Research Output 1968 2019

2017

Arachidonic Acid Metabolism by Human Cardiovascular CYP2J2 Is Modulated by Doxorubicin

Arnold, W. R., Baylon, J. L., Tajkhorshid, E. & Das, A., Dec 26 2017, In : Biochemistry. 56, 51, p. 6700-6712 13 p.

Research output: Contribution to journalArticle

Arachidonic Acid
Metabolism
Doxorubicin
Catalytic Domain
Enzyme kinetics

Brd4 modulates the innate immune response through Mnk2-eIF4E pathway-dependent translational control of IκBα

Bao, Y., Wu, X., Chen, J., Hu, X., Zeng, F., Cheng, J., Jin, H., Lin, X. & Chen, L-F., May 16 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 20, p. E3993-E4001

Research output: Contribution to journalArticle

Eukaryotic Initiation Factor-4E
Eukaryotic Initiation Factors
Innate Immunity
Gene Expression
Macrophages

Bright Dyes Bring Biology into Focus

Yadav, A. K. & Chan, J. K. F., Sep 27 2017, In : ACS Central Science. 3, 9, p. 920-921 2 p.

Research output: Contribution to journalShort survey

Dyes

Bromodomain and extraterminal proteins - A novel class of therapeutic targets in epigenetics

Chen, J. J., Zhao, X. L., Wang, Z. & Chen, L-F., Jan 1 2017, In : Yaoxue Xuebao. 52, 8, p. 1209-1215 7 p.

Research output: Contribution to journalReview article

Staphylococcal Protein A
Epigenomics
Proteins
Therapeutic Uses
Therapeutics

Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function

Trebesch, N., Vermaas, J. V. & Tajkhorshid, E., Jan 1 2017, Computational Biophysics of Membrane Proteins. Hirst, J. & Domene, C. (eds.). 10 ed. Royal Society of Chemistry, p. 197-236 40 p. (RSC Theoretical and Computational Chemistry Series; vol. 2017-January, no. 10).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Membranes
Computational methods
Free energy
Adenosinetriphosphate

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan, J. R., Estrada, P., Covello, P. S. & Nair, S. K., Jun 20 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 25, p. 6551-6556 6 p.

Research output: Contribution to journalArticle

Cyclic Peptides
Enzymes
Peptides
Plant Structures
Libraries

Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads

Olivares, P., Ulrich, E. C., Chekan, J. R., van der Donk, W. A. & Nair, S. K., Feb 17 2017, In : ACS chemical biology. 12, 2, p. 456-463 8 p.

Research output: Contribution to journalArticle

Fosfomycin
Biosynthesis
Enzymes
Anti-Bacterial Agents
Pseudomonas syringae

Chasing the open-state structure of pentameric ligand-gated ion channels

Gonzalez-Gutierrez, G., Wang, Y., Cymes, G. D., Tajkhorshid, E. & Grosman, C., Dec 1 2017, In : Journal of General Physiology. 149, 12, p. 1119-1138 20 p.

Research output: Contribution to journalArticle

Ligand-Gated Ion Channels
Glycine Receptors
Structural Models
Ions
Mutation

Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products

Burkhart, B. J., Kakkar, N., Hudson, G. A., van der Donk, W. A. & Mitchell, D. A., Jun 28 2017, In : ACS Central Science. 3, 6, p. 629-638 10 p.

Research output: Contribution to journalArticle

Protein Sorting Signals
Enzymes
Peptides
Biosynthesis
Substrates

Comparative proteomic investigation of metastatic and non-metastatic osteosarcoma cells of human and canine origin

Roy, J., Wycislo, K. L., Pondenis, H., Fan, T. M. & Das, A., Sep 2017, In : PloS one. 12, 9, e0183930.

Research output: Contribution to journalArticle

osteosarcoma
Osteosarcoma
Proteomics
proteomics
Canidae

Conformational equilibria of light-activated rhodopsin in nanodiscs

Van Eps, N., Caro, L. N., Morizumi, T., Kusnetzow, A. K., Szczepek, M., Hofmann, K. P., Bayburt, T. H., Sligar, S., Ernst, O. P. & Hubbell, W. L., Apr 18 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 16, p. E3268-E3275

Research output: Contribution to journalArticle

Rhodopsin
G-Protein-Coupled Receptors
Light
Electrons
Transducin

Control of leucine-dependent mTORC1 pathway through chemical intervention of leucyl-tRNA synthetase and RagD interaction

Kim, J. H., Lee, C., Lee, M., Wang, H., Kim, K., Park, S. J., Yoon, I., Jang, J., Zhao, H., Kim, H. K., Kwon, N. H., Jeong, S. J., Yoo, H. C., Kim, J. H., Yang, J. S., Lee, M. Y., Lee, C. W., Yun, J., Oh, S. J., Kang, J. S. & 6 others, Martinis, S. A., Hwang, K. Y., Guo, M., Han, G., Han, J. M. & Kim, S., Dec 1 2017, In : Nature communications. 8, 1, 732.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
leucine
Leucine
cancer
catalytic activity

Coupling X-Ray Reflectivity and in Silico Binding to Yield Dynamics of Membrane Recognition by Tim1

Tietjen, G. T., Baylon, J. L., Kerr, D., Gong, Z., Henderson, J. M., Heffern, C. T. R., Meron, M., Lin, B., Schlossman, M. L., Adams, E. J., Tajkhorshid, E. & Lee, K. Y. C., Oct 3 2017, In : Biophysical journal. 113, 7, p. 1505-1519 15 p.

Research output: Contribution to journalArticle

Computer Simulation
X-Rays
Membranes
Membrane Lipids
Membrane Proteins

Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase

Padayatti, P. S., Leung, J. H., Mahinthichaichan, P., Tajkhorshid, E., Ishchenko, A., Cherezov, V., Soltis, S. M., Jackson, J. B., Stout, C. D., Gennis, R. B. & Zhang, Q., Jul 5 2017, In : Structure. 25, 7, p. 1111-1119.e3

Research output: Contribution to journalArticle

Protons
NADP Transhydrogenases
Thermus thermophilus
Proton-Motive Force
Membranes

Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation

Calla, B., Noble, K., Johnson, R. M., Walden, K. K. O., Schuler, M. A., Robertson, H. M. & Berenbaum, M. R., Nov 2017, In : Molecular ecology. 26, 21, p. 6021-6035 15 p.

Research output: Contribution to journalArticle

Moths
cytochrome P-450
generalist
moth
Cytochrome P-450 Enzyme System

Deleting the DAG kinase Dgk1 augments yeast vacuole fusion through increased Ypt7 activity and altered membrane fluidity

Miner, G. E., Starr, M. L., Hurst, L. R. & Fratti, R., May 1 2017, In : Traffic. 18, 5, p. 315-329 15 p.

Research output: Contribution to journalArticle

Diacylglycerol Kinase
Membrane Fluidity
Fluidity
Diglycerides
Vacuoles

Differential membrane binding mechanics of synaptotagmin isoforms observed in atomic detail

Vermaas, J. V. & Tajkhorshid, E., Jan 1 2017, In : Biochemistry. 56, 1, p. 281-293 13 p.

Research output: Contribution to journalArticle

Synaptotagmins
Mechanics
Synaptotagmin I
Protein Isoforms
Membranes

Differential Roles for the Coagulation Factors XI and XII in Regulating the Physical Biology of Fibrin

Sylman, J. L., Daalkhaijav, U., Zhang, Y., Gray, E. M., Farhang, P. A., Chu, T. T., Zilberman-Rudenko, J., Puy, C., Tucker, E. I., Smith, S. A., Morrissey, J. H., Walker, T. W., Nan, X. L., Gruber, A. & McCarty, O. J. T., May 1 2017, In : Annals of Biomedical Engineering. 45, 5, p. 1328-1340 13 p.

Research output: Contribution to journalArticle

Coagulation
Chemical activation
Ellagic acid
Gelation
Tissue

Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters

Yu, X., Yang, G., Yan, C., Baylon, J. L., Jiang, J., Fan, H., Lu, G., Hasegawa, K., Okumura, H., Wang, T., Tajkhorshid, E., Li, S. & Yan, N., Aug 1 2017, In : Cell Research. 27, 8, p. 1020-1033 14 p.

Research output: Contribution to journalArticle

Symporters
Uracil
Protons
Micelles
Detergents

Disproportionate impact of named reactions on chemical biology

Bearrood, T. E. & Chan, J. K. F., Jan 1 2017, In : Aldrichimica Acta. 50, 2, p. 31-41 11 p.

Research output: Contribution to journalReview article

Organic Chemistry
Honey
Bees
Quercetin
Triazoles
Phytochemicals

DNA Aptamer-Based Activatable Probes for Photoacoustic Imaging in Living Mice

Zhang, J., Smaga, L. P., Satyavolu, N. S. R., Chan, J. K. F. & Lu, Y., Dec 6 2017, In : Journal of the American Chemical Society. 139, 48, p. 17225-17228 4 p.

Research output: Contribution to journalArticle

Nucleotide Aptamers
Photoacoustic effect
Thrombin
DNA
probe

Drive the car(go)s—new modalities to control cargo trafficking in live cells

Mondal, P., Khamo, J. S., Krishnamurthy, V. V., Cai, Q. & Zhang, K., Jan 20 2017, In : Frontiers in Molecular Neuroscience. 10, 4.

Research output: Contribution to journalReview article

Synaptic Transmission
Synapses
Neurotransmitter Receptor
Peptide Receptors
Active Biological Transport

Dynamics of the KB Proton Pathway in Cytochrome ba3 from Thermus thermophilus

von Ballmoos, C., Smirnova, I., Poiana, F., Gonska, N., Chang, H. Y., Gennis, R. B., Brzezinski, P. & Ädelroth, P., May 1 2017, In : Israel Journal of Chemistry. 57, 5, p. 424-436 13 p.

Research output: Contribution to journalArticle

Protons
Oxidoreductases
Proton transfer
Pumps
Proton Pumps

Energy transduction and alternating access of the mammalian ABC transporter P-glycoprotein

Verhalen, B., Dastvan, R., Thangapandian, S., Peskova, Y., Koteiche, H. A., Nakamoto, R. K., Tajkhorshid, E. & McHaourab, H. S., Mar 30 2017, In : Nature. 543, 7647, p. 738-741 4 p.

Research output: Contribution to journalArticle

ATP-Binding Cassette Transporters
P-Glycoprotein
Adenosine Triphosphate
Hydrolysis
Nucleotides

Enzymatic N- and C-Protection in Cyanobactin RiPP Natural Products

Sardar, D., Hao, Y., Lin, Z., Morita, M., Nair, S. K. & Schmidt, E. W., Mar 1 2017, In : Journal of the American Chemical Society. 139, 8, p. 2884-2887 4 p.

Research output: Contribution to journalArticle

Biological Products
peptide
Peptides
Biosynthesis
Enzymes

Erratum: Heme Binding Biguanides Target Cytochrome P450-Dependent Cancer Cell Mitochondria (Cell Chemical Biology (2017) 24(10) (1259–1275.e6) (S2451945617302830)(10.1016/j.chembiol.2017.08.009))

Guo, Z., Sevrioukova, I. F., Denisov, I. G., Zhang, X., Chiu, T. L., Thomas, D. G., Hanse, E. A., Cuellar, R. A. D., Grinkova, Y. V., Langenfeld, V. W., Swedien, D. S., Stamschror, J. D., Alvarez, J., Luna, F., Galván, A., Bae, Y. K., Wulfkuhle, J. D., Gallagher, R. I., Petricoin, E. F., Norris, B. & 17 others, Flory, C. M., Schumacher, R. J., O'Sullivan, M. G., Cao, Q., Chu, H., Lipscomb, J. D., Atkins, W. M., Gupta, K., Kelekar, A., Blair, I. A., Capdevila, J. H., Falck, J. R., Sligar, S., Poulos, T. L., Georg, G. I., Ambrose, E. & Potter, D. A., Oct 19 2017, In : Cell chemical biology. 24, 10, 1 p.

Research output: Contribution to journalComment/debate

Biguanides
Mitochondria
Heme
Cytochrome P-450 Enzyme System
Cell Biology

Evolutionary radiation of lanthipeptides in marine cyanobacteria

Cubillos-Ruiz, A., Berta-Thompson, J. W., Becker, J. W., van der Donk, W. A. & Chisholm, S. W., Jul 3 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 27, p. E5424-E5433

Research output: Contribution to journalArticle

Cyanobacteria
Ligases
Radiation
Cyclic Peptides
Peptides

Expression and activity of the BioH esterase of biotin synthesis is independent of genome context

Cao, X., Zhu, L., Hu, Z. & Cronan, J. E., Dec 1 2017, In : Scientific reports. 7, 1, 2141.

Research output: Contribution to journalArticle

Esterases
Operon
Biotin
Genome
Hydrolases

Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents

Vermaas, J. V., Pogorelov, T. V. & Tajkhorshid, E., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3764-3776 13 p.

Research output: Contribution to journalArticle

Computer Simulation
membranes
proteins
Proteins
Membranes

Generation of higher affinity T cell receptors by antigen-driven differentiation of progenitor t cells in vitro

Schmitt, T. M., Aggen, D. H., Ishida-Tsubota, K., Ochsenreither, S., Kranz, D. M. & Greenberg, P. D., Jan 1 2017, In : Nature Biotechnology. 35, 12, p. 1188-1195 8 p.

Research output: Contribution to journalArticle

T-cells
Antigens
T-Cell Antigen Receptor
Stem Cells
Autoantigens
Genes
Genome
Biological Products
Enzymes
Metabolic Networks and Pathways

Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes

Peck, S. C. & van der Donk, W. A., Apr 1 2017, In : Journal of Biological Inorganic Chemistry. 22, 2-3, p. 381-394 14 p.

Research output: Contribution to journalReview article

Iron
Electrons
Oxidation
Enzymes
Biosynthesis

Heme Binding Biguanides Target Cytochrome P450-Dependent Cancer Cell Mitochondria

Guo, Z., Sevrioukova, I. F., Denisov, I. G., Zhang, X., Chiu, T. L., Thomas, D. G., Hanse, E. A., Cuellar, R. A. D., Grinkova, Y. V., Langenfeld, V. W., Swedien, D. S., Stamschror, J. D., Alvarez, J., Luna, F., Galván, A., Bae, Y. K., Wulfkuhle, J. D., Gallagher, R. I., Petricoin, E. F., Norris, B. & 17 others, Flory, C. M., Schumacher, R. J., O'Sullivan, M. G., Cao, Q., Chu, H., Lipscomb, J. D., Atkins, W. M., Gupta, K., Kelekar, A., Blair, I. A., Capdevila, J. H., Falck, J. R., Sligar, S., Poulos, T. L., Georg, G. I., Ambrose, E. & Potter, D. A., Oct 19 2017, In : Cell chemical biology. 24, 10, p. 1259-1275.e6

Research output: Contribution to journalArticle

Biguanides
Cytochrome P-450 CYP3A
Mitochondria
Heme
Cytochrome P-450 Enzyme System

Heterologous expression and characterization of plant Taxadiene-5α-Hydroxylase (CYP725A4) in Escherichia coli

Rouck, J. E., Biggs, B. W., Kambalyal, A., Arnold, W. R., De Mey, M., Ajikumar, P. K. & Das, A., Apr 1 2017, In : Protein Expression and Purification. 132, p. 60-67 8 p.

Research output: Contribution to journalArticle

Mixed Function Oxygenases
Escherichia coli
NADPH-Ferrihemoprotein Reductase
Membranes
Lipid Bilayers

Host and pathogen copper-transporting P-type ATPases function antagonistically during Salmonella infection

Ladomersky, E., Khan, A., Shanbhag, V., Cavet, J. S., Chan, J. K. F., Weisman, G. A. & Petris, M. J., Sep 1 2017, In : Infection and immunity. 85, 9, e00351-17.

Research output: Contribution to journalArticle

Salmonella Infections
Copper
Macrophages
Infection
copper-transporting ATPases

IL-1b inhibits connexin 43 and disrupts decidualization of human endometrial stromal cells through ERK1/2 and p38 MAP kinase

Yu, J., Berga, S. L., Zou, W., Grace Yook, D., Pan, J. C., Andrade, A. A., Zhao, L., Sidell, N., Bagchi, I. C., Bagchi, M. K. & Taylor, R. N., Dec 1 2017, In : Endocrinology. 158, 12, p. 4270-4285 16 p.

Research output: Contribution to journalArticle

Connexin 43
Interleukins
p38 Mitogen-Activated Protein Kinases
Stromal Cells
Phosphotransferases

Insights into the biosynthesis of duramycin

Huo, L., Ökesli, A., Zhao, M. & van der Donk, W. A., Jan 1 2017, In : Applied and environmental microbiology. 83, 3, e02698-16.

Research output: Contribution to journalArticle

phosphatidylethanolamines
peptide
biosynthesis
aspartic acid
Streptomyces cinnamoneus

Interaction of KRas4b with anionic membranes: A special role for PIP2

Gregory, M. C., McLean, M. A. & Sligar, S., May 27 2017, In : Biochemical and Biophysical Research Communications. 487, 2, p. 351-355 5 p.

Research output: Contribution to journalArticle

Unithiol
Membranes
Lipids
Fluorescence Polarization
Monomeric GTP-Binding Proteins

Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism

Arif, W., Datar, G. & Kalsotra, A., Mar 1 2017, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 3, p. 349-362 14 p.

Research output: Contribution to journalReview article

Regulator Genes
Metabolism
Genes
Enzymes
Allosteric Regulation

Introduction: Unusual Enzymology in Natural Product Synthesis

van der Donk, W. A., Apr 26 2017, In : Chemical reviews. 117, 8, p. 5223-5225 3 p.

Research output: Contribution to journalEditorial

Cyclization
Biological Products
Catalysis
Peptides
Enzymes

Isolation of bacterial compartments to track movement of protein synthesis factors

Zhao, H. & Martinis, S. A., Jan 15 2017, In : Methods. 113, p. 120-126 7 p.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
Transfer RNA
Fractionation
Proteins
Membranes

Light-Mediated reversible modulation of the Mitogen-Activated protein Kinase pathway during cell differentiation and xenopus embryonic development

Krishnamurthy, V. V., Turgeon, A. J., Khamo, J. S., Mondal, P., Sharum, S. R., Mei, W., Yang, J. & Zhang, K., Jun 15 2017, In : Journal of Visualized Experiments. 2017, 124, e55823.

Research output: Contribution to journalArticle

Xenopus
Mitogen-Activated Protein Kinases
Embryonic Development
Cell Differentiation
Phosphotransferases

Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase

Jiang, T., Yu, K., Hartzell, H. C. & Tajkhorshid, E., Sep 16 2017, In : eLife. 6, e28671.

Research output: Contribution to journalArticle

Phospholipids
Ions
Membranes
Lipids
Adenosine Triphosphate

Lipid specificity of the membrane binding domain of coagulation factor X

Muller, M. P., Wang, Y., Morrissey, J. H. & Tajkhorshid, E., Oct 2017, In : Journal of Thrombosis and Haemostasis. 15, 10, p. 2005-2016 12 p.

Research output: Contribution to journalArticle

Factor X
Membrane Lipids
Phosphatidylserines
Membranes
Lipids

Localization of Short-Chain Polyphosphate Enhances its Ability to Clot Flowing Blood Plasma

Yeon, J. H., Mazinani, N., Schlappi, T. S., Chan, K. Y. T., Baylis, J. R., Smith, S. A., Donovan, A. J., Kudela, D., Stucky, G. D., Liu, Y., Morrissey, J. H. & Kastrup, C. J., Feb 10 2017, In : Scientific reports. 7, 42119.

Research output: Contribution to journalArticle

blood
plasma
polyp
polymer
fold

Location of the Substrate Binding Site of the Cytochrome bo3 Ubiquinol Oxidase from Escherichia coli

Choi, S. K., Schurig-Briccio, L., Ding, Z., Hong, S., Sun, C. & Gennis, R. B., Jun 21 2017, In : Journal of the American Chemical Society. 139, 24, p. 8346-8354 9 p.

Research output: Contribution to journalArticle

Binding sites
Cytochromes
Escherichia coli
cytochrome
coenzyme Q10

Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

Weisz, D. A., Liu, H., Zhang, H., Thangapandian, S., Tajkhorshid, E., Gross, M. L. & Pakrasi, H. B., Feb 28 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 9, p. 2224-2229 6 p.

Research output: Contribution to journalArticle

Photosystem II Protein Complex
Mass Spectrometry
Proteins
cytochrome b559
Isotopes

Maternal dead-end 1 promotes translation of nanos1 by binding the eiF3 complex

Aguero, T., Jin, Z., Chorghade, S., Kalsotra, A., King, M. L. & Yang, J., Oct 15 2017, In : Development (Cambridge). 144, 20, p. 3755-3765 11 p.

Research output: Contribution to journalArticle

germ cell
embryo
Germ Cells
Mothers
Fertilization

Mdm2 mediates FMRP- and Gp1 mGluR-dependent protein translation and neural network activity

Liu, D. C., Seimetz, J., Lee, K. Y., Kalsotra, A., Chung, H. J., Lu, H. & Tsai, N-P., Oct 15 2017, In : Human molecular genetics. 26, 20, p. 3895-3908 14 p.

Research output: Contribution to journalArticle

Fragile X Mental Retardation Protein
Protein Biosynthesis
Fragile X Syndrome
Neuronal Plasticity
Animal Behavior