Scholars@Duke
Benjamin Bobay

Benjamin Bobay

Assistant Professor in Radiology
Radiology
ben.bobay@duke.edu
308 Research Dr, Durham, NC 27710
308 Research Dr, Durham, NC 27710

Selected Publications

Observation of Dynamic Aggregation Behavior in Thermoresponsive Micro- and Nanoparticles via Diffusion-Ordered NMR Spectroscopy.

Journal Article Journal of the American Chemical Society · March 2025 Stimuli-responsive drug delivery systems have expanded the diversity of potential cargos by protecting payloads, extending circulation, and controlling payload release. However, quantitative characterization methods that accurately describe these complex s ... Full text Cite

Controlling glass forming kinetics in 2D perovskites using organic cation isomers.

Journal Article Chemical science · May 2024 The recent discovery of glass-forming metal halide perovskites (MHPs) provides opportunities to broaden the application domain beyond traditionally celebrated optoelectronic research fueled by associated crystalline counterparts. In this regard, it is cruc ... Full text Cite

Anionic nanoplastic contaminants promote Parkinson's disease-associated α-synuclein aggregation.

Journal Article Sci Adv · November 15, 2023 Recent studies have identified increasing levels of nanoplastic pollution in the environment. Here, we find that anionic nanoplastic contaminants potently precipitate the formation and propagation of α-synuclein protein fibrils through a high-affinity inte ... Full text Link to item Cite

Anionic Nanoplastic Contaminants Promote Parkinson's Disease-Associated α-Synuclein Aggregation.

Journal Article Res Sq · October 13, 2023 Recent studies have identified increasing levels of nanoplastic pollution in the environment. Here we find that anionic nanoplastic contaminants potently precipitate the formation and propagation of α-synuclein protein fibrils through a high-affinity inter ... Full text Link to item Cite

Chiral Cation Doping for Modulating Structural Symmetry of 2D Perovskites.

Journal Article Journal of the American Chemical Society · August 2023 Cation mixing in two-dimensional (2D) hybrid organic-inorganic perovskite (HOIP) structures represents an important degree of freedom for modifying organic templating effects and tailoring inorganic structures. However, the limited number of known cation-m ... Full text Open Access Cite

Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase.

Journal Article Comput Biol Chem · February 2023 Featured Publication Butyrylcholinesterase (BChE) is recognized as a high value biotherapeutic in the treatment of Alzheimer's disease and drug addiction. This study presents the rational design and screening of an in-silico library of trimeric peptides against BChE and the ex ... Full text Link to item Cite

Calcineurin Inhibitor CN585 Exhibits Off-Target Effects in the Human Fungal Pathogen Aspergillus fumigatus.

Journal Article Journal of fungi (Basel, Switzerland) · December 2022 Calcineurin (CN) is an attractive antifungal target as it is critical for growth, stress response, drug resistance, and virulence in fungal pathogens. The immunosuppressive drugs, tacrolimus (FK506) and cyclosporin A (CsA), are fungistatic and specifically ... Full text Open Access Cite

Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus.

Journal Article mBio · June 28, 2022 Calcineurin is an essential virulence factor that is conserved across human fungal pathogens, including Cryptococcus neoformans, Aspergillus fumigatus, and Candida albicans. Although an excellent target for antifungal drug development, the serine-threonine ... Full text Open Access Link to item Cite

Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs.

Journal Article mBio · December 21, 2021 Featured Publication Calcineurin is a critical enzyme in fungal pathogenesis and antifungal drug tolerance and, therefore, an attractive antifungal target. Current clinically accessible calcineurin inhibitors, such as FK506, are immunosuppressive to humans, so exploiting calci ... Full text Open Access Link to item Cite

Salmonella Typhi Vi capsule prime-boost vaccination induces convergent and functional antibody responses.

Journal Article Sci Immunol · October 29, 2021 Vaccine development to prevent Salmonella Typhi infections has accelerated over the past decade, resulting in licensure of new vaccines, which use the Vi polysaccharide (Vi PS) of the bacterium conjugated to an unrelated carrier protein as the active compo ... Full text Open Access Link to item Cite

Characterizing azobenzene disperse dyes in commercial mixtures and children's polyester clothing.

Journal Article Environmental pollution (Barking, Essex : 1987) · October 2021 Azobenzene disperse dyes are the fastest-growing class of dyestuffs, yet little is known about dye occurrences, sources, and transformations; azo dyes are also underrepresented in chemical standard catalogs, molecular databases, and mass spectral libraries ... Full text Open Access Cite

Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep.

Journal Article Biochemistry · September 2021 Featured Publication The geminivirus replication protein, Rep, has long been recognized as a high-value target for control of geminivirus infections as this protein is highly conserved and essential for viral replication and proliferation. In addition, inhibition of viral repl ... Full text Open Access Cite

The Protein Kinase A-Dependent Phosphoproteome of the Human Pathogen Aspergillus fumigatus Reveals Diverse Virulence-Associated Kinase Targets.

Journal Article mBio · December 15, 2020 Protein kinase A (PKA) signaling plays a critical role in the growth and development of all eukaryotic microbes. However, few direct targets have been characterized in any organism. The fungus Aspergillus fumigatus is a leading infectious cause of death in ... Full text Open Access Link to item Cite

Structure-Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes.

Journal Article Plant physiology · July 2020 Auxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in genes involved in glucosinolate ... Full text Open Access Cite

FKBP12 dimerization mutations effect FK506 binding and differentially alter calcineurin inhibition in the human pathogen Aspergillus fumigatus.

Journal Article Biochem Biophys Res Commun · May 21, 2020 The 12-kDa FK506-binding protein (FKBP12) is the target of the commonly used immunosuppressive drug FK506. The FKBP12-FK506 complex binds to calcineurin and inhibits its activity, leading to immunosuppression and preventing organ transplant rejection. Our ... Full text Open Access Link to item Cite

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 Article Journal of molecular biology · January 2020 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 ... Full text Open Access Cite

Leveraging Fungal Calcineurin-Inhibitor Structures, Biophysics and Dynamics to Design Selective and Non-Immunosuppressive FK506 Analogs

Journal Article · 2020 Calcineurin is a critical enzyme in fungal pathogenesis and antifungal drug tolerance and, therefore, an attractive antifungal target. Current clinically-accessible calcineurin inhibitors, such as FK506, are immunosuppressive to humans, so exploiting calci ... Full text Open Access Cite

Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents.

Journal Article Nat Commun · September 19, 2019 Calcineurin is important for fungal virulence and a potential antifungal target, but compounds targeting calcineurin, such as FK506, are immunosuppressive. Here we report the crystal structures of calcineurin catalytic (CnA) and regulatory (CnB) subunits c ... Full text Open Access Link to item Cite

Translating antibody-binding peptides into peptoid ligands with improved affinity and stability.

Journal Article Journal of chromatography. A · September 2019 A great number of protein-binding peptides are known and utilized as drugs, diagnostic reagents, and affinity ligands. Recently, however, peptide mimetics have been proposed as valuable alternative to peptides by virtue of their excellent biorecognition ac ... Full text Open Access Cite

A Lysine Residue Essential for Geminivirus Replication Also Controls Nuclear Localization of the Tomato Yellow Leaf Curl Virus Rep Protein.

Journal Article Journal of virology · May 2019 Geminiviruses are single-stranded DNA (ssDNA) viruses that infect a wide range of plants. To promote viral replication, geminiviruses manipulate the host cell cycle. The viral protein Rep is essential to reprogram the cell cycle and then initiate viral DNA ... Full text Open Access Cite

15N, 13C and 1H resonance assignments of FKBP12 proteins from the pathogenic fungi Mucor circinelloides and Aspergillus fumigatus.

Journal Article Biomol NMR Assign · April 2019 Invasive fungal infections are a leading cause of death in immunocompromised patients and remain difficult to treat since fungal pathogens, like mammals, are eukaryotes and share many orthologous proteins. As a result, current antifungal drugs have limited ... Full text Open Access Link to item Cite

Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection.

Journal Article Plant physiology · September 2018 Geminiviruses are single-stranded DNA viruses that infect a wide variety of plants and cause severe crop losses worldwide. The geminivirus replication initiator protein (Rep) binds to the viral replication origin and catalyzes DNA cleavage and ligation to ... Full text Open Access Cite

The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism.

Journal Article Journal of molecular biology · March 2018 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 infectio ... Full text Open Access Cite

Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds.

Journal Article Molecular microbiology · October 2017 With antibiotic resistance increasing at alarming rates, targets for new antimicrobial therapies must be identified. A particularly promising target is the bacterial two-component system. Two-component systems allow bacteria to detect, evaluate and protect ... Full text Open Access Cite

Design, selection, and development of cyclic peptide ligands for human erythropoietin.

Journal Article Journal of chromatography. A · June 2017 This work presents the selection and characterization of erythropoietin (EPO)-binding cyclic peptide ligands. The sequences were selected by screening a focused library of cyclic depsipeptides cyclo[(Nα-Ac)Dap(A)-X1-X6-AE], ... Full text Open Access Cite

Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain.

Journal Article Applied microbiology and biotechnology · February 2017 A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing id ... Full text Open Access Cite

Human Norovirus Aptamer Exhibits High Degree of Target Conformation-Dependent Binding Similar to That of Receptors and Discriminates Particle Functionality.

Journal Article mSphere · November 2016 Although two in vitro cultivation methods have been reported, discrimination of infectious human norovirus particles for study of viral inactivation is still a challenge, as both rely on reverse transcriptase quantitative PCR. Histo-blood group anti ... Full text Open Access Cite

A combined approach for predicting the cytotoxic effect of drug-nanoaggregates.

Journal Article Journal of materials chemistry. B · October 2016 We present a combined spectroscopic and computational approach aimed to elucidate the mechanism of formation and activity of etoposide nanoaggregates upon release from dextran-etoposide conjugates. Etoposide is an anticancer drug that inhibits cell growth ... Full text Open Access Cite

Design of protease-resistant peptide ligands for the purification of antibodies from human plasma.

Journal Article Journal of chromatography. A · May 2016 A strategy is presented for developing variants of peptide ligands with enhanced biochemical stability for the purification of antibodies from animal sera. Antibody-binding sequences HWRGWV, HYFKFD, and HFRRHL, previously discovered by our group, were modi ... Full text Open Access Cite

Cyclic peptide ligands for the purification of erythropoietin by affinity chromatography

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2016 Cite

NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.

Journal Article J Biol Chem · August 14, 2015 The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the ... Full text Open Access Link to item Cite

Structure and DNA-binding traits of the transition state regulator AbrB.

Journal Article Structure · November 4, 2014 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, ext ... Full text Open Access Link to item Cite

A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA.

Journal Article J Mol Biol · May 1, 2014 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 tra ... Full text Open Access Link to item Cite

Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum.

Journal Article Biomolecular NMR assignments · April 2014 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. ... Full text Open Access Cite

Solution NMR studies of the plant peptide hormone CEP inform function.

Journal Article FEBS letters · December 2013 The C-terminally Encoded Peptide (CEP) family of regulatory peptides controls root development in vascular plants. Here, we present the first NMR structures of CEP. We show that root-knot nematode (RKN: Meloidogyne spp.) also encodes CEP, presumably to mim ... Full text Open Access Cite

Identification of BfmR, a response regulator involved in biofilm development, as a target for a 2-Aminoimidazole-based antibiofilm agent.

Journal Article Biochemistry · December 2012 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 acti ... Full text Open Access Cite

Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3.

Journal Article FEBS letters · October 2012 The regulation of apoptosis involves a complicated cascade requiring numerous protein interactions including the pro-apoptotic executioner protein caspase-3 and the anti-apoptotic calcium-binding protein calbindin-D28K. Using isothermal titration calorimet ... Full text Cite

¹H, ¹³C, and ¹⁵N resonance assignments and secondary structure prediction of the full-length transition state regulator AbrB from Bacillus anthracis.

Journal Article Biomolecular NMR assignments · April 2012 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 ... Full text Open Access Cite

Dynamics and activation in response regulators: the β4-α4 loop.

Journal Article Biomolecular concepts · February 2012 Two-component signal transduction systems of microbes are a primary means to respond to signals emanating from environmental and metabolic fluctuations as well as to signals coordinating the cell cycle with macromolecular syntheses, among a large variety o ... Full text Open Access Cite

Long range dynamic effects of point-mutations trap a response regulator in an active conformation.

Journal Article FEBS letters · October 2010 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 r ... Full text Open Access Cite

Binding site on human immunoglobulin G for the affinity ligand HWRGWV.

Journal Article Journal of molecular recognition : JMR · May 2010 Affinity ligand HWRGWV has demonstrated the ability to isolate human immunoglobulin G (hIgG) from mammalian cell culture media. The ligand specifically binds hIgG through its Fc portion. This work shows that deglycosylation of hIgG has no influence on its ... Full text Open Access Cite

NMR solution structure and DNA-binding model of the DNA-binding domain of competence protein A.

Journal Article Journal of molecular biology · April 2010 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 ... Full text Cite

Determination of separate inhibitor and substrate binding sites in the dehaloperoxidase-hemoglobin from Amphitrite ornata.

Journal Article Biochemistry · February 2010 Dehaloperoxidase-hemoglobin (DHP A) is a dual function protein found in the terrebellid polychaete Amphitrite ornata. A. ornata is an annelid, which inhabits estuary mudflats with other polychaetes that secrete a range of toxic brominated phenols. DHP A is ... Full text Cite

Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry.

Journal Article Biochemistry · September 2009 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 import ... Full text Cite

Insights into the nature of DNA binding of AbrB-like transcription factors.

Journal Article Structure (London, England : 1993) · November 2008 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 "transit ... Full text Cite

Co-evolving motions at protein-protein interfaces of two-component signaling systems identified by covariance analysis.

Journal Article Biochemistry · July 2008 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 ... Full text Cite

Targeting RNA with cysteine-constrained peptides.

Journal Article Bioorganic & medicinal chemistry letters · January 2008 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. Subs ... Full text Cite

Abh and AbrB control of Bacillus subtilis antimicrobial gene expression.

Journal Article Journal of bacteriology · November 2007 The Bacillus subtilis abh gene encodes a protein whose N-terminal domain has 74% identity to the DNA-binding domain of the global regulatory protein AbrB. Strains with a mutation in abh showed alterations in the production of antimicrobial compounds direct ... Full text Cite

Peptide binding proclivities of calcium loaded calbindin-D28k.

Journal Article FEBS Lett · October 2, 2007 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 change ... Full text Link to item Cite

Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition.

Journal Article FEBS letters · April 2007 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 alpha4-helix and hence the beta4-alpha4 kinase ... Full text Cite

Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents.

Journal Article Rapid Commun Mass Spectrom · 2007 Chemical crosslinking combined with mass spectrometry is a useful tool for studying the topological organization of multiprotein interactions, but it is technically challenging to identify peptides involved in a crosslink using tandem mass spectrometry (MS ... Full text Link to item Cite

NMR structure of AbhN and comparison with AbrBN: FIRST insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins.

Journal Article J Biol Chem · July 28, 2006 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, lit ... Full text Link to item Cite

Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins.

Journal Article FEBS letters · October 2005 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 sha ... Full text Cite

Evaluation of the DNA binding tendencies of the transition state regulator AbrB.

Journal Article Biochemistry · December 2004 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 ... Full text Cite

Macromolecular assembly of the transition state regulator AbrB in its unbound and complexed states probed by microelectrospray ionization mass spectrometry.

Journal Article Analytical biochemistry · July 2002 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 shar ... Full text Cite

Stoichiometries of protein-protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry.

Journal Article Biochemistry · June 2002 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 ... Full text Cite

Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer.

Journal Article Biochemistry · November 2001 We have investigated the oligomeric properties of procaspase-3 and a mutant that lacks the pro-domain (called pro-less variant). In addition, we have examined the interactions of the 28 amino acid pro-peptide when added in trans to the pro-less variant. By ... Full text Cite