Publications

Sample publications from CBI students and affiliates.

2020

Schatzman SS, Peterson RL, Teka M, He B, Cabelli DE, Cormack BP, Culotta VC. (2020) Copper-only superoxide dismutase enzymes and iron starvation stress in Candida fungal pathogens. J. Biol. Chem. 295(2):570-583. [DOI: 10.1074/jbc.RA119.011084]

Henager SH, Henriquez S, Dempsey DR, Cole PA. (2020) Analysis of Site-Specific Phosphorylation of PTEN by Using Enzyme-Catalyzed Expressed Protein Ligation. ChemBioChem. 21(1-2):64-68. [DOI: 10.1002/cbic.201900316]

Abraham R, McPherson RL, Dasovich M, Badiee M, Leung AKL, Griffin DE. (2020) Both ADP-Ribosyl-Binding and Hydrolase Activities of the Alphavirus nsP3 Macrodomain Affect Neurovirulence in Mice. mBio.11;11(1).[DOI: 10.1128/mBio.03253-19]

Khodade VS, Pharoah BM, Paolocci N, Toscano JP. (2020) Alkylamine-Substituted Perthiocarbamates: Dual Precursors to Hydropersulfide and Carbonyl Sulfide with Cardioprotective Actions. Journal of the American Chemical Society. 142(9):4309-4316. [DOI: 10.1021/jacs.9b12180]

Cairns L, Patterson A, Weingartner KA, Koehler TJ, DeAngelis DR, Tripp KW, Bothner B, Kavran JM. (2020) Biophysical characterization of SARAH domain-mediated multimerization of Hippo pathway complexes in Drosophila. Journal of Biological Chemistry. 295(18):6202-6213. [DOI: 10.1074/jbc.RA120.012679]

Hutchinson MA, Deeyaa BD, Byrne SR, Williams SJ, Rokita SE. (2020) Directing Quinone Methide-Dependent Alkylation and Cross-Linking of Nucleic Acids with Quaternary Amines. Bioconjugate Chemistry. 31(5):1486-1496. [DOI: 10.1021/acs.bioconjchem.0c00166]

Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. (2020) Molecular & Cellular Proteomics 19(6):916-927. [DOI: 10.1074/mcp.R120.001936]

Chu N, Viennet T, Bae H, Salguero A, Boeszoermenyi A, Arthanari H, Cole PA. (2020) The structural determinants of PH domain-mediated regulation of Akt revealed by segmental labeling. eLife.[DOI: 10.7554/eLife.59151]

Cohen DR, Townsend CA. (2020) C-N-Coupled Metabolites Yield Insights into Dynemicin A Biosynthesis. ChemBioChem. 21(15):2137-2142.[DOI: 10.1002/cbic.202000177]

Gonzalez-Gil A, Li TA, Porell RN, Fernandes SM, Tarbox HE, Lee HS, Aoki K, Tiemeyer M, Kim J, Schnaar RL. (2020) Isolation, identification, and characterization of the human airway ligand for the eosinophil and mast cell immunoinhibitory receptor Siglec-8. Journal of Allergy and Clinical Immunology. August 2020 [DOI: 10.1016/j.jaci.2020.08.001]

Spisak S, Ostermeier M. (2020) Engineered protein switches for exogenous control of gene expression. Biochemical Society Transactions. 48(5):2205-2212. [DOI: 10.1042/BST20200441]

Byrne SR, Rokita SE. (2020) Unraveling Reversible DNA Cross-Links with a Biological Machine. Chemical Research in Toxicology. 33(11):2903-2913. [DOI: 10.1021/acs.chemrestox.0c00413]

2019

Mazanek Z, Sohn J. (2019) Tracking the polymerization of DNA sensors and inflammasomes using FRET. Methods in Enzymology. 625:87-94. [DOI: 10.1016/bs.mie.2019.06.006.]

Dasovich M, Leung AKL. (2019) A Nucleolar PARtnership Expands PARP Roles in RNA Biology and the Clinical Potential of PARP Inhibitors. Molecular Cell. 75(6):1089-1091. [DOI: 10.1016/j.molcel.2019.09.001]

DeColli AA, Zhang X, Heflin KL, Jordan F, Freel Meyers CL. (2019) Active Site Histidines Link Conformational Dynamics with Catalysis on Anti-Infective Target 1-Deoxy-d-xylulose 5-Phosphate Synthase. Biochemistry 58(49):4970-4982. [DOI: 10.1021/acs.biochem.9b00878]

Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA. (2019) Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme. Chemical Communications. 55(99):14934-14937. [DOI: 10.1039/c9cc07197k]

Okafor IC, Singh D, Wang Y, Jung M, Wang H, Mallon J, Bailey S, Lee JK, Ha T. (201) Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding. Nucleic Acids Research. 47(22):11880-11888. [DOI: 10.1093/nar/gkz1058]

Ando Y, Elkayam E, McPherson RL, Dasovich M, Cheng SJ, Voorneveld J, Filippov DV, Ong SE, Joshua-Tor L, Leung AKL. (2019) ELTA: Enzymatic Labeling of Terminal ADP-Ribose. Molecular cell. 73(4):845-856.e5. [DOI: 10.1016/j.molcel.2018.12.022.]

Bartee D, Sanders S, Phillips PD, Harrison MJ, Koppisch AT, Freel Meyers (2019) Enamide Prodrugs of Acetyl Phosphonate Deoxy-d-xylulose-5-phosphate Synthase Inhibitors as Potent Antibacterial Agents. ACS Infectious Diseases. 5(3):406-417. [DOI: 10.1021/acsinfecdis.8b00307.]

Byrne SR, Yang K, Rokita SE. Effect of Nucleosome Assembly on Alkylation by a Dynamic Electrophile. (2019) Chemical Research in Toxicology. 32(5):917-925. [DOI: 10.1021/acs.chemrestox.9b00057]

Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. (2019) Structural Features of Transcription Factors Associating with Nucleosome Binding. Molecular Cell 75(5):921-932.e6. [DOI: 10.1016/j.molcel.2019.06.009]

Cole PA, Chu N, Salguero AL, Bae H. AKTivation mechanisms. Current opinion in structural biology. 2019 December;59:47-53. PubMed PMID:30901610; PubMed Central PMCID: PMC6752985; DOI: 10.1016/j.sbi.2019.02.004

Nye DB, Johnson EA, Mai MH, Lecomte JTJ. (2019) Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1. (2019) J. Inorganic Biochemistry.  201:110824. [DOI: 10.1016/j.jinorgbio.2019.110824]

2018

Singh D, Mallon J, Poddar A, Wang Y, Tippana R, Yang O, Bailey S, Ha T. (2018) Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). Proceedings of the National Academy of Sciences of the United States of America. 115(21):5444-5449.[DOI: 10.1073/pnas.1718686115]

Boucher LE, Hopp CS, Muthinja JM, Frischknecht F, Bosch J. (2018)Discovery of Plasmodium (M)TRAP-Aldolase Interaction Stabilizers Interfering with Sporozoite Motility and Invasion. ACS Infectious Diseases. 4(4):620-634. [DOI: 10.1021/acsinfecdis.7b00225]

Herbst DA, Huitt-Roehl CR, Jakob RP, Kravetz JM, Storm PA, Alley JR, Townsend CA, Maier T. (2018) The structural organization of substrate loading in iterative polyketide synthases. Nat. Chem. Biol. 14:474-479. [doi: 10.1038/s41589-018-0026-3]

Schatzman SS, Culotta VC.(2018)  Chemical Warfare at the Microorganismal Level: A Closer Look at the Superoxide Dismutase Enzymes of Pathogens. ACS Infect. Dis.  4:893–903. [doi: 10.1021/acsinfecdis.8b00026]

Singh D, Wang Y, Mallon J, Yang O, Fei J, Poddar A, Ceylan D, Bailey S, Ha T. (2018) Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis. Nat. Struct. Mol. Biol. 25:347-354.  [doi: 10.1038/s41594-018-0051-7]

Cohen DR, Townsend CA. (2018) A dual role for a polyketide synthase in dynemicin enediyne and anthraquinone biosynthesis. Nat. Chem. 10:231-236.  [doi: 10.1038/nchem.2876]

Cohen DR, Townsend CA. (2018) Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis. Angew. Chem. Int. Ed. Engl. 57:5650-5654.  [doi: 10.1002/anie.201802036]

Saraiva RG, Huitt-Roehl CR, Tripathi A, Cheng YQ, Bosch J, Townsend CA, Dimopoulos G. (2018) Chromobacterium spp. mediate their anti-Plasmodium activity through secretion of the histone deacetylase inhibitor romidepsin. Sci. Rep. 8:6176. [doi: 10.1038/s41598-018-24296-0]

Nye DB, Preimesberger MR, Majumdar A, Lecomte JTJ. (2018) Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates. Biochemistry 57:631-644. [doi: 10.1021/acs.biochem.7b01155.]

Boucher LE, Hopp CS, Muthinja JM, Frischknecht F, Bosch J. (2018) Discovery of Plasmodium (M)TRAP-Aldolase Interaction Stabilizers Interfering with Sporozoite Motility and Invasion. ACS Infect. Dis. 4:620-634.  [doi: 10.1021/acsinfecdis.7b00225]

2017

Sanders S, Vierling RJ, Bartee D, DeColli AA, Harrison MJ, Aklinski JL, Koppisch AT, Freel Meyers CL. (2017) Challenges and Hallmarks of Establishing Alkylacetylphosphonates as Probes of Bacterial 1-Deoxy-d-xylulose 5-Phosphate Synthase. ACS Infect. Dis. 3:467-478. [doi: 10.1021/acsinfecdis.6b00168]

Storm PA, Townsend CA. (2017) In trans hydrolysis of carrier protein bound acyl intermediates by CitA during citrinin biosynthesis. Chem. Commun. (Camb). 54:50-53.  [doi: 10.1039/c7cc07079a]

Kosowicz JG, Lee J, Peiffer B, Guo Z, Chen J, Liao G, Hayward SD, Liu JO, Ambinder RF. Drug Modulators of B Cell Signaling Pathways and Epstein-Barr Virus Lytic Activation. (2017) J Virol. 91(16).  [doi: 10.1128/JVI.00747-17.]

Barajas JF, Shakya G, Moreno G, Rivera H Jr, Jackson DR, Topper CL, Vagstad AL, La Clair JJ, Townsend CA, Burkart MD, Tsai SC. (2017) Polyketide mimetics yield structural and mechanistic insights into product template domain function in nonreducing polyketide synthases. Proc. Natl. Acad. Sci. U S A. 114:E4142-E4148. [doi: 10.1073/pnas.1609001114]

Rossi DCP, Gleason JE, Sanchez H, Schatzman SS, Culbertson EM, Johnson CJ, McNees CA, Coelho C, Nett JE, Andes DR, Cormack BP, Culotta VC. (2017) Candida albicans FRE8 encodes a member of the NADPH oxidase family that produces a burst of ROS during fungal morphogenesis. PLoS Pathog. 13(12):e1006763. [doi: 10.1371/journal.ppat.1006763]

Preimesberger MR, Johnson EA, Nye DB, Lecomte JTJ. (2017) Covalent attachment of the heme to Synechococcus hemoglobin alters its reactivity toward nitric oxide. J Inorg Biochem.  177:171-182. [doi: 10.1016/j.jinorgbio.2017.09.018]

Head SA, Shi WQ, Yang EJ, Nacev BA, Hong SY, Pasunooti KK, Li RJ, Shim. JS, Liu JO. (2017) Simultaneous targeting of NPC1 and VDAC1 by itraconazole leads to synergistic inhibition of mTOR signaling and angiogenesis. ACS Chem Biol.12:174-182.

Shelat NY, Parhi S, Ostermeier M. (2017) Development of a cancer-marker activated enzymatic switch from the herpes simplex virus thymidine kinase. Protein Eng Des Sel. 30:95-103.

Yu H, Gonzalez-Gil A, Wei Y, Fernandes SM, Porell RN, Vajn K, Paulson JC, Nycholat CM, Schnaar RL. (2017) Siglec-8 and Siglec-9 binding specificities and endogenous airway ligand distributions and properties. Glycobiology 27:657-668.

Ingavat N, Kavran JM, Sun Z, Rokita SE (2017) Active site binding is not sufficient for reductive deiodination by iodotyrosine deiodinase. Biochemistry 56:1130-1139.

Su Q, Boucher PA, Rokita SE (2017) Conversion of a dehalogenase to a nitroreductase by swapping its flavin cofactor with a 5-deazaflavin analog. (2017) Angew. Chem. Int. Ed. 56:10862-10866

Storm PA, Herbst DA, Maier T, Townsend CA. (2017) Functional and structural analysis of programmed C-methylation in the biosynthesis of the fungal polyketide citrinin. Cell Chem Biol. 24:316-325.

2016

Henager S, Chu N, Chen Z, Bolduc DM, Dempsey DR, Hwang Y, Wells J, Cole PA (2016) Enzyme-catalyzed expressed protein ligation. Nature Methods 13: 925-927.

Nemeria NS, Shome B, DeColli AA, Heflin K, Begley TP, Freel Meyers CF, Jordan F. (2016) Competence of thiamin diphosphate-dependent enzymes with 2′-methoxythiamin diphosphate derived from bacimethrin, a naturally occurring thiamin anti-vitamin. Biochemistry 55:1135-1148.

Choi, JH, Xiong T, Ostermeier M. (2016) The interplay between effector binding and allostery in an engineered protein switch. Protein Sci. 25:1605-1616.

Steinberg B, Ostermeier M. (2016) Shifting fitness and epistatic landscapes reflect tradeoffs along an evolutionary pathway. J. Mol. Biol. 428:2730-2743,

Steinberg B, Ostermeier M (2016) Environmental changes bridge evolutionary valleys. Sci. Adv. 2:e1500921.

Shelat NY, Parhi S, Ostermeier M. (2016) A positive selection for nucleoside kinases in E. coli. PLoS One. 11:e0162921.

Saha S, Rokita SE (2016) An activator of an adenylation domain revealed by activity but not sequence homology. ChemBioChem 17:1818-1823.

Phatarphekar A, Rokita SE (2016) Functional analysis of iodotyrosine deiodinase from Drosophila melanogaster.  Protein Science 25:2187-2195.

Millikin R, Bianco CL, White C, Saund SS, Henriquez S, Sosa V, Akaike T, Kumagai Y, Soeda S, Toscano JP, Lin J, Fukuto JM. (2016) The chemical biology of protein hydropersulfides: Studies of a possible protective function of biological hydropersulfide generation. Free Radic Biol Med. 97:136-47.

Hansen EC, Ransom M, Hesselberth JR, Hosmane NN, Zhang H, Capoferri AA, Drummond MB, Siliciano JM, Siliciano RF. Stivers JT (2016) Diverse fates of uracilated HIV DNA during infection of myeloid lineage cells. eLIFE 5:e18447.

Newman, AG. Townsend CA (2016) Molecular characterization of the cercosporin biosynthetic pathway in the fungal plant pathogen Cercospora nicotianae. (2016) J. Am. Chem. Soc. 138:4219-4228.

Barajas JF, Finzel K, Valentic TR, Shakya G, Gamarra N, Martinez D, Meier JL, Vagstad AL, Newman AG, Townsend CA, Burkart MD, Tsai S-C (2016) Structural and biochemical analysis of protein-protein interactions between the acyl carrier protein and product template domain. Angew. Chem. Int. Ed. 55:13005-13009.

Panja S, Paul R, Greenberg MM, Woodson SA. (2016) Light-triggered RNA annealing by an RNA chaperone. Angew Chem Int Ed Engl. 54:7281-7284.

Reiter KH, Ramachandran A, Xia X, Boucher LE, Bosch J, Matunis MJ. (2016) characterization and Structural Insights into Selective E1-E2 Interactions in the Human and Plasmodium falciparum SUMO Conjugation Systems. J Biol Chem. 291:3860-3870.

Mallon J, Bailey S. (2016) A molecular arms race: new insights into anti-CRISPR mechanisms. Nat Struct Mol Biol. 23:765-766.

Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E. (2016) Altered stoichiometry Escherichia coli cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Nucleic Acids Res. 44:10849-10861.

Moore CD, Ajala OZ, Zhu H. (2016) Applications in high-content functional protein microarrays. Curr Opin Chem Biol. 30:21-27.

2015

Boucher LE, Bosch J. (2015) The apicomplexan glideosome and adhesins -structures and function. J Struct Biol. 190:93-114.

Zuckerman DM, Boucher LE, Xie K, Engelhardt H, Bosch J, Hoiczyk E. (2015) The bactofilin cytoskeleton protein BacM of Myxococcus xanthus forms an extended β-sheet structure likely mediated by hydrophobic interactions. PLoS One 10:e0121074.

Rice SL, Boucher LE, Schlessman JL, Preimesberger MR, Bosch J, Lecomte JT. (2015) Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine-lysine heme ligation. Acta Crystallogr F Struct Biol Commun. 71:718-725.

Bartee D, Morris F, Al-Khouja A, Freel Meyers CL (2015) Hydroxybenzaldoximes Are D-GAP-competitive inhibitors of E. coli 1-deoxy-D-xylulose-5-phosphate synthase. Chembiochem. 16:1771-1781.

Cravens SL, Schonhoft JD, Rowland MM, Rodriguez AA, Anderson BG, Stivers JT. (2015) Molecular crowding enhances facilitated diffusion of two human DNA glycosylases. Nucleic Acids Res.43:4087-4097.

Gaudelli NM, Long DH, Townsend CA. (2015) β-Lactam formation by a nonribosomal peptide synthetase during antibiotic biosynthesis. Nature 520:383-387.

Huitt-Roehl CR, Hill EA, Adams MM, Vagstad AL, Li JW, Townsend CA. (2015) Starter unit flexibility for engineered product synthesis by the nonreducing polyketide synthase PksA. ACS Chem Biol. 10:1443-1449.

Gonzalez-Gil A, Porell R, Fernandes SM, Aoki K, Tiemeyer M, Schnaar RL. (2015) “Siglec-8 binds to sialylated keratan sulfate chains on aggrecan extracted from human airways” Glycobiology 25:1249.

Zuckerman DM, Boucher LE, Xie K, Engelhardt H, Bosch J, Hoiczyk E. (2015) The bactofilin cytoskeleton protein BacM of Myxococcus xanthus forms an extended β-sheet structure likely mediated by hydrophobic interactions. PLoS One 10:e0121074.

Boucher LE, Bosch J. (2015) The apicomplexan glideosome and adhesins – structures and function. J Struct Biol. 190:93-114.

Jia Y, Yu H, Fernandes SM, Wei Y, Gonzalez-Gil A, Motari MG, Vajn K, Stevens WW, Peters AT, Bochner BS, Kern RC, Schleimer RP, Schnaar RL. (2015) Expression of ligands for Siglec-8 and Siglec-9 in human airways and airway cells. J Allergy Clin Immunol. 135:799-810.