Research Output 1968 2019

2015

Antiinfectives targeting enzymes and the proton motive force

Feng, X., Zhu, W., Schurig-Briccio, L. A., Lindert, S., Shoen, C., Hitchings, R., Li, J., Wang, Y., Baig, N., Zhou, T., Kim, B. K., Crick, D. C., Cynamon, M., McCammon, J. A., Gennis, R. B. & Oldfield, E., Dec 22 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 51, p. E7073-E7082

Research output: Contribution to journalArticle

Proton-Motive Force
Mycobacterium tuberculosis
undecaprenyl pyrophosphate synthetase
Membranes
Staphylococcus aureus

An unexpected role for ergothioneine

Huang, Z. & van der Donk, W. A., Dec 1 2015, In : National Science Review. 2, 4, p. 382-383 2 p.

Research output: Contribution to journalArticle

Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage

Tang, W., Dong, S. H., Repka, L. M., He, C., Nair, S. K. & van der Donk, W. A., Sep 2 2015, In : Chemical Science. 6, 11, p. 6270-6279 10 p.

Research output: Contribution to journalArticle

Peptide Hydrolases
Peptides
Biosynthesis
Subtilisin
Bacteriocins

A Reaction-Based Fluorescent Probe for Imaging of Formaldehyde in Living Cells

Roth, A., Li, H., Anorma, C. & Chan, J. K. F., Sep 2 2015, In : Journal of the American Chemical Society. 137, 34, p. 10890-10893 4 p.

Research output: Contribution to journalArticle

Fluorescent Dyes
formaldehyde
Formaldehyde
Cells
probe

A series of medium and high copy number arabinose-inducible Escherichia coli expression vectors compatible with pBR322 and pACYC184

Chakravartty, V. & Cronan, J. E., Sep 1 2015, In : Plasmid. 81, p. 21-26 6 p.

Research output: Contribution to journalArticle

Arabinose
Plasmids
Escherichia coli
Spectinomycin
Ampicillin Resistance

Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:Phosphate antiporter

Moradi, M., Enkavi, G. & Tajkhorshid, E., Sep 29 2015, In : Nature communications. 6, 8393.

Research output: Contribution to journalArticle

thermodynamic cycles
Antiporters
Facings
Membrane Transport Proteins
Structural Models

ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58

Wichelecki, D. J., Vetting, M. W., Chou, L., Al-Obaidi, N., Bouvier, J. T., Almo, S. C. & Gerlt, J. A., Nov 27 2015, In : Journal of Biological Chemistry. 290, 48, p. 28963-28976 14 p.

Research output: Contribution to journalArticle

Galactitol
Agrobacterium tumefaciens
Carrier Proteins
Adenosine Triphosphate
Enzymes

A unique cis -3-hydroxy- l -proline dehydratase in the enolase superfamily

Zhang, X., Kumar, R., Vetting, M. W., Zhao, S., Jacobson, M. P., Almo, S. C. & Gerlt, J. A., Feb 4 2015, In : Journal of the American Chemical Society. 137, 4, p. 1388-1391 4 p.

Research output: Contribution to journalArticle

Hydroxyproline
Hydro-Lyases
Phosphopyruvate Hydratase
Proline
dehydration

Bacteria do it differently: An alternative path to squalene

van der Donk, W. A., May 27 2015, In : ACS Central Science. 1, 2, p. 64-65 2 p.

Research output: Contribution to journalShort survey

Bacteria

Biochemical Studies of Mycobacterial Fatty Acid Methyltransferase: A Catalyst for the Enzymatic Production of Biodiesel

Petronikolou, N. & Nair, S. K., Nov 19 2015, In : Chemistry and Biology. 22, 11, p. 1480-1490 11 p.

Research output: Contribution to journalArticle

Biofuels
Fatty Acids
Metabolism
Biological Products
Catalysts

Biosynthesis of fosfazinomycin is a convergent process

Huang, Z., Wang, K. K. A., Lee, J. & van der Donk, W. A., Feb 1 2015, In : Chemical Science. 6, 2, p. 1282-1287 6 p.

Research output: Contribution to journalArticle

Biosynthesis
Phosphonoacetic Acid
Methyltransferases
Acetates
Dioxygenases

Biosynthesis of squalene from farnesyl diphosphate in Bacteria: Three steps catalyzed by three enzymes

Pan, J. J., Solbiati, J. O., Ramamoorthy, G., Hillerich, B. S., Seidel, R. D., Cronan, J. E., Almo, S. C. & Poulter, C. D., May 27 2015, In : ACS Central Science. 1, 2, p. 77-82 6 p.

Research output: Contribution to journalArticle

Squalene
Biosynthesis
Bacteria
Enzymes
Genes

C3-OH of Amphotericin B Plays an Important Role in Ion Conductance

Davis, S. A., Della Ripa, L. A., Hu, L., Cioffi, A. G., Pogorelov, T. V., Rienstra, C. M. & Burke, M. D., Dec 9 2015, In : Journal of the American Chemical Society. 137, 48, p. 15102-15104 3 p.

Research output: Contribution to journalArticle

Amphotericin B
Ion Channels
Ions
ion
Hydroxyl Radical

Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide

Baylon, J. L. & Tajkhorshid, E., Jun 25 2015, In : Journal of Physical Chemistry B. 119, 25, p. 7882-7893 12 p.

Research output: Contribution to journalArticle

influenza
Hemagglutinins
viruses
Orthomyxoviridae
Viruses

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

Qi, Y., Cheng, X., Lee, J., Vermaas, J. V., Pogorelov, T. V., Tajkhorshid, E., Park, S., Klauda, J. B. & Im, W., Nov 17 2015, In : Biophysical journal. 109, 10, p. 2012-2022 11 p.

Research output: Contribution to journalArticle

Membranes
Lipids
Proteins
Membrane Proteins

Clotting activity of polyphosphate-functionalized silica Nanoparticles

Kudela, D., Smith, S. A., May-Masnou, A., Braun, G. B., Pallaoro, A., Nguyen, C. K., Chuong, T. T., Nownes, S., Allen, R., Parker, N. R., Rashidi, H. H., Morrissey, J. H. & Stucky, G. D., Mar 23 2015, In : Angewandte Chemie - International Edition. 54, 13, p. 4018-4022 5 p.

Research output: Contribution to journalArticle

Polyphosphates
Silicon Dioxide
Silica
Nanoparticles
Blood

Computational characterization of structural dynamics underlying function in active membrane transporters

Li, J., Wen, P. C., Moradi, M. & Tajkhorshid, E., Apr 1 2015, In : Current Opinion in Structural Biology. 31, p. 96-105 10 p.

Research output: Contribution to journalReview article

Membrane Transport Proteins
Active Biological Transport
Molecular Dynamics Simulation
Hydrolysis
Adenosine Triphosphate

Contribution of clinically derived mutations in ERG11 to azole resistance in Candida albicans

Flowers, S. A., Colón, B., Whaley, S. G., Schuler, M. A. & David Rogers, P., Jan 1 2015, In : Antimicrobial Agents and Chemotherapy. 59, 1, p. 450-460 11 p.

Research output: Contribution to journalArticle

Azoles
Amino Acid Substitution
Candida albicans
Fluconazole
Mutation

CYP2J2 epoxygenase membrane anchor plays an important role in facilitating electron transfer from CPR

Meling, D. D., McDougle, D. R. & Das, A., Jan 2015, In : Journal of Inorganic Biochemistry. 142, p. 47-53 7 p.

Research output: Contribution to journalArticle

NADPH-Ferrihemoprotein Reductase
Anchors
Electrons
Membranes
Cytochrome P-450 Enzyme System

Developmental insights into the pathology of and therapeutic strategies for DM1: Back to the basics

Chau, A. & Kalsotra, A., Mar 1 2015, In : Developmental Dynamics. 244, 3, p. 377-390 14 p.

Research output: Contribution to journalReview article

Poisons
Trinucleotide Repeat Expansion
RNA
Fetal Proteins
Pathology

Direct Capture of Functional Proteins from Mammalian Plasma Membranes into Nanodiscs

Roy, J., Pondenis, H., Fan, T. M. & Das, A., Oct 20 2015, In : Biochemistry. 54, 41, p. 6299-6302 4 p.

Research output: Contribution to journalArticle

Cell membranes
Membrane Proteins
Cell Membrane
Proteome
Blood Proteins

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes

Ju, K. S., Gao, J., Doroghazi, J. R., Wang, K. K. A., Thibodeaux, C. J., Li, S., Metzger, E., Fudala, J., Su, J., Zhang, J. K., Lee, J., Cioni, J. P., Evans, B. S., Hirota, R., Labeda, D. P., van der Donk, W. A. & Metcalf, W. W., Sep 29 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 39, p. 12175-12180 6 p.

Research output: Contribution to journalArticle

Actinobacteria
Organophosphonates
Biological Products
Genome
Phosphorous Acids

Disease modeling and gene therapy of copper storage disease in canine hepatic organoids

Nantasanti, S., Spee, B., Kruitwagen, H. S., Chen, C., Geijsen, N., Oosterhoff, L. A., Van Wolferen, M. E., Pelaez, N., Fieten, H., Wubbolts, R. W., Grinwis, G. C., Chan, J., Huch, M., Vries, R. R. G., Clevers, H., De Bruin, A., Rothuizen, J., Penning, L. C. & Schotanus, B. A., Nov 10 2015, In : Stem Cell Reports. 5, 5, p. 895-907 13 p.

Research output: Contribution to journalArticle

Organoids
Gene therapy
Hepatolenticular Degeneration
Genetic Therapy
Liver

Division of labor in transhydrogenase by alternating proton translocation and hydride transfer

Leung, J. H., Schurig-Briccio, L. A., Yamaguchi, M., Moeller, A., Speir, J. A., Gennis, R. B. & Stout, C. D., Jan 9 2015, In : Science. 347, 6218, p. 178-181 4 p.

Research output: Contribution to journalArticle

NADP
Protons
NADP Transhydrogenases
Thermus thermophilus
Proton-Motive Force

Dual suppression of estrogenic and inflammatory activities for targeting of endometriosis

Zhao, Y., Gong, P., Chen, Y., Nwachukwu, J. C., Srinivasan, S., Ko, C., Bagchi, M. K., Taylor, R. N., Korach, K. S., Nettles, K. W., Katzenellenbogen, J. A. & Katzenellenbogen, B. S., Jan 21 2015, In : Science Translational Medicine. 7, 271, 271ra9.

Research output: Contribution to journalArticle

Endometriosis
Estrogen Receptors
Estrogens
Fertility
Ligands

Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution

Vermaas, J. V., Baylon, J. L., Arcario, M. J., Muller, M. P., Wu, Z., Pogorelov, T. V. & Tajkhorshid, E., Jun 1 2015, In : Journal of Membrane Biology. 248, 3, p. 563-582 20 p.

Research output: Contribution to journalArticle

Membranes
Lipids
Lipid Bilayers
Molecular Dynamics Simulation
Phospholipids

Endocannabinoid metabolism by cytochrome P450 monooxygenases

Zelasko, S., Arnold, W. R. & Das, A., Jan 1 2015, In : Prostaglandins and Other Lipid Mediators. 116-117, p. 112-123 12 p.

Research output: Contribution to journalReview article

Endocannabinoids
Mixed Function Oxygenases
Metabolism
Cytochrome P-450 Enzyme System
Lipoxygenase

Enzyme function initiative-enzyme similarity tool (EFI-EST): A web tool for generating protein sequence similarity networks

Gerlt, J. A., Bouvier, J. T., Davidson, D. B., Imker, H. J., Sadkhin, B., Slater, D. R. & Whalen, K. L., Aug 1 2015, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1854, 8, p. 1019-1037 19 p.

Research output: Contribution to journalReview article

Enzymes
Proteins
National Institute of General Medical Sciences (U.S.)
Orotidine-5'-Phosphate Decarboxylase
Biota
Qi
Rhodobacter sphaeroides
Ubiquinone
Methionine
Biochemistry

Erratum: Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas (Nature Chemical Biology (2014) 10 (1034-1042))

Hong-Hermesdorf, A., Miethke, M., Gallaher, S. D., Kropat, J., Dodani, S. C., Chan, J. K. F., Barupala, D., Domaille, D. W., Shirasaki, D. I., Loo, J. A., Weber, P. K., Pett-Ridge, J., Stemmler, T. L., Chang, C. J. & Merchant, S. S., Mar 2015, In : Nature chemical biology. 11, 3, 1 p.

Research output: Contribution to journalComment/debate

Chlamydomonas
Metals

Escherichia coli Auxotroph Host Strains for Amino Acid-Selective Isotope Labeling of Recombinant Proteins

Lin, M. T., Fukazawa, R., Miyajima-Nakano, Y., Matsushita, S., Choi, S. K., Iwasaki, T. & Gennis, R. B., Jan 1 2015, Methods in Enzymology. Academic Press Inc., p. 45-66 22 p. (Methods in Enzymology; vol. 565).

Research output: Chapter in Book/Report/Conference proceedingChapter

Isotope Labeling
Recombinant Proteins
Isotopes
Labeling
Escherichia coli

ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation

Bhate, A., Parker, D. J., Bebee, T. W., Ahn, J., Arif, W., Rashan, E. H., Chorghade, S., Chau, A., Lee, J. H., Anakk, S., Carstens, R. P., Xiao, X. & Kalsotra, A., Nov 4 2015, In : Nature communications. 6, 8768.

Research output: Contribution to journalArticle

Protein Splicing
splicing
liver
Liver
Hepatocytes

Estrogen receptor α inhibitor activates the unfolded protein response, blocks protein synthesis, and induces tumor regression

Andruska, N. D., Zheng, X., Yang, X., Mao, C., Cherian, M. M., Mahapatra, L., Helferich, W. G. & Shapiro, D. J., Apr 14 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 15, p. 4737-4742 6 p.

Research output: Contribution to journalArticle

Unfolded Protein Response
Estrogen Receptors
Endoplasmic Reticulum
Neoplasms
Peptide Elongation Factor 2

Experimental protein structure verification by scoring with a single, unassigned NMR spectrum

Courtney, J. M., Ye, Q., Nesbitt, A. E., Tang, M., Tuttle, M. D., Watt, E. D., Nuzzio, K. M., Sperling, L. J., Comellas, G., Peterson, J. R., Morrissey, J. H. & Rienstra, C. M., Oct 6 2015, In : Structure. 23, 10, p. 1958-1966 9 p.

Research output: Contribution to journalArticle

Magnetic Resonance Spectroscopy
Proteins
Structural Models
Thromboplastin
Ubiquitin

Experimental strategies for functional annotation and metabolism discovery: Targeted screening of solute binding proteins and unbiased panning of metabolomes

Vetting, M. W., Al-Obaidi, N., Zhao, S., San Francisco, B., Kim, J., Wichelecki, D. J., Bouvier, J. T., Solbiati, J. O., Vu, H., Zhang, X., Rodionov, D. A., Love, J. D., Hillerich, B. S., Seidel, R. D., Quinn, R. J., Osterman, A. L., Cronan, J. E., Jacobson, M. P., Gerlt, J. A. & Almo, S. C., Jan 27 2015, In : Biochemistry. 54, 3, p. 909-931 23 p.

Research output: Contribution to journalArticle

Metabolome
Metabolism
Carrier Proteins
Screening
Libraries

Facile Removal of Leader Peptides from Lanthipeptides by Incorporation of a Hydroxy Acid

Bindman, N. A., Bobeica, S. C., Liu, W. R. & van der Donk, W. A., Jun 10 2015, In : Journal of the American Chemical Society. 137, 22, p. 6975-6978 4 p.

Research output: Contribution to journalArticle

Hydroxy Acids
Protein Sorting Signals
peptide
Peptides
Acids

From Synthesis to Function via Iterative Assembly of N-Methyliminodiacetic Acid Boronate Building Blocks

Li, J., Grillo, A. S. & Burke, M. D., Jul 22 2015, In : Accounts of chemical research. 48, 8, p. 2297-2307 11 p.

Research output: Contribution to journalArticle

Molecules
Biological Products
Polyenes
Poisons
Aldehydes

Functional role of the conserved I-helix residue I346 in CYP5A1-Nanodiscs

Meling, D. D., Zelasko, S., Kambalyal, A., Roy, J. & Das, A., Jul 1 2015, In : Biophysical Chemistry. 200-201, p. 34-40 7 p.

Research output: Contribution to journalArticle

Prostaglandin H2
Thromboxane A2
Threonine
Isomerization
Catalytic Domain

FXIa and platelet polyphosphate as therapeutic targets during human blood clotting on collagen/tissue factor surfaces under flow

Zhu, S., Travers, R. J., Morrissey, J. H. & Diamond, S. L., Sep 17 2015, In : Blood. 126, 12, p. 1494-1502 9 p.

Research output: Contribution to journalArticle

Factor XIa
Polyphosphates
Thromboplastin
Blood Coagulation
Platelets

Helical antimicrobial polypeptides with radial amphiphilicity

Xiong, M., Lee, M. W., Mansbach, R. A., Song, Z., Bao, Y., Peek, R. M., Yao, C., Chen, L-F., Ferguson, A., Wong, G. C. L. & Cheng, J., Oct 27 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 43, p. 13155-13160 6 p.

Research output: Contribution to journalArticle

Peptides
Bacteria
Eukaryotic Cells
Gram-Negative Bacteria
Blood Proteins

Herman N. Eisen: Mentor to many

Kranz, D. M. & Sykulev, Y., Feb 10 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 6, p. 1650-1651 2 p.

Research output: Contribution to journalArticle

21st Century History
20th Century History
Career Choice
Mentors
Allergy and Immunology

How it all starts: Initiation of the clotting cascade

Smith, S. A., Travers, R. J. & Morrissey, J. H., Jul 4 2015, In : Critical Reviews in Biochemistry and Molecular Biology. 50, 4, p. 326-336 11 p.

Research output: Contribution to journalReview article

Thrombosis
Blood
Blood Coagulation
Hemostasis
Thromboplastin

Impaired mitochondrial energy production causes light-induced photoreceptor degeneration independent of oxidative stress

Jaiswal, M., Haelterman, N. A., Sandoval, H., Xiong, B., Donti, T., Kalsotra, A., Yamamoto, S., Cooper, T. A., Graham, B. H. & Bellen, H. J., Jan 1 2015, In : PLoS biology. 13, 7

Research output: Contribution to journalArticle

Oxidative stress
photoreceptors
Oxidative Stress
oxidative stress
Light

Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2-lipid bilayer interactions

McDougle, D. R., Baylon, J. L., Meling, D. D., Kambalyal, A., Grinkova, Y. V., Hammernik, J., Tajkhorshid, E. & Das, A., Aug 17 2015, In : Biochimica et Biophysica Acta - Biomembranes. 1848, 10, p. 2460-2470 11 p., 81959.

Research output: Contribution to journalArticle

Lipid bilayers
Lipid Bilayers
Membranes
Molecular Dynamics Simulation
Molecular dynamics

Insights into Methyltransferase Specificity and Bioactivity of Derivatives of the Antibiotic Plantazolicin

Hao, Y., Blair, P. M., Sharma, A., Mitchell, D. A. & Nair, S. K., May 15 2015, In : ACS chemical biology. 10, 5, p. 1209-1216 8 p.

Research output: Contribution to journalArticle

Methyltransferases
Bioactivity
Biological Products
Bacillus anthracis
Anti-Bacterial Agents

Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways

Cho, K., Evans, B. S., Wood, B. M. K., Kumar, R., Erb, T. J., Warlick, B. P., Gerlt, J. A. & Sweedler, J. V., Jun 1 2015, In : Metabolomics. 11, 3, p. 503-517 15 p.

Research output: Contribution to journalArticle

Metabolomics
Metabolic Networks and Pathways
Salvaging
Methionine
Metabolites

Intracellular delivery system for antibody-peptide drug conjugates

Berguig, G. Y., Convertine, A. J., Frayo, S., Kern, H. B., Procko, E., Roy, D., Srinivasan, S., Margineantu, D. H., Booth, G., Palanca-Wessels, M. C., Baker, D., Hockenbery, D., Press, O. W. & Stayton, P. S., May 9 2015, In : Molecular Therapy. 23, 5, p. 907-917 11 p.

Research output: Contribution to journalArticle

Peptides
Antibodies
Pharmaceutical Preparations
Neoplasms
Biomarkers

In Vitro Biosynthesis of the Core Scaffold of the Thiopeptide Thiomuracin

Hudson, G. A., Zhang, Z., Tietz, J. I., Mitchell, D. A. & van der Donk, W. A., Dec 30 2015, In : Journal of the American Chemical Society. 137, 51, p. 16012-16015 4 p.

Research output: Contribution to journalArticle

Biosynthesis
Scaffolds
Antibiotics
Proteins
Dehydration

Mechanism of Drug-Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer

Denisov, I. G., Grinkova, Y. V., Baylon, J. L., Tajkhorshid, E. & Sligar, S. G., Apr 7 2015, In : Biochemistry. 54, 13, p. 2227-2239 13 p.

Research output: Contribution to journalArticle

Drug interactions
Allosteric Site
Cytochrome P-450 CYP3A
Carbamazepine
Drug Interactions

Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail

Madsen, J. J., Ohkubo, Y. Z., Peters, G. H., Faber, J. H., Tajkhorshid, E. & Olsen, O. H., Oct 6 2015, In : Biochemistry. 54, 39, p. 6123-6131 9 p.

Research output: Contribution to journalArticle

Factor VIIIa
Membranes
Discoidin Domain
Molecular orientation
Missense Mutation