Benjamin Bobay

Benjamin G. Bobay

Box 3711
Duke University Medical Center
Durham, NC  27710
Work Phone: (919)-613-8884  Fax: (919)-684-8885
e-mail: ben.bobay@duke.edu
linkedin profile: linkedin.com/in/benjaminbobay
Google Scholar profile: goo.gl/UjJFrp
Pubmed (citation list): goo.gl/eqeEnB
ORCID profile: goo.gl/KngUK2

EDUCATION

Ph.D., Structural Biochemistry – August, 2004

Department of Molecular and Structural Biochemistry  North Carolina State University, Raleigh, North Carolina

Bachelor of Science, Chemistry/Biochemistry – ACS certified – April, 2000

Department of Chemistry, Purdue University, West Lafayette, Indiana

 

PROFESSIONAL EXPERIENCE          

Senior Research Associate
 – July 2016 – to present, Duke University, Radiology, NMR facility

  • Initiated the partnering with several academic departments within Duke.
  • Maintained NMR facility operation and user base.
  • Provided research support, user training, and maintenance to the NMR facility.
  • Developed partnerships to teach a short tutorial about small molecule characterization through nuclear magnetic resonance.

Research Assistant Professor – January, 2011 – July 2016, North Carolina State University (NCSU), Dept. of Molecular and Structural Biochemistry

  • The underlying theme of my research is to better understand how the specific structure and inherent flexibility of proteins help them carry out their biological roles (structure to function relationships). We have been successfully utilizing structural biology to characterize the molecular mechanisms behind replication of ssDNA viruses, bioseparations via modified amino acid peptides, and hosts:parasite interactions.

Assistant NMR Supervisor – February, 2007 – July 2016, NCSU BIO-Nuclear Magnetic Resonance Facility

  • Maintained facility operation and user base despite significant budget cuts and the retirement of the only full time employee
  • Initiated the partnering with several academic departments within NCSU.
  • Provided research support, user training, and maintenance to the BIO-NMR facility

NMR Director – March, 2009-March, 2011, Plants for Human Health Institute NC Research Campus, NCSU at Kannapolis

  • Designed and implemented the specific NMR research projects for users of various backgrounds in industry and academia.
  • Provided research support, user training, and facility maintenance to the NMR center.

 

BOARDS/PANELS/VOLUNTEER WORK

  • Sycamore Creek Elementary PTA – VP for track 1 – May 2017 – to present
  • North Carolina School of Science and Mathematics – February 2017 – to present Short tutorial on small molecule characterization
  • Raleigh’s First Citizen Police Academy – April 2017 – May 2017
  • Committee chair, Structural Biochemistry Resource, NCSU – August, 2015 – July 2016
  • Member, Graduate student search committee, NCSU – May, 2014

 

CONSULTATION

  • Macromolecular structure determination: Dole Foods, Monsanto, and David H. Murdock Research Institute.
  • Expert Witness / Consultant – Small molecule characterization: Winston & Strawn LLP, Chicago IL

 

TEACHING SUMMARY

Instructor – BCH701: Proteins and Molecular MechanismsAugust 2015 – July 2016

  • 7-10 students
  • Principles of protein structure and function, protein folding, enzymology, ligand binding, protein transport, and metabolic pathways.

Instructor – BCH455/555: Proteins and Molecular Mechanisms  – January 2013 – July 2016

  • 40-70+ students
  • Principles of protein structure and function, protein folding, enzymology, ligand binding, protein transport, and metabolic pathways.

Instructor – BCH590A: Analytical Methods in Structural BiochemistryJuly 2012

  • 8-10 students
  • Hands-on approach to analytical structural biochemistry including mass spectrometry, NMR, and x-ray crystallography.

 

Post-graduate dissertation committees                                                        

Degrees awarded to date

  • Kimberly Harris – Ph.D. – Department of Molecular and Structural Biochemistry, NCSU
  • Andrew Argo – MS – Department of Molecular and Structural Biochemistry, NCSU
  • George Logan Draughn – Ph.D. candidate – Department of Molecular and Structural Biochemistry, NCSU

Ongoing in 2017

  • Caroline Smith – Ph.D. candidate – Department of Plant and Microbial Biology, NCSU

Awards to students under my supervision (2013-15)

  • Gabrielle Dailey – NCSU Undergraduate Research Grant – Reduction of geminivirus replication through inhibitory peptide:AL1 interactions – 2014 – $3,000
  • Logan Butler – NCSU Undergraduate Research Grant – Inhibiting the interaction of pro-apoptotic caspase-3 and anti-apoptotic Calbindin-D28k through use of cyclic peptides to prevent cancer – 2014 – $3,000
  • Amanda Mintz – Jimmy V Research Scholarship – 2014 – $500
  • Gabrielle Dailey – Jimmy V Research Scholarship – 2014 – $500
  • Logan Butler – Jimmy V Research Scholarship – 2014 – $500
  • Amanda Mintz – NCSU Undergraduate Research Grant – Structural characterization of the master control regulator for replication in geminivirus – 2013 – $1,000

 

PATENTS

  • Protease-Resistant Peptide Ligands, PCT Application No. PCT/US14/46660, filed July 15, 2014, claiming the benefit of U. S. Provisional Application Serial No. 61/846,326, filed July 15, 2013.

 

JOURNAL COVERS

  • NMR-based structural analysis of threonylcarbamoyl-AMP synthase and its substrate interactions. J Biol Chem. 2015 Jun 9.
  • A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA. J Mol Biol. 2014 May 1

 

INVITED RESEARCH PRESENTATIONS

  • 10/2014 Symposium on Plant Systems and Synthetic Biology: Solutions to Global Food Security (poster) – Title: Structure to function relationships in plant biology: Utilizing structural biology to characterize unique functions of individual members within large gene families
  • 10/2104 Symposium on Plant Systems and Synthetic Biology: Solutions to Global Food Security (poster) – Title: Increasing photosynthetic CO2 capture in Camelina with a synthetic carbon fixation cycle composed of select microbial enzymes
  • 10/2014 Symposium on Plant Systems and Synthetic Biology: Solutions to Global Food Security (poster) – Title: Use of MS to understand geminivirus infections in Arabidopsis
  • 09/2013 ARPA-E Petro (poster) – Title: Increasing Photosynthetic CO2 capture in Camelina with a Synthetic Carbon Fixation Cycle Composed of Select Microbial Enzymes
  • 01/2011 NCSU – Department of Forest Biosciences (seminar). Title: Analytical Approaches to the Structural Characterization of Macromolecules
  • 03/2010 NCSU – Department of Molecular and Structural Biochemistry (seminar). Title: Rationale Structure Based Design
  • Fall/2009 Results (magazine) – Research and Graduate Studies at NCSU. Title: Guardian Protein Could Keep Alzheimer’s at Bay
  • 10/2008 University of South Alabama – Department of Chemistry (seminar). Title: Bacterial Cell Protection
  • 04/2007 ENC (poster) – Title: Comparative Structural Analysis of Hyper-sporulation Spo0F Mutants from Bacillus subtilis
  • 04/2007 ENC (poster) – Title: Structural Model of the AbrB/abrb8 Complex Revealed by Combining NMR, Mutagenesis, and Docking Approaches

PUBLICATIONS – full list

  • Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Appl Microbiol Biotechnol. 2017 Feb;101(4):1615-1630. doi: 10.1007/s00253-016-7978-6. Epub 2016 Nov 19. PubMed PMID: 27866253.
  • Kish WS, Sachi H, Naik AD, Roach MK, Bobay BG, Blackburn RK, Menegatti S, Carbonell RG. Design, selection, and development of cyclic peptide ligands for human erythropoietin. J Chromatogr A. 2017 Jun 2;1500:105-120. doi: 10.1016/j.chroma.2017.04.019. Epub 2017 Apr 12. PubMed PMID: 28433433.
  • Moore MD, Bobay BG, Mertens B, Jaykus LA. Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to that of Receptors and Discriminates Particle Functionality. mSphere. 2016 Nov 2;1(6). pii: e00298-16. PubMed PMID: 27830193.
  • Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Appl Microbiol Biotechnol. 2017 Feb;101(4):1615-1630. doi: 10.1007/s00253-016-7978-6. PubMed PMID: 27866253.
  • Menegatti S, Bobay BG, Ward KL, Islam T, Kish WS, Naik AD, Carbonell RG. Design of protease-resistant peptide ligands for the purification of antibodies from human plasma. J Chromatogr A. 2016 May 6;1445:93-104. doi: 10.1016/j.chroma.2016.03.087. PubMed PMID: 27072524.
  • Wojnilowicz M, Tortora M, Bobay BG, Santiso E, Caruso M, Micheli L, Venanzi M, Menegatti S, Cavalieri F. A combined approach for predicting the cytotoxic effect of drug-nanoaggregates. Journal of Materials Chemistry B 4 (40), 6516-6523
  • NMR-based structural analysis of threonylcarbamoyl-AMP synthase and its substrate interactions. Harris KA, Bobay BG*, Sarachan KL, Sims AF, Bilbille Y, Deutsch C, Iwata-Reuyl D, Agris PF. J Biol Chem. 2015 Aug 14;290(33):20032-43. *co-first author
  • Structure and DNA-binding traits of the transition state regulator AbrB. Olson AL, Tucker AT, Bobay BG, Soderblom EJ, Moseley MA, Thompson RJ, Cavanagh J. Structure. 2014 Nov 4;22(11):1650-6.
  • A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA. Tucker AT, Bobay BG*, Banse AV, Olson AL, Soderblom EJ, Moseley MA, Thompson RJ, Varney KM, Losick R, Cavanagh J. J Mol Biol. 2014 May 1;426(9):1911-24. *co-first author
  • Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum. Bobay BG, Thompson RJ, Milton DL, Cavanagh J. Biomol NMR Assign. 2014 Apr;8(1):177-9.
  • Solution NMR studies of the plant peptide hormone CEP inform function. Bobay BG*, DiGennaro P, Scholl E, Imin N, Djordjevic MA, Mck Bird D. FEBS Lett. 2013 Dec 11;587(24):3979-85. *co-first author
  • Identification of BfmR, a Response Regulator Involved in Biofilm Development, as a Target for a 2-Aminoimidazole-Based Anti-Biofilm Agent. Thompson RJ, Bobay BG, Stowe S, Olson A, Su Z, Peng L, Actis L, Melander C, and Cavanagh J. Biochemistry. 2012 Dec 11;51(49):9776-8.
  • Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3. Bobay BG, Stewart AL, Tucker AT, Thompson RJ, Varney K and Cavanagh J. FEBS Lett. 2012 Oct 19;586(20):3582-9
  • Dynamics and activation in response regulators: the β4-α4 loop. Bobay BG, James A. Hoch, and John Cavanagh. BioMolecular Concepts2 (2012): 175-182.
  • (1)H, (13)C, and (15)N resonance assignments and secondary structure prediction of the full-length transition state regulator AbrB from Bacillus anthracis. Olson AL, Bobay BG, Melander C, Cavanagh Biomol NMR Assign. 2011 Aug 4.
  • Long range dynamic effects of point-mutations trap a response regulator in an active conformation. Bobay BG, Thompson RJ, Hoch JA, Cavanagh J. FEBS Lett. 2010 Oct 8;584(19):4203-7.
  • NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A. Hobbs CA, Bobay BG, Thompson RJ, Perego M, Cavanagh J. J Mol Biol. 2010 Apr 30;398(2):248-63.
  • Determination of separate inhibitor and substrate binding sites in the dehaloperoxidase-hemoglobin from Amphitrite ornata. Davis MF, Bobay BG, Franzen S. Biochemistry. 2010 Feb 16;49(6):1199-206.
  • Binding site on human immunoglobulin G for the affinity ligand HWRGWV. Yang H, Gurgel PV, Williams DK Jr, Bobay BG, Cavanagh J, Muddiman DC, Carbonell RG. J Mol Recognit. 2010 May-Jun;23(3):271-82.
  • Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Hobbs CA, Deterding LJ, Perera L, Bobay BG, Thompson RJ, Darden TA, Cavanagh J, Tomer KB. Biochemistry. 2009 Sep 15;48(36):8603-14.
  • Insights into the nature of DNA binding of AbrB-like transcription factors. Sullivan DM, Bobay BG*, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J. Structure. 2008 Nov 12;16(11):1702-13. *co-first author
  • Co-evolving motions at protein-protein interfaces of two-component signaling systems identified by covariance analysis. Szurmant H, Bobay BG, White RA, Sullivan DM, Thompson RJ, Hwa T, Hoch JA, Cavanagh J. Biochemistry. 2008 Jul 29;47(30):7782-4.
  • Targeting RNA with cysteine-constrained peptides. Burns VA, Bobay BG, Basso A, Cavanagh J, Melander C. Bioorg Med Chem Lett. 2008 Jan 15;18(2):565-7.
  • Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents. Soderblom EJ, Bobay BG, Cavanagh J, Goshe MB. Rapid Commun Mass Spectrom. 2007;21(21):3395-408.
  • Peptide binding proclivities of calcium loaded calbindin-D28k. Kordys DR, Bobay BG, Thompson RJ, Venters RA, Cavanagh J. FEBS Lett. 2007 Oct 2;581(24):4778-82.
  • Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. Strauch MA, Bobay BG, Cavanagh J, Yao F, Wilson A, Le Breton Y. J Bacteriol. 2007 Nov;189(21):7720-32.
  • Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. McLaughlin PD, Bobay BG, Regel EJ, Thompson RJ, Hoch JA, Cavanagh J. FEBS Lett. 2007 Apr 3;581(7):1425-9.
  • NMR structure of AbhN and comparison with AbrBN: FIRST insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins. Bobay BG, Mueller GA, Thompson RJ, Murzin AG, Venters RA, Strauch MA, Cavanagh J. J Biol Chem. 2006 Jul 28;281(30):21399-409.
  • Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. Bobay BG, Andreeva A, Mueller GA, Cavanagh J, Murzin AG. FEBS Lett. 2005 Oct 24;579(25):5669-74.
  • Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Bobay BG, Benson L, Naylor S, Feeney B, Clark AC, Goshe MB, Strauch MA, Thompson R, Cavanagh J. Biochemistry. 2004 Dec 28;43(51):16106-18.
  • Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry. Benson LM, Vaughn JL, Strauch MA, Bobay BG, Thompson R, Naylor S, Cavanagh J. Anal Biochem. 2002 Jul 15;306(2):222-7.
  • Stoichiometries of protein-protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry. Cavanagh J, Thompson R, Bobay B, Benson LM, Naylor S. Biochemistry. 2002 Jun 25;41(25):7859-65.
  • Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer. Pop C, Chen YR, Smith B, Bose K, Bobay B, Tripathy A, Franzen S, Clark AC. Biochemistry. 2001 Nov 27;40(47):14224-35.