Michael F., Benjamin G. Bobay, and Stefan Franzen. “Determination of separate inhibitor and substrate binding sites in the dehaloperoxidase-hemoglobin from Amphitrite ornata.” Biochemistry 49, no. 6 (February 2010): 1199–1206. https://doi.org/10.1021/bi9018576.Full Text
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Hobbs, Carey A., Leesa J. Deterding, Lalith Perera, Benjamin G. Bobay, Richele J. Thompson, Thomas A. Darden, John Cavanagh, and Kenneth B. Tomer. “Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry.” Biochemistry 48, no. 36 (September 2009): 8603–14. https://doi.org/10.1021/bi900350q.Full Text
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Cavanagh, J., B. G. Bobay, D. M. Sullivan, and R. J. Thompson. “DNA bound structure of the N-terminal domain of AbrB,” November 11, 2008. https://doi.org/10.2210/pdb2k1n/pdb.Full Text
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Sullivan, D. M., B. G. Bobay, D. J. Kojetin, R. J. Thompson, M. Rance, M. A. Strauch, and J. Cavanagh. “RDC-refined solution structure of the N-terminal DNA recognition domain of the Bacillus subtilis transition-state regulator SpoVT,” November 11, 2008. https://doi.org/10.2210/pdb2ro5/pdb.Full Text
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Sullivan, D. M., B. G. Bobay, D. J. Kojetin, R. J. Thompson, M. Rance, M. A. Strauch, and J. Cavanagh. “RDC-refined Solution Structure of the N-terminal DNA Recognition Domain of the Bacillus subtilis Transition-state Regulator AbrB,” November 11, 2008. https://doi.org/10.2210/pdb2ro4/pdb.Full Text
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Sullivan, D. M., B. G. Bobay, K. J. Douglas, R. J. Thompson, M. Rance, M. A. Strauch, and J. Cavanagh. “RDC-refined Solution Structure of the N-terminal DNA Recognition Domain of the Bacillus subtilis Transition-state Regulator Abh,” November 11, 2008. https://doi.org/10.2210/pdb2ro3/pdb.Full Text
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Sullivan, Daniel M., Benjamin G. Bobay, Douglas J. Kojetin, Richele J. Thompson, Mark Rance, Mark A. Strauch, and John Cavanagh. “Insights into the nature of DNA binding of AbrB-like transcription factors.” Structure (London, England : 1993) 16, no. 11 (November 2008): 1702–13. https://doi.org/10.1016/j.str.2008.08.014.Full Text
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Szurmant, Hendrik, Benjamin G. Bobay, Robert A. White, Daniel M. Sullivan, Richele J. Thompson, Terence Hwa, James A. Hoch, and John Cavanagh. “Co-evolving motions at protein-protein interfaces of two-component signaling systems identified by covariance analysis.” Biochemistry 47, no. 30 (July 2008): 7782–84. https://doi.org/10.1021/bi8009604.Full Text
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Bobay, B. G., P. D. McLaughlin, R. J. Thompson, J. A. Hoch, and J. Cavanagh. “NMR Solution Structure of the Hyper-Sporulation Response Regulator Spo0F Mutant H101A from Bacillus subtilis,” February 5, 2008. https://doi.org/10.2210/pdb2jvi/pdb.Full Text
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Bobay, B. G., P. D. McLaughlin, R. J. Thompson, J. A. Hoch, and J. Cavanagh. “NMR Solution Structure of the Hyper-Sporulation Response Regulator Spo0F Mutant L66A from Bacillus subtilis,” February 5, 2008. https://doi.org/10.2210/pdb2jvk/pdb.Full Text
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Bobay, B. G., P. D. McLaughlin, R. J. Thompson, J. A. Hoch, and J. Cavanagh. “NMR Solution Structure of the Hyper-Sporulation Response Regulator Spo0F Mutant I90A from Bacillus subtilis,” February 5, 2008. https://doi.org/10.2210/pdb2jvj/pdb.Full Text
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Burns, Virginia A., Benjamin G. Bobay, Anne Basso, John Cavanagh, and Christian Melander. “Targeting RNA with cysteine-constrained peptides.” Bioorganic & Medicinal Chemistry Letters 18, no. 2 (January 2008): 565–67. https://doi.org/10.1016/j.bmcl.2007.11.096.Full Text
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Strauch, Mark A., Benjamin G. Bobay, John Cavanagh, Fude Yao, Angelo Wilson, and Yoann Le Breton. “Abh and AbrB control of Bacillus subtilis antimicrobial gene expression.” Journal of Bacteriology 189, no. 21 (November 2007): 7720–32. https://doi.org/10.1128/jb.01081-07.Full Text
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Kordys, David R., Benjamin G. Bobay, Richele J. Thompson, Ronald A. Venters, and John Cavanagh. “Peptide binding proclivities of calcium loaded calbindin-D28k.” Febs Lett 581, no. 24 (October 2, 2007): 4778–82. https://doi.org/10.1016/j.febslet.2007.09.004.Full Text Link to Item
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McLaughlin, Patrick D., Benjamin G. Bobay, Erin J. Regel, Richele J. Thompson, James A. Hoch, and John Cavanagh. “Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition.” Febs Letters 581, no. 7 (April 2007): 1425–29. https://doi.org/10.1016/j.febslet.2007.02.061.Full Text
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Soderblom, Erik J., Benjamin G. Bobay, John Cavanagh, and Michael B. Goshe. “Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents.” Rapid Commun Mass Spectrom 21, no. 21 (2007): 3395–3408. https://doi.org/10.1002/rcm.3213.Full Text Link to Item
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Bobay, Benjamin G., Geoffrey A. Mueller, Richele J. Thompson, Alexey G. Murzin, Ronald A. Venters, Mark A. Strauch, and John Cavanagh. “NMR structure of AbhN and comparison with AbrBN: FIRST insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins.” J Biol Chem 281, no. 30 (July 28, 2006): 21399–409. https://doi.org/10.1074/jbc.M601963200.Full Text Link to Item
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Cavanagh, J., and B. G. Bobay. “Solution Structure of the N-Terminal DNA Recognition Domain of the Bacillus Subtilis Transcription-State Regulator ABH,” May 23, 2006. https://doi.org/10.2210/pdb2fy9/pdb.Full Text
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Bobay, Benjamin G., Antonina Andreeva, Geoffrey A. Mueller, John Cavanagh, and Alexey G. Murzin. “Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins.” Febs Letters 579, no. 25 (October 2005): 5669–74. https://doi.org/10.1016/j.febslet.2005.09.045.Full Text
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Bobay, B. G., A. Andreeva, G. A. Mueller, J. Cavanagh, and A. G. Murzin. “Solution Structure of the N-terminal DNA Recognition Domain of the Bacillus subtilis Transcription-State Regulator AbrB,” March 15, 2005. https://doi.org/10.2210/pdb1z0r/pdb.Full Text
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Bobay, Benjamin G., Linda Benson, Stephen Naylor, Brett Feeney, A Clay Clark, Michael B. Goshe, Mark A. Strauch, Richele Thompson, and John Cavanagh. “Evaluation of the DNA binding tendencies of the transition state regulator AbrB.” Biochemistry 43, no. 51 (December 2004): 16106–18. https://doi.org/10.1021/bi048399h.Full Text
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Benson, Linda M., Jeffrey L. Vaughn, Mark A. Strauch, Benjamin G. Bobay, Richele Thompson, Stephen Naylor, and John Cavanagh. “Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry.” Analytical Biochemistry 306, no. 2 (July 2002): 222–27. https://doi.org/10.1006/abio.2002.5704.Full Text
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Cavanagh, John, Richele Thompson, Benjamin Bobay, Linda M. Benson, and Stephen Naylor. “Stoichiometries of protein-protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry.” Biochemistry 41, no. 25 (June 2002): 7859–65. https://doi.org/10.1021/bi0202225.Full Text
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Pop, C., Y. R. Chen, B. Smith, K. Bose, B. Bobay, A. Tripathy, S. Franzen, and A. C. Clark. “Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer.” Biochemistry 40, no. 47 (November 2001): 14224–35. https://doi.org/10.1021/bi011037e.Full Text
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Conference Papers
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Milton, Morgan Eilise, G Logan Draughn, Benjamin G. Bobay, Sean D. Stowe, Andrew L. Olson, Erik A. Feldmann, Richele J. Thompson, et al. “Filling in the gaps for the master regulator of biofilm formation in Bacillus subtilis: A structural and biochemical look at SinR and SinI.” In Faseb Journal, Vol. 33, 2019.Link to Item
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Venters, Ronald, Sophie Gobeil, Leonard Spicer, and Benjamin Bobay. “SELECTIVE INHIBITION OF CALCINEURIN ACTIVITY IN PATHOGENIC FUNGI.” In Protein Science, 28:93–93, 2019.Link to Item
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Draughn, George Logan, Benjamin G. Bobay, Sean D. Stowe, Andrew L. Olson, Erik A. Feldmann, Richele J. Thompson, Daniel B. Kearns, and John Cavanagh. “Solution structures of biofilm-controlling proteins SinI and SinR from Bacillus subtilis reveal details of DNA-binding and regulatory mechanism.” In Faseb Journal, Vol. 31, 2017.Link to Item
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Gobeil, Sophie, Leonard Spicer, Ben Bobay, and Ron Venters. “Selective Inhibition of Calcineurin Activity in Pathogenic Fungii.” In Protein Science, 26:182–83, 2017.Link to Item
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Kish, William, Amith Naik, Hiroyuki Sachi, Benjamin Bobay, Stefano Menegatti, and Ruben Carbonell. “Cyclic peptide ligands for the purification of erythropoietin by affinity chromatography.” In Abstracts of Papers of the American Chemical Society, Vol. 251, 2016.Link to Item
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DiGennaro, P., B. G. Bobay, and D. M. Bird. “STRUCTURAL APPROACHES TO UNDERSTANDING PLANT AND NEMATODE DEVELOPMENTAL SIGNALS.” In Journal of Nematology, 47:233–233, 2015.Link to Item
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DiGennaro, P., B. Bobay, and D McK Bird. “TERTIARY STRUCTURES OF ROOT-KNOT NEMATODE EFFECTORS INFORM FUNCTION.” In Journal of Nematology, 46:153–54, 2014.Link to Item
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Harris, Kimberly A., Victoria Jones, Yann Bilbille, Benjamin G. Bobay, and Paul F. Agris. “Structural characteristics of E. coli YrdC suggest a role in the enzymatic biosynthesis of the tRNA modification N6-threonylcarbamoyladenosine.” In Faseb Journal, Vol. 25, 2011.Link to Item
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- Scholarly, Clinical, & Service Activities
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Outreach & Engaged Scholarship
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