Research Output 1968 2019

2018

Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides

Ongpipattanakul, C. & Nair, S. K., Jun 12 2018, In : Biochemistry. 57, 23, p. 3201-3209 9 p.

Research output: Contribution to journalArticle

Peptide Hydrolases
Peptides
Macrocyclic Compounds
Proteolysis
Small Molecule Libraries
Peritoneal Macrophages
Epigenomics
Histone Code
Gene Expression
Scavenger Receptors

BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis

Dong, X., Hu, X., Chen, J., Hu, D. & Chen, L-F., Feb 1 2018, In : Cell Death and Disease. 9, 2, 203.

Research output: Contribution to journalArticle

Cell Aging
Stomach Neoplasms
Neoplasms
3' Untranslated Regions
Proteins

Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane

Hallock, M. J., Greenwood, A. I., Wang, Y., Morrissey, J. H., Tajkhorshid, E., Rienstra, C. M. & Pogorelov, T. V., Dec 18 2018, In : Biochemistry. 57, 50, p. 6897-6905 9 p.

Research output: Contribution to journalArticle

Nanoclusters
Cell membranes
Cell Membrane
Calcium
Lipids

Carbon dots with induced surface oxidation permits imaging at single-particle level for intracellular studies

Misra, S. K., Srivastava, I., Khamo, J. S., Krishnamurthy, V. V., Sar, D., Schwartz-Duval, A. S., Soares, J. A. N. T., Zhang, K. & Pan, D., Aug 16 2018, In : Nanoscale. 10, 39, p. 18510-18519 10 p.

Research output: Contribution to journalArticle

Carbon
Imaging techniques
Oxidation
Oxides
Photoluminescence

Characterization of Leader Peptide Binding during Catalysis by the Nisin Dehydratase NisB

Repka, L. M., Hetrick, K. J., Chee, S. H. & van der Donk, W. A., Mar 28 2018, In : Journal of the American Chemical Society. 140, 12, p. 4200-4203 4 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Nisin
catalysis
Protein Sorting Signals
Catalysis

Chemical Physics in Living Cells-using Light to Visualize and Control Intracellular Signal Transduction

Krishnamurthy, V. V. & Zhang, K., 2018, In : Chinese Journal of Chemical Physics. 31, 4, p. 375-392 18 p.

Research output: Contribution to journalReview article

Comparison of t cell activities mediated by human TCRs and CARs that use the same recognition domains

Harris, D. T., Hager, M. V., Smith, S. N., Cai, Q., Stone, J. D., Kruger, P., Lever, M., Dushek, O., Schmitt, T. M., Greenberg, P. D. & Kranz, D. M., Feb 1 2018, In : Journal of Immunology. 200, 3, p. 1088-1100 13 p.

Research output: Contribution to journalArticle

Human Activities
HLA-A2 Antigen
Single-Chain Antibodies
Cell- and Tissue-Based Therapy
T-Lymphocytes

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination

Zeng, F. & Jin, H., Dec 1 2018, In : Scientific reports. 8, 1, 2349.

Research output: Contribution to journalArticle

Peptide Termination Factors
Translational Peptide Chain Termination
Peptidyl Transferases
Amino Acid Motifs
Methylation

Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons

Wang, Y., Shekhar, M., Thifault, D., Williams, C. J., McGreevy, R., Richardson, J., Singharoy, A. & Tajkhorshid, E., Nov 2018, In : Journal of Structural Biology. 204, 2, p. 319-328 10 p.

Research output: Contribution to journalArticle

Structural Models
Molecular Dynamics Simulation
Galactosidases
Electrons
Research

Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system

Xiao, T., Ackerman, C. M., Carroll, E. C., Jia, S., Hoagland, A., Chan, J. K. F., Thai, B., Liu, C. S., Isacoff, E. Y. & Chang, C. J., Jul 1 2018, In : Nature chemical biology. 14, 7, p. 655-663 9 p.

Research output: Contribution to journalArticle

Activity Cycles
Locus Coeruleus
Copper
Norepinephrine
Arousal

Cross-talk of cannabinoid and endocannabinoid metabolism is mediated via human cardiac CYP2J2

Arnold, W. R., Weigle, A. T. & Das, A., Jul 2018, In : Journal of Inorganic Biochemistry. 184, p. 88-99 12 p.

Research output: Contribution to journalArticle

Endocannabinoids
Cannabinoids
Metabolism
Dronabinol
Cytochrome P-450 Enzyme System

Cytochrome aa 3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures to Deliver O2 for Catalysis

Mahinthichaichan, P., Gennis, R. B. & Tajkhorshid, E., Apr 10 2018, In : Biochemistry. 57, 14, p. 2150-2161 12 p.

Research output: Contribution to journalArticle

Electron Transport Complex IV
Cytochromes
Catalysis
Tunnels
Oxidoreductases

Cytochrome b5 enhances androgen synthesis by rapidly reducing the CYP17A1 oxy-complex in the lyase step

Duggal, R., Denisov, I. G. & Sligar, S., Jul 2018, In : FEBS Letters. 592, 13, p. 2282-2288 7 p.

Research output: Contribution to journalLetter

Cytochromes b5
Lyases
Cytochrome P-450 Enzyme System
Androgens
NADPH-Ferrihemoprotein Reductase

Cytochromes bd-I and bo3 are essential for the bactericidal effect of microcin J25 on Escherichia coli cells

Galván, A. E., Chalón, M. C., Schurig-Briccio, L. A., Salomón, R. A., Minahk, C. J., Gennis, R. B. & Bellomio, A., Feb 2018, In : Biochimica et Biophysica Acta - Bioenergetics. 1859, 2, p. 110-118 9 p.

Research output: Contribution to journalArticle

Open Access
Cytochromes
Escherichia coli
Cell Respiration
Oxygen
Membranes

Damage-Responsive Microcapsules for Amplified Photoacoustic Detection of Microcracks in Polymers

Geng, J. L., Li, W., Smaga, L. P., Sottos, N. R. & Chan, J. K. F., Apr 10 2018, In : Chemistry of Materials. 30, 7, p. 2198-2202 5 p.

Research output: Contribution to journalArticle

Photoacoustic effect
Microcracks
Polymers

DEER Spectroscopy Measurements Reveal Multiple Conformations of HIV-1 SOSIP Envelopes that Show Similarities with Envelopes on Native Virions

Stadtmueller, B. M., Bridges, M. D., Dam, K. M., Lerch, M. T., Huey-Tubman, K. E., Hubbell, W. L. & Bjorkman, P. J., Aug 21 2018, In : Immunity. 49, 2, p. 235-246.e4

Research output: Contribution to journalArticle

Virion
HIV-1
Spectrum Analysis
Electrons
Neutralizing Antibodies

Deregulation of RNA metabolism in microsatellite expansion diseases

Misra, C., Lin, F. & Kalsotra, A., Jan 1 2018, Advances in Neurobiology. Springer New York LLC, p. 213-238 26 p. (Advances in Neurobiology; vol. 20).

Research output: Chapter in Book/Report/Conference proceedingChapter

Deregulation
Metabolism
Microsatellite Repeats
Trinucleotide Repeat Expansion
RNA

Development and Application of Yeast and Phage Display of Diverse Lanthipeptides

Hetrick, K. J., Walker, M. C. & van der Donk, W. A., Apr 25 2018, In : ACS Central Science. 4, 4, p. 458-467 10 p.

Research output: Contribution to journalArticle

Bacteriophages
Yeast
Display devices
Peptides
Bioactivity
Glycine
Keto Acids
Proteins
Oxidoreductases
Bacillus subtilis

Development of Photoacoustic Probes for in Vivo Molecular Imaging

Reinhardt, C. J. & Chan, J. K. F., Jan 16 2018, In : Biochemistry. 57, 2, p. 194-199 6 p.

Research output: Contribution to journalReview article

Molecular imaging
Biological Models
Molecular Imaging
Photoacoustic effect
Optical Imaging

Direct protein-lipid interactions shape the conformational landscape of secondary transporters

Martens, C., Shekhar, M., Borysik, A. J., Lau, A. M., Reading, E., Tajkhorshid, E., Booth, P. J. & Politis, A., Dec 1 2018, In : Nature communications. 9, 1, 4151.

Research output: Contribution to journalArticle

transporter
lipids
proteins
Lipids
Switches

Double methylation of tRNA-U54 to 2-O-methylthymidine (Tm) synergistically decreases immune response by Toll-like receptor 7

Keller, P., Freund, I., Marchand, V., Bec, G., Huang, R. H., Motorin, Y., Eigenbrod, T., Dalpke, A. & Helm, M., Jan 1 2018, In : Nucleic acids research. 46, 18, p. 9764-9775 12 p.

Research output: Contribution to journalArticle

Open Access
Toll-Like Receptor 7
Transfer RNA
Methylation
RNA
RNA, Transfer, Lys

Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4

Denisov, I. G., Baylon, J. L., Grinkova, Y. V., Tajkhorshid, E. & Sligar, S. G., Feb 6 2018, In : Biochemistry. 57, 5, p. 805-816 12 p.

Research output: Contribution to journalArticle

Drug interactions
Cytochrome P-450 CYP3A
Drug Interactions
Lactones
Pharmaceutical Preparations

Editorial overview: Novel enzymes, coenzymes, and metabolic pathways

Gerlt, J. A. & Erb, T. J., Dec 2018, In : Current Opinion in Chemical Biology. 47, p. A4-A6

Research output: Contribution to journalEditorial

Enzymes and Coenzymes
Metabolic Networks and Pathways

Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE

Vermaas, J. V., Rempe, S. B. & Tajkhorshid, E., Aug 7 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 32, p. E7502-E7511

Research output: Contribution to journalArticle

Multiple Drug Resistance
Static Electricity
Glutamic Acid
Protons
Hydrogen

Elucidation of the roles of conserved residues in the biosynthesis of the lasso peptide paeninodin

Hegemann, J. D., Schwalen, C. J., Mitchell, D. A. & van der Donk, W. A., Jan 1 2018, In : Chemical Communications. 54, 65, p. 9007-9010 4 p.

Research output: Contribution to journalArticle

Biosynthesis
Peptides
Assays
Proteolysis
Substrates

Endocannabinoid Virodhamine Is an Endogenous Inhibitor of Human Cardiovascular CYP2J2 Epoxygenase

Carnevale, L. N., Arango, A. S., Arnold, W. R., Tajkhorshid, E. & Das, A., Nov 20 2018, In : Biochemistry. 57, 46, p. 6489-6499 11 p.

Research output: Contribution to journalArticle

Endocannabinoids
Anti-Inflammatory Agents
Arachidonic Acid
Cannabinoids
Cytochrome P-450 Enzyme System

Enzymatic reconstitution of ribosomal peptide backbone thioamidation

Mahanta, N., Liu, A., Dong, S., Nair, S. K. & Mitchell, D. A., Mar 20 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 12, p. 3030-3035 6 p.

Research output: Contribution to journalArticle

Oxidoreductases
Peptides
Archaea
Post Translational Protein Processing
Proteins

Enzyme Architecture: Breaking Down the Catalytic Cage that Activates Orotidine 5′-Monophosphate Decarboxylase for Catalysis

Reyes, A. C., Plache, D. C., Koudelka, A. P., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Dec 19 2018, In : Journal of the American Chemical Society. 140, 50, p. 17580-17590 11 p.

Research output: Contribution to journalArticle

Carboxy-Lyases
catalysis
Catalysis
Yeast
Enzymes

Erratum: Correction: Impaired Mitochondrial Energy Production Causes Light-Induced Photoreceptor Degeneration Independent of Oxidative Stress (PLoS biology (2015) 13 7 (e1002197))

Jaiswal, M., Haelterman, N. A., Sandoval, H., Xiong, B., Donti, T., Kalsotra, A., Yamamoto, S., Cooper, T. A., Graham, B. H. & Bellen, H. J., Mar 1 2018, In : PLoS biology. 16, 3, p. e1002622

Research output: Contribution to journalComment/debate

Open Access
Oxidative stress
photoreceptors
Oxidative Stress
oxidative stress
Light

Erratum to: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. (Nature Genetics, (2018), 50, 11, (1565-1573), 10.1038/s41588-018-0237-2)

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., Zhu, F., Jones, T., Zhu, X., Bowers, J., Wai, C. M., Zheng, C., Shi, Y., Chen, S., Xu, X., Yue, J., Nelson, D. R., Huang, L., Li, Z., Xu, H. & 88 others, Zhou, D., Wang, Y., Hu, W., Lin, J., Deng, Y., Pandey, N., Mancini, M., Zerpa, D., Nguyen, J. K., Wang, L., Yu, L., Xin, Y., Ge, L., Arro, J., Han, J. O., Chakrabarty, S., Pushko, M., Zhang, W., Ma, Y., Ma, P., Lv, M., Chen, F., Zheng, G., Xu, J., Yang, Z., Deng, F., Chen, X., Liao, Z., Zhang, X., Lin, Z., Lin, H., Yan, H., Kuang, Z., Zhong, W., Liang, P., Wang, G., Yuan, Y., Shi, J., Hou, J., Lin, J., Jin, J., Cao, P., Shen, Q., Jiang, Q., Zhou, P., Ma, Y., Zhang, X., Xu, R., Liu, J., Zhou, Y., Jia, H., Ma, Q., Qi, R., Zhang, Z., Fang, J., Fang, H., Song, J., Wang, M., Dong, G., Wang, G., Chen, Z., Ma, T., Liu, H., Dhungana, S. R., Huss, S. E., Yang, X., Sharma, A., Trujillo, J. H., Martinez, M. C., Hudson, M., Riascos, J. J., Schuler, M. A., Chen, L., Braun, D. M., Li, L., Yu, Q., Wang, J., Wang, K., Schatz, M. C., Heckerman, D., Van Sluys, M. A., Souza, G. M., Moore, P. H., Sankoff, D., VanBuren, R., Paterson, A. H., Nagai, C. & Ming, R. R., Dec 1 2018, In : Nature Genetics. 50, 12, 1 p.

Research output: Contribution to journalComment/debate

Saccharum
Alleles
Genome
Molecular Sequence Annotation
Databases

FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity

Yien, Y. Y., Shi, J., Chen, C., Cheung, J. T. M., Grillo, A. S., Shrestha, R., Li, L., Zhang, X., Kafina, M. D., Kingsley, P. D., King, M. J., Ablain, J., Li, H., Zon, L. I., Palis, J., Burke, M., Bauer, D. E., Orkin, S. H., Koehler, C. M., Phillips, J. D. & 4 others, Kaplan, J., Ward, D. M., Lodish, H. F. & Paw, B. H., Jan 1 2018, In : Journal of Biological Chemistry. 293, 51, p. 19797-19811 15 p.

Research output: Contribution to journalArticle

Ferrochelatase
Erythropoietin
Heme
Iron
Erythropoiesis

Functional assignment of multiple catabolic pathways for d-apiose article

Carter, M. S., Zhang, X., Huang, H., Bouvier, J. T., Francisco, B. S., Vetting, M. W., Al-Obaidi, N., Bonanno, J. B., Ghosh, A., Zallot, R. G., Andersen, H. M., Almo, S. C. & Gerlt, J. A., Jul 1 2018, In : Nature chemical biology. 14, 7, p. 696-705 10 p.

Research output: Contribution to journalArticle

Methylmalonyl-CoA carboxytransferase
Carrier Proteins
Phosphates
Genome
Pentoses
Cytochromes
Escherichia coli
Protons
Glutamic Acid
Electrons

Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin

Wang, K. K. A., Ng, T. L., Wang, P., Huang, Z., Balskus, E. P. & van der Donk, W. A., Dec 1 2018, In : Nature communications. 9, 1, 3687.

Research output: Contribution to journalArticle

hydrazine
glutamic acid
biosynthesis
Biosynthesis
hydrazines

Human Cytochrome CYP17A1: The Structural Basis for Compromised Lyase Activity with 17-Hydroxyprogesterone

Mak, P. J., Duggal, R., Denisov, I. G., Gregory, M. C., Sligar, S. & Kincaid, J. R., Jun 13 2018, In : Journal of the American Chemical Society. 140, 23, p. 7324-7331 8 p.

Research output: Contribution to journalArticle

17-alpha-Hydroxyprogesterone
Pregnenolone
Lyases
androgen
Cytochromes

Human P450 CYP17A1: Control of Substrate Preference by Asparagine 202

Gregory, M. C., Mak, P. J., Khatri, Y., Kincaid, J. R. & Sligar, S. G., Feb 6 2018, In : Biochemistry. 57, 5, p. 764-771 8 p.

Research output: Contribution to journalArticle

17-alpha-Hydroxyprogesterone
Asparagine
Substrates
Enzymes
Pregnenes

Incorporation of Nonproteinogenic Amino Acids in Class i and II Lantibiotics

Kakkar, N., Perez, J. G., Liu, W. R., Jewett, M. C. & van der Donk, W. A., Apr 20 2018, In : ACS chemical biology. 13, 4, p. 951-957 7 p.

Research output: Contribution to journalArticle

Bacteriocins
Amino Acids
Nisin
Amber
Terminator Codon

Investigation of Amide Bond Formation during Dehydrophos Biosynthesis

Ulrich, E. C., Bougioukou, D. J. & van der Donk, W. A., Mar 16 2018, In : ACS chemical biology. 13, 3, p. 537-541 5 p.

Research output: Contribution to journalArticle

Biosynthesis
Transfer RNA
Amides
RNA, Transfer, Leu
Enzymes

Investigation of Substrate Recognition and Biosynthesis in Class IV Lanthipeptide Systems

Hegemann, J. D. & van der Donk, W. A., May 2 2018, In : Journal of the American Chemical Society. 140, 17, p. 5743-5754 12 p.

Research output: Contribution to journalArticle

Biosynthesis
peptide
Peptides
Enzymes
substrate

Ionophoric effects of the antitubercular drug bedaquiline

Hards, K., McMillan, D. G. G., Schurig-Briccio, L. A., Gennis, R. B., Lill, H., Bald, D. & Cook, G. M., Jul 10 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. 7326-7331 6 p.

Research output: Contribution to journalArticle

bedaquiline
Antitubercular Agents
Adenosine Triphosphate
Escherichia coli
Proton-Motive Force

Lanthionine synthetase C-like protein 2 (LanCL2) is important for adipogenic differentiation

Dutta, D., Lai, K. Y., Reyes-Ordoñez, A., Chen, J. & van der Donk, W. A., Jan 1 2018, In : Journal of Lipid Research. 59, 8, p. 1433-1445 13 p.

Research output: Contribution to journalArticle

Peroxisome Proliferator-Activated Receptors
Ligases
Protein C
CCAAT-Enhancer-Binding Proteins
Proteins

Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor

Cao, X., Koch, T., Steffens, L., Finkensieper, J., Zigann, R., Cronan, J. E. & Dahl, C., Jul 13 2018, In : eLife. 7, e37439.

Research output: Contribution to journalArticle

Sulfur
Carrier Proteins
Oxidation
Genes
Bacillus subtilis

Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside

Petronikolou, N., Hollatz, A. J., Schuler, M. A. & Nair, S. K., Apr 16 2018, In : ChemBioChem. 19, 8, p. 784-788 5 p.

Research output: Contribution to journalArticle

Iridoid Glycosides
Methylation
Methyltransferases
Secologanin Tryptamine Alkaloids
Indole Alkaloids

Loss of function mutations in VARS encoding cytoplasmic valyl-tRNA synthetase cause microcephaly, seizures, and progressive cerebral atrophy

Stephen, J., Nampoothiri, S., Banerjee, A., Tolman, N. J., Penninger, J. M., Elling, U., Agu, C. A., Burke, J. D., Devadathan, K., Kannan, R., Huang, Y., Steinbach, P. J., Martinis, S. A., Gahl, W. A. & Malicdan, M. C. V., Apr 1 2018, In : Human Genetics. 137, 4, p. 293-303 11 p.

Research output: Contribution to journalArticle

Valine-tRNA Ligase
Microcephaly
Atrophy
Seizures
Mutation

Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor

Infield, D. T., Matulef, K., Galpin, J. D., Lam, K., Tajkhorshid, E., Ahern, C. A. & Valiyaveetil, F. I., Dec 1 2018, In : Nature communications. 9, 1, 5055.

Research output: Contribution to journalArticle

mutagenesis
Mutagenesis
Hydrogen Bonding
Ion Channels
Amides

Mapping interaction sites on human chemokine receptors by deep mutational scanning

Heredia, J. D., Park, J., Brubaker, R. J., Szymanski, S. K., Gill, K. S. & Procko, E., Jun 1 2018, In : Journal of Immunology. 200, 11, p. 3825-3839 15 p.

Research output: Contribution to journalArticle

Chemokine Receptors
Chemokines
HIV Envelope Protein gp120
Mutation
Ligands

Mechanism of proton transfer through the KC proton pathway in the Vibrio cholerae cbb3 terminal oxidase

Ahn, Y. O., Albertsson, I., Gennis, R. B. & Ädelroth, P., Nov 2018, In : Biochimica et Biophysica Acta - Bioenergetics. 1859, 11, p. 1191-1198 8 p.

Research output: Contribution to journalArticle

Proton transfer
Vibrio cholerae
Protons
Oxidoreductases
Oxygen

Menthol stereoisomers exhibit different effects on α4β2 nAChR upregulation and dopamine neuron spontaneous firing

Henderson, B. J., Grant, S., Wong, B. K., Shahoei, R., Huard, S. M., Saladi, S. S. M., Tajkhorshid, E., Dougherty, D. A. & Lester, H. A., Nov 1 2018, In : eNeuro. 5, 6, e0465-18.2018.

Research output: Contribution to journalArticle

Menthol
Stereoisomerism
Dopaminergic Neurons
Up-Regulation
Aptitude