Research Output 1967 2020

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2014

Biotin and lipoic acid: Synthesis, attachment, and regulation

Cronan, J. E., Jan 1 2014, In : EcoSal Plus. 6, 1, p. 1-39 39 p.

Research output: Contribution to journalArticle

Thioctic Acid
Biotin
Coenzymes
Synthetic Genes
Proteins

Brd4 maintains constitutively active NF-κB in cancer cells by binding to acetylated RelA

Zou, Z., Huang, B., Wu, X., Zhang, H., Qi, J., Bradner, J., Nair, S. & Chen, L. F., May 1 2014, In : Oncogene. 33, 18, p. 2395-2404 10 p.

Research output: Contribution to journalArticle

Lysine
Neoplasms
Proteins
Severe Combined Immunodeficiency
Ubiquitination

Changing the peptide specificity of a human T-cell receptor by directed evolution

Smith, S. N., Wang, Y., Baylon, J. L., Singh, N. K., Baker, B. M., Tajkhorshid, E. & Kranz, D. M., 2014, In : Nature communications. 5, 5223.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor
T-cells
peptides
clone cells
Peptides

Characterization of the type 2 NADH:menaquinone oxidoreductases from Staphylococcus aureus and the bactericidal action of phenothiazines

Schurig-Briccio, L. A., Yano, T., Rubin, H. & Gennis, R. B., Jul 2014, In : Biochimica et Biophysica Acta - Bioenergetics. 1837, 7, p. 954-963 10 p.

Research output: Contribution to journalArticle

Phenothiazines
Vitamin K 2
NAD
Staphylococcus aureus
Oxidoreductases

Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase

Hung, J. E., Fogle, E. J., Garg, N., Chekan, J. R., Nair, S. K. & Van Der Donk, W. A., Jan 31 2014, In : PloS one. 9, 1, e87134.

Research output: Contribution to journalArticle

Phosphites
mutants
catalytic activity
active sites
Catalytic Domain
Free energy
Sampling
Membrane Transport Proteins
free energy
Membranes

Conformational coupling between the active site and residues within the KC-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase

Ahn, Y. O., Mahinthichaichan, P., Lee, H. J., Ouyang, H., Kaluka, D., Yeh, S. R., Arjona, D., Rousseau, D. L., Tajkhorshid, E., Ädelroth, P. & Gennis, R. B., Oct 21 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 42, p. E4419-E4428

Research output: Contribution to journalArticle

Vibrio cholerae
Catalytic Domain
Oxidoreductases
Oxygen
Protons

Conformational dynamics at the inner gate of KcsA during activation

Hulse, R. E., Sachleben, J. R., Wen, P. C., Moradi, M., Tajkhorshid, E. & Perozo, E., Apr 29 2014, In : Biochemistry. 53, 16, p. 2557-2559 3 p.

Research output: Contribution to journalArticle

Chemical activation
Potassium Channels
Electron Spin Resonance Spectroscopy
Lipid Bilayers
Micelles

Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

Mishra, S., Verhalen, B., Stein, R. A., Wen, P. C., Tajkhorshid, E. & Mchaourab, H. S., May 16 2014, In : eLife. 2014, 3

Research output: Contribution to journalArticle

ATP-Binding Cassette Transporters
Nucleotides
Adenosine Triphosphate
Stroke
Hydrolysis

Conformational heterogeneity of α-synuclein in membrane

Vermaas, J. V. & Tajkhorshid, E., Dec 2014, In : Biochimica et Biophysica Acta - Biomembranes. 1838, 12, p. 3107-3117 11 p.

Research output: Contribution to journalArticle

Synucleins
Membranes
Conformations
Lipids
Monomers

Conjugation to albumin-binding molecule tags as a strategy to improve both efficacy and pharmacokinetic properties of the complement inhibitor compstatin

Huang, Y., Reis, E. S., Knerr, P. J., van der Donk, W. A., Ricklin, D. & Lambris, J. D., Oct 1 2014, In : ChemMedChem. 9, 10, p. 2223-2226 4 p.

Research output: Contribution to journalArticle

Complement Inactivating Agents
Pharmacokinetics
Albumins
Protein Binding
Molecules

Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs

Orlando, B. J., McDougle, D. R., Lucido, M. J., Eng, E. T., Graham, L. A., Schneider, C., Stokes, D. L., Das, A. & Malkowski, M. G., Apr 15 2014, In : Archives of Biochemistry and Biophysics. 546, p. 33-40 8 p.

Research output: Contribution to journalArticle

Lipid bilayers
Lipid Bilayers
Cyclooxygenase 2
Catalysis
Arachidonic Acid

Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis

Dunbar, K. L., Chekan, J. R., Cox, C. L., Burkhart, B. J., Nair, S. K. & Mitchell, D. A., Oct 1 2014, In : Nature chemical biology. 10, 10, p. 823-829 7 p.

Research output: Contribution to journalArticle

Oxazoles
Thiazoles
Protein C
Adenosine Triphosphate
Catalysis

Discovery of a novel l -lyxonate degradation pathway in Pseudomonas aeruginosa PAO1

Ghasempur, S., Eswaramoorthy, S., Hillerich, B. S., Seidel, R. D., Swaminathan, S., Almo, S. C. & Gerlt, J. A., May 27 2014, In : Biochemistry. 53, 20, p. 3357-3366 10 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Pseudomonas aeruginosa
mandelate racemase
Degradation
Dehydration

Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the d-mannonate dehydratase subgroup

Wichelecki, D. J., Balthazor, B. M., Chau, A. C., Vetting, M. W., Fedorov, A. A., Fedorov, E. V., Lukk, T., Patskovsky, Y. V., Stead, M. B., Hillerich, B. S., Seidel, R. D., Almo, S. C. & Gerlt, J. A., Apr 29 2014, In : Biochemistry. 53, 16, p. 2722-2731 10 p.

Research output: Contribution to journalArticle

gluconate dehydratase
Phosphopyruvate Hydratase
Dehydration
mandelate racemase
Sugar Acids

Dynamic association of the PI3P-interacting Mon1-Ccz1 GEF with vacuoles is controlled through its phosphorylation by the type 1 casein kinase Yck3

Lawrence, G., Brown, C. C., Flood, B. A., Karunakaran, S., Cabrera, M., Nordmann, M., Ungermann, C. & Fratti, R. A., May 15 2014, In : Molecular biology of the cell. 25, 10, p. 1608-1619 12 p.

Research output: Contribution to journalArticle

Casein Kinase I
Vacuoles
Phosphorylation
Recycling
Class III Phosphatidylinositol 3-Kinases

Endocannabinoids anandamide and 2-arachidonoylglycerol are substrates for human CYP2J2 epoxygenase

McDougle, D. R., Kambalyal, A., Meling, D. D. & Das, A., Dec 1 2014, In : Journal of Pharmacology and Experimental Therapeutics. 351, 3, p. 616-627 12 p.

Research output: Contribution to journalArticle

Endocannabinoids
Arachidonic Acid
Epoxy Compounds
Ligands
NADPH-Ferrihemoprotein Reductase

Enzymatic and structural characterization of rTSγ provides insights into the function of rTSβ

Wichelecki, D. J., Froese, D. S., Kopec, J., Muniz, J. R. C., Yue, W. W. & Gerlt, J. A., Apr 29 2014, In : Biochemistry. 53, 16, p. 2732-2738 7 p.

Research output: Contribution to journalArticle

Thymidylate Synthase
Protein Isoforms
Gene encoding
Hydro-Lyases
Biosynthesis

Enzyme architecture: Deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5′-monophosphate decarboxylase

Goldman, L. M., Amyes, T. L., Goryanova, B., Gerlt, J. A. & Richard, J. P., Jul 16 2014, In : Journal of the American Chemical Society. 136, 28, p. 10156-10165 10 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Binding energy
Enzymes
enzyme
Grippers

Evidence against translational repression by the carboxyltransferase component of Escherichia coli acetyl coenzyme a carboxylase

Smith, A. C. & Cronan, J. E., Jan 1 2014, In : Journal of bacteriology. 196, 21, p. 3768-3775 8 p.

Research output: Contribution to journalArticle

Carboxyl and Carbamoyl Transferases
Coenzymes
Escherichia coli
Messenger RNA
Acetyl-CoA Carboxylase

Evidence for distinct electron transfer processes in terminal oxidases from different origin by means of protein film voltammetry

Meyer, T., Melin, F., Xie, H., Von Der Hocht, I., Choi, S. K., Noor, M. R., Michel, H., Gennis, R. B., Soulimane, T. & Hellwig, P., Aug 6 2014, In : Journal of the American Chemical Society. 136, 31, p. 10854-10857 4 p.

Research output: Contribution to journalArticle

Voltammetry
Oxidoreductases
Enzymes
Electrons
enzyme

Evolution of enzymatic activities in the enolase superfamily: Galactarate dehydratase III from agrobacterium tumefaciens C58

Groninger-Poe, F. P., Bouvier, J. T., Vetting, M. W., Kalyanaraman, C., Kumar, R., Almo, S. C., Jacobson, M. P. & Gerlt, J. A., Jul 1 2014, In : Biochemistry. 53, 25, p. 4192-4203 12 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Agrobacterium tumefaciens
Phosphopyruvate Hydratase
Sugar Acids
Biochemistry

Exploring the substrate promiscuity of an antibiotic inactivating enzyme

Agarwal, V., Vondenhoff, G., Gadakh, B., Severinov, K., Van Aerschot, A. & Nair, S. K., Oct 1 2014, In : MedChemComm. 5, 10, p. 1567-1570 4 p.

Research output: Contribution to journalArticle

Nucleotides
Anti-Bacterial Agents
Aspartate-tRNA Ligase
Substrates
Enzymes

Factor XII inhibition reduces thrombus formation in a primate thrombosis model

Matafonov, A., Leung, P. Y., Gailani, A. E., Grach, S. L., Puy, C., Cheng, Q., Sun, M. F., McCarty, O. J. T., Tucker, E. I., Kataoka, H., Renné, T., Morrissey, J. H., Gruber, A. & Gailani, D., Mar 13 2014, In : Blood. 123, 11, p. 1739-1746 8 p.

Research output: Contribution to journalArticle

Factor XII
Primates
Thrombosis
Factor XI
Fibrin

Functional investigations of Thromboxane synthase (CYP5A1) in lipid bilayers of nanodiscs

Das, A., Varma, S. S., Mularczyk, C. & Meling, D. D., Jan 1 2014, In : ChemBioChem. 15, 6, p. 892-899 8 p.

Research output: Contribution to journalArticle

Lipid bilayers
Thromboxanes
Lipid Bilayers
Cyanides
Lipids

Galactaro δ-lactone isomerase: Lactone isomerization by a member of the amidohydrolase superfamily

Bouvier, J. T., Groninger-Poe, F. P., Vetting, M., Almo, S. C. & Gerlt, J. A., Feb 4 2014, In : Biochemistry. 53, 4, p. 614-616 3 p.

Research output: Contribution to journalArticle

Amidohydrolases
Isomerases
Lactones
Isomerization
4 alpha-glucanotransferase

High divergence of the precursor peptides in combinatorial lanthipeptide biosynthesis

Zhang, Q., Yang, X., Wang, H. & Van Der Donk, W. A., Nov 21 2014, In : ACS chemical biology. 9, 11, p. 2686-2694 9 p.

Research output: Contribution to journalArticle

Peptide Biosynthesis
Biosynthesis
Peptides
Protein Sorting Signals
Biological Products

High-throughput fluorescence anisotropy screen for inhibitors of the oncogenic mrna binding protein, IMP-1

Mahapatra, L., Mao, C., Andruska, N., Zhang, C. & Shapiro, D. J., Mar 1 2014, In : Journal of Biomolecular Screening. 19, 3, p. 427-436 10 p.

Research output: Contribution to journalArticle

Inosine Monophosphate
Fluorescence Polarization
Carrier Proteins
Anisotropy
Fluorescence

Identification of the in vivo function of the high-efficiency d -mannonate dehydratase in caulobacter crescentus NA1000 from the enolase superfamily

Wichelecki, D. J., Graff, D. C., Al-Obaidi, N., Almo, S. C. & Gerlt, J. A., Jul 1 2014, In : Biochemistry. 53, 25, p. 4087-4089 3 p.

Research output: Contribution to journalArticle

Caulobacter crescentus
Phosphopyruvate Hydratase
Glucuronic Acid
Biochemistry
Metabolism

Inefficient translation renders the enterococcus faecalis fabk enoyl- acyl carrier protein reductase phenotypically cryptic

Bi, H., Zhu, L., Wang, H. & Cronan, J. E., Jan 1 2014, In : Journal of bacteriology. 196, 1, p. 170-179 10 p.

Research output: Contribution to journalArticle

Acyl Carrier Protein
Enterococcus faecalis
Oxidoreductases
Growth
Mutation

Interpretation and deconvolution of nanodisc native mass spectra

Marty, M. T., Zhang, H., Cui, W., Gross, M. L. & Sligar, S. G., Feb 1 2014, In : Journal of the American Society for Mass Spectrometry. 25, 2, p. 269-277 9 p.

Research output: Contribution to journalArticle

Deconvolution
Lipids
Charge distribution
Gases
Dimyristoylphosphatidylcholine

Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: Pathways for the catabolism of L-gulonate and L-idonate

Wichelecki, D. J., Vendiola, J. A. F., Jones, A. M., Al-Obaidi, N., Almo, S. C. & Gerlt, J. A., Sep 9 2014, In : Biochemistry. 53, 35, p. 5692-5699 8 p.

Research output: Contribution to journalArticle

gluconate dehydratase
Phosphopyruvate Hydratase
Dehydration
Biochemistry
Chromohalobacter

Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

Desai, B. J., Goto, Y., Cembran, A., Fedorov, A. A., Almo, S. C., Gao, J., Suga, H. & Gerlt, J. A., Oct 21 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 42, p. 15066-15071 6 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
Amides
Hydrogen
Esters
Amber

Kinetics and intermediates of the reaction of fully reduced escherichia coli bo 3 ubiquinol oxidase with O2

Szundi, I., Kittredge, C., Choi, S. K., McDonald, W., Ray, J., Gennis, R. B. & Einarsdóttir, Ó., Jan 1 2014, In : Biochemistry. 53, 33, p. 5393-5404 12 p.

Research output: Contribution to journalArticle

Escherichia coli
Heme
Kinetics
Cytochromes
Oxidation

Kinetic solvent isotope effect in steady-state turnover by CYP19A1 suggests involvement of Compound 1 for both hydroxylation and aromatization steps

Khatri, Y., Luthra, A., Duggal, R. & Sligar, S. G., Aug 25 2014, In : FEBS Letters. 588, 17, p. 3117-3122 6 p.

Research output: Contribution to journalArticle

Aromatization
Hydroxylation
Lyases
Isotopes
Reaction intermediates

Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth

Zhang, K., Duan, L., Ong, Q., Lin, Z., Varman, P. M., Sung, K. & Cui, B., Mar 25 2014, In : PloS one. 9, 3, e92917.

Research output: Contribution to journalArticle

neurites
MAP Kinase Signaling System
PC12 Cells
Mitogen-Activated Protein Kinase Kinases
Chemical activation

Mechanistic studies on the substrate-tolerant lanthipeptide synthetase ProcM

Mukherjee, S. & Van Der Donk, W. A., Jul 23 2014, In : Journal of the American Chemical Society. 136, 29, p. 10450-10459 10 p.

Research output: Contribution to journalArticle

Ligases
peptide
Alkynes
substrate
Protein Sorting Signals

Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3

Arcario, M. J. & Tajkhorshid, E., Nov 4 2014, In : Biophysical journal. 107, 9, p. 2059-2069 11 p.

Research output: Contribution to journalArticle

Talin
Membranes
Static Electricity
Integrins

Mode of action and structure-activity relationship studies of geobacillin i

Garg, N., Oman, T. J., Andrew Wang, T. S., De Gonzalo, C. V. G., Walker, S. & Van Der Donk, W. A., Jan 1 2014, In : Journal of Antibiotics. 67, 1, p. 133-136 4 p.

Research output: Contribution to journalArticle

Bacterial Drug Resistance
Nisin
Bacteriocins
Microbial Sensitivity Tests
Structure-Activity Relationship

Modulating the copper-sulfur interaction in type 1 blue copper azurin by replacing Cys112 with nonproteinogenic homocysteine

Clark, K. M., Yu, Y., Van Der Donk, W. A., Blackburn, N. J. & Lu, Y., Feb 1 2014, In : Inorganic Chemistry Frontiers. 1, 2, p. 153-158 6 p.

Research output: Contribution to journalArticle

Azurin
Homocysteine
Sulfur
Copper
Amino Acids

Myxoma virus expressing a fusion protein of interleukin-15 (IL15) and IL15 receptor alpha has enhanced antitumor activity

Tosic, V., Thomas, D. L., Kranz, D. M., Liu, J., McFadden, G., Shisler, J. L., MacNeill, A. L. & Roy, E. J., Oct 16 2014, In : PloS one. 9, 10, e109801.

Research output: Contribution to journalArticle

Interleukin-15 Receptor alpha Subunit
Myxoma virus
viral fusion proteins
Interleukin-15
Viruses

NMR structure of the S-linked glycopeptide sublancin 168

Garcia De Gonzalo, C. V., Zhu, L., Oman, T. J. & Van Der Donk, W. A., Mar 21 2014, In : ACS chemical biology. 9, 3, p. 796-801 6 p.

Research output: Contribution to journalArticle

Glycopeptides
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Amino Acids
Peptides

Nontoxic polyphosphate inhibitors reduce thrombosis while sparing hemostasis

Travers, R. J., Shenoi, R. A., Kalathottukaren, M. T., Kizhakkedathu, J. N. & Morrissey, J. H., Nov 20 2014, In : Blood. 124, 22, p. 3183-3190 8 p.

Research output: Contribution to journalArticle

Polyphosphates
Hemostasis
Heparin
Thrombosis
Hemorrhage

Partitioning of amino acids into a model membrane: Capturing the interface

Pogorelov, T. V., Vermaas, J. V., Arcario, M. J. & Tajkhorshid, E., Feb 13 2014, In : Journal of Physical Chemistry B. 118, 6, p. 1481-1492 12 p.

Research output: Contribution to journalArticle

amino acids
Amino acids
membranes
Membranes
Amino Acids

PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis

Feng, Y. & Cronan, J. E., Jul 2014, In : Research in Microbiology. 165, 6, p. 429-438 10 p.

Research output: Contribution to journalArticle

Thioctic Acid
Pyruvic Acid
Oxidoreductases
Binding Sites
Galactosidases

Peptidoglycan Recognition Proteins Kill Bacteria by Inducing Oxidative, Thiol, and Metal Stress

Kashyap, D. R., Rompca, A., Gaballa, A., Helmann, J. D., Chan, J., Chang, C. J., Hozo, I., Gupta, D. & Dziarski, R., Jul 2014, In : PLoS pathogens. 10, 7, e1004280.

Research output: Contribution to journalArticle

Sulfhydryl Compounds
Metals
Bacteria
Anti-Bacterial Agents
Reactive Oxygen Species

Polyphosphate: A new player in the field of hemostasis

Smith, S. A. & Morrissey, J. H., Sep 2014, In : Current Opinion in Hematology. 21, 5, p. 388-394 7 p.

Research output: Contribution to journalArticle

Polyphosphates
Blood Coagulation
Hemostasis
Polyps
Blood Cells

Polyphosphate suppresses complement via the terminal pathway

Wat, J. M., Foley, J. H., Krisinger, M. J., Ocariza, L. M., Lei, V., Wasney, G. A., Lameignere, E., Strynadka, N. C., Smith, S. A., Morrissey, J. H. & Conway, E. M., Jan 30 2014, In : Blood. 123, 5, p. 768-776 9 p.

Research output: Contribution to journalArticle

Polyphosphates
Assays
Coagulation
Innate Immunity
Polymers

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine

Kumar, R., Zhao, S., Vetting, M. W., Wood, B. M. K., Sakai, A., Cho, K., Solbiati, J., Almo, S. C., Sweedler, J. V., Jacobson, M. P., Gerlt, J. A. & Cronan, J. E., Feb 11 2014, In : mBio. 5, 1, e00933-13.

Research output: Contribution to journalArticle

Betaine
Paracoccus denitrificans
Metabolomics
Hydroxyproline
Rhodobacter sphaeroides

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

Zhao, S., Sakai, A., Zhang, X., Vetting, M. W., Kumar, R., Hillerich, B., Francisco, B. S., Solbiati, J., Steves, A., Brown, S., Akiva, E., Barber, A., Seidel, R. D., Babbitt, P. C., Almo, S. C., Gerlt, J. A. & Jacobson, M. P., Jun 30 2014, In : eLife. 2014, 3, 03275.

Research output: Contribution to journalArticle

Metabolic Networks and Pathways
Genes
Genome
Enzymes
Archaea