Research Output

2020

Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy

Misra, C., Bangru, S., Lin, F., Lam, K., Koenig, S. N., Lubbers, E. R., Hedhli, J., Murphy, N. P., Parker, D. J., Dobrucki, L. W., Cooper, T. A., Tajkhorshid, E., Mohler, P. J. & Kalsotra, A., Feb 1 2020, (Accepted/In press) In : Developmental cell.

Research output: Contribution to journalArticle

A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli

North, J. A., Wildenthal, J. A., Erb, T. J., Evans, B. S., Byerly, K. M., Gerlt, J. A. & Tabita, F. R., Jan 1 2020, (Accepted/In press) In : Molecular Microbiology.

Research output: Contribution to journalArticle

A Computer Conquers Tactical Combinations

Blair, D. J. & Burke, M. D., Jan 9 2020, In : Chem. 6, 1, p. 12-13 2 p.

Research output: Contribution to journalArticle

An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells

Yadav, A. K., Reinhardt, C. J., Arango, A. S., Huff, H. C., Dong, L., Malkowski, M. G., Das, A., Tajkhorshid, E. & Chan, J., Feb 17 2020, In : Angewandte Chemie - International Edition. 59, 8, p. 3307-3314 8 p.

Research output: Contribution to journalArticle

Bacteroidetes can be a rich source of novel lanthipeptides: The case study of Pedobacter lusitanus

Caetano, T., van der Donk, W. & Mendo, S., May 2020, In : Microbiological Research. 235, 126441.

Research output: Contribution to journalArticle

Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae

Huo, L., Zhao, X., Acedo, J. Z., Estrada, P., Nair, S. K. & van der Donk, W. A., Jan 15 2020, In : ChemBioChem. 21, 1-2, p. 190-199 10 p.

Research output: Contribution to journalArticle

Characterization of an l -Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations

Stack, T. M. M., Morrison, K. N., Dettmer, T. M., Wille, B., Kim, C., Joyce, R., Jermain, M., Naing, Y. T., Bhatti, K., Francisco, B. S., Carter, M. S. & Gerlt, J. A., Jan 29 2020, In : Journal of the American Chemical Society. 142, 4, p. 1657-1661 5 p.

Research output: Contribution to journalArticle

Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer

Kumar, P., Wang, Y., Zhang, Z., Zhao, Z., Cymes, G. D., Tajkhorshid, E. & Grosman, C., Jan 21 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 3, p. 1788-1798 11 p.

Research output: Contribution to journalArticle

Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions

Weitzel, C. S., Li, L., Zhang, C., Eilts, K. K., Bretz, N. M., Gatten, A. L., Whitaker, R. J. & Martinis, S. A., Feb 26 2020, (Accepted/In press) In : Journal of Biological Chemistry. jbc.RA118.006481.

Research output: Contribution to journalArticle

Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans

Nayak, D. D., Liu, A., Agrawal, N., Rodriguez-Carerro, R., Dong, S. H., Mitchell, D. A., Nair, S. K. & Metcalf, W. W., Jan 1 2020, In : PLoS biology. 18, 2, e3000507.

Research output: Contribution to journalArticle

Open Access

Membrane-Bound Ras as a Conformational Clock

Gorfe, A. A. & Sligar, S. G., Jan 1 2020, (Accepted/In press) In : Biophysical journal.

Research output: Contribution to journalArticle

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes

Pant, S. & Tajkhorshid, E., Mar 5 2020, In : Journal of Computational Chemistry. 41, 6, p. 489-499 11 p.

Research output: Contribution to journalArticle

Molecular Insights into the Loading and Dynamics of Doxorubicin on PEGylated Graphene Oxide Nanocarriers

Mahdavi, M., Fattahi, A., Tajkhorshid, E. & Nouranian, S., Jan 1 2020, (Accepted/In press) In : ACS Applied Bio Materials.

Research output: Contribution to journalArticle

Molecular Orientation Determination in Nanodiscs at the Single-Molecule Level

Camp, T., Mehta, K., Sligar, S. G. & Zhang, K., Jan 21 2020, In : Analytical chemistry. 92, 2, p. 2229-2236 8 p.

Research output: Contribution to journalArticle

Natural product biosynthesis: What’s next? An introduction to the JBC Reviews Thematic Series

Nair, S. K. & Jez, J. M., Jan 1 2020, In : Journal of Biological Chemistry. 295, 2, p. 335-336 2 p.

Research output: Contribution to journalReview article

Open Access

Nitric oxide imaging in cancer enabled by steric relaxation of a photoacoustic probe platform

Reinhardt, C. J., Xu, R. & Chan, J., Feb 14 2020, In : Chemical Science. 11, 6, p. 1587-1592 6 p.

Research output: Contribution to journalArticle

Open Access

PLK4 deubiquitination by Spata2-CYLD suppresses NEK7-mediated NLRP3 inflammasome activation at the centrosome

Yang, X. D., Li, W., Zhang, S., Wu, D., Jiang, X., Tan, R., Niu, X., Wang, Q., Wu, X., Liu, Z., Chen, L. F., Qin, J. & Su, B., Jan 15 2020, In : EMBO Journal. 39, 2, e102201.

Research output: Contribution to journalArticle

Probing cholesterol binding and translocation in P-glycoprotein

Thangapandian, S., Kapoor, K. & Tajkhorshid, E., Jan 1 2020, In : Biochimica et Biophysica Acta - Biomembranes. 1862, 1, 183090.

Research output: Contribution to journalArticle

The carboxy-terminal insert in the Q-loop is needed for functionality of Escherichia coli cytochrome bd-I

Goojani, H. G., Konings, J., Hakvoort, H., Hong, S., Gennis, R. B., Sakamoto, J., Lill, H. & Bald, D., Jun 1 2020, In : Biochimica et Biophysica Acta - Bioenergetics. 1861, 5-6, 148175.

Research output: Contribution to journalArticle

The fellowship of the rings: Macrocyclic antibiotic peptides reveal an anti-gram-negative target

McLaughlin, M. I. & Van Der Donk, W. A., Jan 1 2020, (Accepted/In press) In : Biochemistry.

Research output: Contribution to journalComment/debate

Open Access

The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus

Garber, J. M., Nothaft, H., Pluvinage, B., Stahl, M., Bian, X., Porfirio, S., Enriquez, A., Butcher, J., Huang, H., Glushka, J., Line, E., Gerlt, J. A., Azadi, P., Stintzi, A., Boraston, A. B. & Szymanski, C. M., Dec 1 2020, In : Communications Biology. 3, 1, 2.

Research output: Contribution to journalArticle

Open Access
2019

A Chalcogen-Bonding Cascade Switch for Planarizable Push–Pull Probes

Macchione, M., Goujon, A., Strakova, K., Humeniuk, H. V., Licari, G., Tajkhorshid, E., Sakai, N. & Matile, S., Oct 28 2019, In : Angewandte Chemie - International Edition. 58, 44, p. 15752-15756 5 p.

Research output: Contribution to journalArticle

A Conformationally Restricted Aza-BODIPY Platform for Stimulus-Responsive Probes with Enhanced Photoacoustic Properties

Zhou, E. Y., Knox, H. J., Liu, C., Zhao, W. & Chan, J., Nov 6 2019, In : Journal of the American Chemical Society. 141, 44, p. 17601-17609 9 p.

Research output: Contribution to journalArticle

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Safarian, S., Hahn, A., Mills, D. J., Radloff, M., Eisinger, M. L., Nikolaev, A., Meier-Credo, J., Melin, F., Miyoshi, H., Gennis, R. B., Sakamoto, J., Langer, J. D., Hellwig, P., Kühlbrandt, W. & Michel, H., Oct 4 2019, In : Science. 366, 6461, p. 100-104 5 p.

Research output: Contribution to journalArticle

Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213

Denisov, I. G., Grinkova, Y. V., Nandigrami, P., Shekhar, M., Tajkhorshid, E. & Sligar, S. G., Mar 12 2019, In : Biochemistry. 58, 10, p. 1411-1422 12 p.

Research output: Contribution to journalArticle

A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl channel ANO1 (TMEM16A)

Yu, K., Jiang, T., Cui, Y. Y., Tajkhorshid, E. & Criss Hartzell, H., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 40, p. 19952-19962 11 p.

Research output: Contribution to journalArticle

Open Access

A novel synthesis of trans-unsaturated fatty acids by the Gram-positive commensal bacterium Enterococcus faecalis FA2-2

Kondakova, T., Kumar, S. & Cronan, J. E., Aug 2019, In : Chemistry and Physics of Lipids. 222, p. 23-35 13 p.

Research output: Contribution to journalArticle

A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion

Sparks, R. P., Arango, A. S., Starr, M. L., Aboff, Z. L., Hurst, L. R., Rivera-Kohr, D. A., Zhang, C., Harnden, K. A., Jenkins, J. L., Guida, W. C., Tajkhorshid, E. & Fratti, R. A., Jan 1 2019, In : Journal of Biological Chemistry. 294, 46, p. 17168-17185 18 p.

Research output: Contribution to journalReview article

Open Access

A specific small-molecule inhibitor of protein kinase CI activity improves metabolic dysfunction in human adipocytes from obese individuals

Sparks, R., Lui, A., Bader, D., Patel, R., Murr, M., Guida, W., Fratti, R. & Patel, N. A., Jan 1 2019, In : Journal of Biological Chemistry. 294, 41, p. 14896-14910 15 p.

Research output: Contribution to journalArticle

Open Access

Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications

Hegemann, J. D., Bobeica, S. C., Walker, M. C., Bothwell, I. R. & van der Donk, W. A., May 17 2019, In : ACS synthetic biology. 8, 5, p. 1204-1214 11 p.

Research output: Contribution to journalArticle

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P., Hunter, C. N. & 3 others, Tajkhorshid, E., Aksimentiev, A. & Schulten, K., Nov 14 2019, In : Cell. 179, 5, p. 1098-1111.e23

Research output: Contribution to journalArticle

Axial shielding of Pd(II) complexes enables perfect stereoretention in Suzuki-Miyaura cross-coupling of Csp 3 boronic acids

Lehmann, J. W., Crouch, I. T., Blair, D. J., Trobe, M., Wang, P., Li, J. & Burke, M., Dec 1 2019, In : Nature communications. 10, 1, 1263.

Research output: Contribution to journalArticle

Open Access

Bacterial expression of membrane-associated cytochrome P450s and their activity assay in nanodiscs

Maroutsos, D., Huff, H. & Das, A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 47-72 26 p. (Methods in Molecular Biology; vol. 1927).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Duan, Y., Llorente, C., Lang, S., Brandl, K., Chu, H., Jiang, L., White, R. C., Clarke, T. H., Nguyen, K., Torralba, M., Shao, Y., Liu, J., Hernandez-Morales, A., Lessor, L., Rahman, I. R., Miyamoto, Y., Ly, M., Gao, B., Sun, W., Kiesel, R. & 26 others, Hutmacher, F., Lee, S., Ventura-Cots, M., Bosques-Padilla, F., Verna, E. C., Abraldes, J. G., Brown, R. S., Vargas, V., Altamirano, J., Caballería, J., Shawcross, D. L., Ho, S. B., Louvet, A., Lucey, M. R., Mathurin, P., Garcia-Tsao, G., Bataller, R., Tu, X. M., Eckmann, L., van der Donk, W. A., Young, R., Lawley, T. D., Stärkel, P., Pride, D., Fouts, D. E. & Schnabl, B., Nov 21 2019, In : Nature. 575, 7783, p. 505-511 7 p.

Research output: Contribution to journalArticle

Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling

Terekhova, K., Pokutta, S., Kee, Y. S., Li, J., Tajkhorshid, E., Fuller, G., Dunn, A. R. & Weis, W. I., Dec 1 2019, In : Scientific reports. 9, 1, 15375.

Research output: Contribution to journalArticle

Open Access

Biodegradable Biliverdin Nanoparticles for Efficient Photoacoustic Imaging

Fathi, P., Knox, H. J., Sar, D., Tripathi, I., Ostadhossein, F., Misra, S. K., Esch, M. B., Chan, J. & Pan, D., Jul 23 2019, In : ACS Nano. 13, 7, p. 7690-7704 15 p.

Research output: Contribution to journalArticle

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor

Dong, S. H., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K. & Nair, S. K., Jan 1 2019, In : Chemical Science. 10, 8, p. 2391-2395 5 p.

Research output: Contribution to journalArticle

Open Access

Biotransformation of the mycotoxin enniatin b1 by CYP P450 3A4 and potential for drug-drug interactions

Ivanova, L., Denisov, I. G., Grinkova, Y. V., Sligar, S. G. & Fæste, C. K., Aug 2019, In : Metabolites. 9, 8, 158.

Research output: Contribution to journalArticle

Open Access

Breaking tolerance with engineered class I antigen-presenting molecules

Parks, C. A., Henning, K. R., Pavelko, K. D., Hansen, M. J., Van Keulen, V. P., Reed, B. K., Stone, J. D., Schrum, A. G., Gil, D., Kranz, D. M., Bordner, A. J., Barry, M. A. & Pease, L. R., Feb 19 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 8, p. 3136-3145 10 p.

Research output: Contribution to journalArticle

Bulk-state and single-particle imaging are central to understanding carbon dot photo-physics and elucidating the effects of precursor composition and reaction temperature

Fathi, P., Khamo, J. S., Huang, X., Srivastava, I., Esch, M. B., Zhang, K. & Pan, D., Apr 2019, In : Carbon. 145, p. 572-585 14 p.

Research output: Contribution to journalArticle

Cell-type specific polysome profiling from mammalian tissues

Seimetz, J., Arif, W., Bangru, S., Hernaez, M. & Kalsotra, A., Feb 15 2019, In : Methods. 155, p. 131-139 9 p.

Research output: Contribution to journalArticle

Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus

Lencina, A. M., Koepke, J., Preu, J., Muenke, C., Gennis, R. B., Michel, H. & Schurig-Briccio, L. A., Nov 1 2019, In : Biochimica et Biophysica Acta - Bioenergetics. 1860, 11, 148080.

Research output: Contribution to journalArticle

Characterization of glutamyl-tRNA–dependent dehydratases using nonreactive substrate mimics

Bothwell, I. R., Cogan, D. P., Kim, T., Reinhardt, C. J., van der Donk, W. A. & Nair, S. K., Aug 27 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17245-17250 6 p.

Research output: Contribution to journalArticle

Open Access

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A. & Tajkhorshid, E., May 8 2019, In : Chemical reviews. 119, 9, p. 6086-6161 76 p.

Research output: Contribution to journalReview article

Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H. & Nair, S. K., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 6, p. 1506-1518 13 p.

Research output: Contribution to journalArticle

Coaction of Electrostatic an Hyrophobic Interactions: Dynamic Constraints on Disorere TrkA Juxtamembrane Domain

Wang, Z., Fan, H., Hu, X., Khamo, J., Diao, J., Zhang, K. & Pogorelov, T. V., Dec 19 2019, In : Journal of Physical Chemistry B. 123, 50, p. 10709-10717 9 p.

Research output: Contribution to journalArticle

Combined ∆ 9 -tetrahydrocannabinol and moderate alcohol administration: effects on ingestive behaviors in adolescent male rats

Nelson, N. G., Law, W. X., Weingarten, M. J., Carnevale, L. N., Das, A. & Liang, N. C., Feb 14 2019, In : Psychopharmacology. 236, 2, p. 671-684 14 p.

Research output: Contribution to journalArticle

Computational Dissection of Membrane Transport at a Microscopic Level

Jiang, T., Wen, P. C., Trebesch, N., Zhao, Z., Pant, S., Kapoor, K., Shekhar, M. & Tajkhorshid, E., Jan 1 2019, (Accepted/In press) In : Trends in Biochemical Sciences.

Research output: Contribution to journalReview article

Conformational engineering of HIV-1 Env based on mutational tolerance in the CD4 and PG16 bound states

Heredia, J. D., Park, J., Choi, H., Gill, K. S. & Procko, E., Jan 1 2019, In : Journal of virology. 93, 11, e0021919.

Research output: Contribution to journalArticle