Research Output 1968 2019

2015

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

Metalloproteins: The long and the short of it

Denisov, I. G. & Sligar, S., Aug 20 2015, In : Nature Chemistry. 7, 9, p. 687-688 2 p.

Research output: Contribution to journalShort survey

Archaeal Proteins
Chloride Peroxidase
Metalloproteins
Sulfur
Cytochrome P-450 Enzyme System

Michael-Type Cyclizations in Lantibiotic Biosynthesis Are Reversible

Yang, X. & van der Donk, W. A., May 15 2015, In : ACS chemical biology. 10, 5, p. 1234-1238 5 p.

Research output: Contribution to journalArticle

Bacteriocins
Cyclization
Biosynthesis
Sulfides
Addition reactions

Minimum Information about a Biosynthetic Gene cluster

Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., De Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A., Hadjithomas, M. & 134 others, Haines, A. S., Helfrich, E. J. N., Hillwig, M. L., Ishida, K., Jones, A. C., Jones, C. S., Jungmann, K., Kegler, C., Kim, H. U., Kötter, P., Krug, D., Masschelein, J., Melnik, A. V., Mantovani, S. M., Monroe, E. A., Moore, M., Moss, N., Nützmann, H. W., Pan, G., Pati, A., Petras, D., Reen, F. J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N. J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A. K., Balibar, C. J., Balskus, E. P., Barona-Gómez, F., Bechthold, A., Bode, H. B., Borriss, R., Brady, S. F., Brakhage, A. A., Caffrey, P., Cheng, Y. Q., Clardy, J., Cox, R. J., De Mot, R., Donadio, S., Donia, M. S., Van Der Donk, W. A., Dorrestein, P. C., Doyle, S., Driessen, A. J. M., Ehling-Schulz, M., Entian, K. D., Fischbach, M. A., Gerwick, L., Gerwick, W. H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S. E., Ju, J., Katz, L., Kaysser, L., Klassen, J. L., Keller, N. P., Kormanec, J., Kuipers, O. P., Kuzuyama, T., Kyrpides, N. C., Kwon, H. J., Lautru, S., Lavigne, R., Lee, C. Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D. A., Moore, B. S., Moreira, L. M., Müller, R., Neilan, B. A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M. S., Ostash, B., Payne, S. M., Pernodet, J. L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J. M., Salas, J. A., Schmitt, E. K., Scott, B., Seipke, R. F., Shen, B., Sherman, D. H., Sivonen, K., Smanski, M. J., Sosio, M., Stegmann, E., Süssmuth, R. D., Tahlan, K., Thomas, C. M., Tang, Y., Truman, A. W., Viaud, M., Walton, J. D., Walsh, C. T., Weber, T., Van Wezel, G. P., Wilkinson, B., Willey, J. M., Wohlleben, W., Wright, G. D., Ziemert, N., Zhang, C., Zotchev, S. B., Breitling, R., Takano, E. & Glöckner, F. O., Aug 18 2015, In : Nature chemical biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journalReview article

Multigene Family
Information Storage and Retrieval
Fungi
Bacteria

Multiplex gene removal by two-step polymerase chain reactions

Krishnamurthy, V. V., Khamo, J. S., Cho, E., Schornak, C. & Zhang, K., Jun 3 2015, In : Analytical Biochemistry. 481, p. 7-9 3 p.

Research output: Contribution to journalArticle

Polymerase chain reaction
Genes
Cloning
Polymerase Chain Reaction
Organism Cloning

Mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site

Von Ballmoos, C., Gonska, N., Lachmann, P., Gennis, R. B., Ädelroth, P. & Brzezinski, P., Mar 17 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 11, p. 3397-3402 6 p.

Research output: Contribution to journalArticle

Protons
Oxidoreductases
Mutation
Electron Transport Complex IV
Electrons

Nanodiscs as a modular platform for multimodal MR-optical imaging

Carney, C. E., Lenov, I. L., Baker, C. J., Macrenaris, K. W., Eckermann, A. L., Sligar, S. & Meade, T. J., May 20 2015, In : Bioconjugate Chemistry. 26, 5, p. 899-905 7 p.

Research output: Contribution to journalArticle

Optical Imaging
Contrast Media
Imaging techniques
Membrane Proteins
Lipid bilayers

Nanoscale synaptic membrane mimetic allows unbiased high throughput screen that targets binding sites for Alzheimer's-associated Aβ oligomers

Wilcox, K. C., Marunde, M. R., Das, A., Velasco, P. T., Kuhns, B. D., Marty, M. T., Jiang, H., Luan, C. H., Sligar, S. & Klein, W. L., Apr 1 2015, In : PloS one. 10, 4, e0125263.

Research output: Contribution to journalArticle

Synaptic Membranes
amyloid
Oligomers
Amyloid
binding sites

Nontoxic antimicrobials that evade drug resistance

Davis, S. A., Vincent, B. M., Endo, M. M., Whitesell, L., Marchillo, K., Andes, D. R., Lindquist, S. & Burke, M. D., Jul 20 2015, In : Nature chemical biology. 11, 7, p. 481-487 7 p.

Research output: Contribution to journalArticle

Amphotericin B
Microbial Drug Resistance
Poisons
Ergosterol
Sterols

Optogenetic control of intracellular signaling pathways

Zhang, K. & Cui, B., Feb 1 2015, In : Trends in Biotechnology. 33, 2, p. 92-100 9 p.

Research output: Contribution to journalReview article

Optogenetics
Aptitude
Molecular Biology
Light

Optogenetic control of molecular motors and organelle distributions in cells

Duan, L., Che, D., Zhang, K., Ong, Q., Guo, S. & Cui, B., May 30 2015, In : Chemistry and Biology. 22, 5, p. 671-682 12 p.

Research output: Contribution to journalArticle

Optogenetics
Organelles
Light
Cryptochromes
Cells

Oxygen-18 Kinetic Isotope Effects of Nonheme Iron Enzymes HEPD and MPnS Support Iron(III) Superoxide as the Hydrogen Abstraction Species

Zhu, H., Peck, S. C., Bonnot, F., van der Donk, W. A. & Klinman, J. P., Aug 12 2015, In : Journal of the American Chemical Society. 137, 33, p. 10448-10451 4 p.

Research output: Contribution to journalArticle

Dioxygenases
Enzyme kinetics
Catalyst supports
Superoxides
Isotopes

P450s in plants, insects, and their fungal pathogens

Schuler, M. A., Jan 1 2015, Cytochrome P450: Structure, Mechanism, and Biochemistry, Fourth Edition. Springer International Publishing, p. 409-449 41 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Pathogens
Insects
Genes
Mixed Function Oxygenases
Biosynthetic Pathways

Photoacoustic Probes for Ratiometric Imaging of Copper(II)

Li, H., Zhang, P., Smaga, L. P., Hoffman, R. A. & Chan, J. K. F., Dec 23 2015, In : Journal of the American Chemical Society. 137, 50, p. 15628-15631 4 p.

Research output: Contribution to journalArticle

Photoacoustic effect
ester
Copper
Esters
Metals

Plasticity in the High Affinity Menaquinone Binding Site of the Cytochrome aa3-600 Menaquinol Oxidase from Bacillus subtilis

Yi, S. M., Taguchi, A. T., Samoilova, R. I., O'Malley, P. J., Gennis, R. B. & Dikanov, S. A., Jul 21 2015, In : Biochemistry. 54, 32, p. 5030-5044 15 p.

Research output: Contribution to journalArticle

Vitamin K 2
Electron Transport Complex IV
Bacilli
Bacillus subtilis
Plasticity

Polymerase chain reaction-based gene removal from plasmids

Krishnamurthy, V. V., Khamo, J. S., Cho, E., Schornak, C. & Zhang, K., Sep 1 2015, In : Data in Brief. 4, p. 75-82 8 p.

Research output: Contribution to journalArticle

manipulation
flexibility

Polyphosphate, platelets, and coagulation

Travers, R. J., Smith, S. A. & Morrissey, J. H., May 1 2015, In : International Journal of Laboratory Hematology. 37, S1, p. 31-35 5 p.

Research output: Contribution to journalReview article

Polyphosphates
Platelets
Coagulation
Blood Platelets
Inflammation

Polyphosphate accelerates factor V activation by factor XIa

Choi, S. H., Smith, S. A. & Morrissey, J. H., Jan 1 2015, In : Thrombosis and Haemostasis. 113, 3, p. 599-604 6 p.

Research output: Contribution to journalArticle

Factor XIa
Polyphosphates
Factor V
Factor Va
Thrombin

Polyphosphate as modulator of hemostasis, thrombosis, and inflammation

Morrissey, J. H. & Smith, S. A., Jun 1 2015, In : Journal of Thrombosis and Haemostasis. 13, S1, p. S92-S97

Research output: Contribution to journalReview article

Polyphosphates
Hemostasis
Thrombosis
Polyps
Inflammation
Alanine
peptide
Peptides
Oxidoreductases
Amino acids

Product formation by the promiscuous lanthipeptide synthetase ProcM is under kinetic control

Yu, Y., Mukherjee, S. & van der Donk, W. A., Apr 22 2015, In : Journal of the American Chemical Society. 137, 15, p. 5140-5148 9 p.

Research output: Contribution to journalArticle

Cyclization
Ligases
Regioselectivity
kinetics
Kinetics

Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5′-Monophosphate Decarboxylase

Goryanova, B., Goldman, L. M., Ming, S., Amyes, T. L., Gerlt, J. A. & Richard, J. P., Jul 28 2015, In : Biochemistry. 54, 29, p. 4555-4564 10 p.

Research output: Contribution to journalArticle

Decarboxylation
Carboxy-Lyases
Equilibrium constants
Catalysis
Rate constants

Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex

Wang, P., Selvadurai, K. & Huang, R. H., Apr 17 2015, In : Nature communications. 6, 6876.

Research output: Contribution to journalArticle

Bacterial Structures
immunity
Repair
rhomboids
RNA

Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides

Vermaas, J. V., Taguchi, A. T., Dikanov, S. A., Wraight, C. A. & Tajkhorshid, E., Mar 31 2015, In : Biochemistry. 54, 12, p. 2104-2116 13 p.

Research output: Contribution to journalArticle

Photosynthetic Reaction Center Complex Proteins
Rhodobacter sphaeroides
Quinones
Ubiquinone
Oxidation-Reduction

Restored physiology in protein-deficient yeast by a small molecule channel

Cioffi, A. G., Hou, J., Grillo, A. S., Diaz, K. A. & Burke, M. D., Aug 19 2015, In : Journal of the American Chemical Society. 137, 32, p. 10096-10099 4 p.

Research output: Contribution to journalArticle

Fungal Proteins
Physiology
yeast
physiology
Proteins

Retrograde NGF axonal transport - Motor coordination in the unidirectional motility regime

Chowdary, P. D., Che, D. L., Zhang, K. & Cui, B., Jun 3 2015, In : Biophysical journal. 108, 11, p. 2691-2703 13 p., 6557.

Research output: Contribution to journalArticle

Axonal Transport
Endosomes
Nerve Growth Factor
Kinesin
Dyneins

Review and Hypothesis. New insights into the reaction mechanism of transhydrogenase: Swivelling the dIII component may gate the proton channel

Jackson, J. B., Leung, J. H., Stout, C. D., Schurig-Briccio, L. A. & Gennis, R. B., Jul 20 2015, In : FEBS Letters. 589, 16, p. 2027-2033 7 p.

Research output: Contribution to journalReview article

NADP
Protons
Thermus thermophilus
Mitochondria
Enzymes

Small-angle scattering determination of the shape and localization of human cytochrome P450 embedded in a phospholipid nanodisc environment

Skar-Gislinge, N., Kynde, S. A. R., Denisov, I. G., Ye, X., Lenov, I., Sligar, S. & Arleth, L., Jan 1 2015, In : Acta Crystallographica Section D: Biological Crystallography. 71, p. 2412-2421 10 p.

Research output: Contribution to journalArticle

Small Angle Scattering
Cytochrome P-450 CYP3A
Cytochrome P-450 Enzyme System
Phospholipids
Membrane Proteins

Structural Basis for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase

Li, Z. & Nair, S. K., Nov 3 2015, In : Structure. 23, 11, p. 2032-2042 11 p.

Research output: Contribution to journalArticle

Coenzyme A Ligases
Adenosine Monophosphate
Tobacco
Protein Isoforms
Adenosine Triphosphate

Structural determinants of the mechanical stability of α-Catenin

Li, J., Newhall, J., Ishiyama, N., Gottardi, C., Ikura, M., Leckband, D. E. & Tajkhorshid, E., Jul 31 2015, In : Journal of Biological Chemistry. 290, 31, p. 18890-18903 14 p.

Research output: Contribution to journalArticle

Catenins
Mechanical stability
Cell adhesion
Molecular Dynamics Simulation
Cell Adhesion

Structure, Function and Inhibition of the Phosphoethanolamine Methyltransferases of the Human Malaria Parasites Plasmodium vivax and Plasmodium knowlesi

Garg, A., Lukk, T., Kumar, V., Choi, J. Y., Augagneur, Y., Voelker, D. R., Nair, S. K. & Mamoun, C. B., 2015, In : Scientific reports. 5, 9064.

Research output: Contribution to journalArticle

Plasmodium knowlesi
Vivax Malaria
Antimalarials
Parasites
Phosphatidylcholines

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

Ortega, M. A., Hao, Y., Zhang, Q., Walker, M. C., van der Donk, W. A. & Nair, S. K., Jan 22 2015, In : Nature. 517, 7535, p. 509-512 4 p.

Research output: Contribution to journalArticle

Hydro-Lyases
Bacteriocins
Transfer RNA
Dehydration
Nisin

Structure-Function Relationship of the Interaction between Tissue Factor and Factor VIIa

Gajsiewicz, J. M. & Morrissey, J. H., Sep 26 2015, In : Seminars in Thrombosis and Hemostasis. 41, 7, p. 682-690 9 p.

Research output: Contribution to journalArticle

Factor VIIa
Thromboplastin
Membrane Proteins
Proteins
Protein Folding

Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor

Cobb, R. E., Bae, B., Li, Z., Desieno, M. A., Nair, S. K. & Zhao, H., Feb 14 2015, In : Chemical Communications. 51, 13, p. 2526-2528 3 p.

Research output: Contribution to journalArticle

Biosynthesis
Phosphates
Antimalarials
Derivatives
xylulose-5-phosphate

Studies of the TLR4-associated protein MD-2 using yeast-display and mutational analyses

Mattis, D. M., Chervin, A. S., Ranoa, D. R., Kelley, S. L., Tapping, R. I. & Kranz, D. M., May 8 2015, In : Molecular Immunology. 68, 2, p. 203-212 10 p.

Research output: Contribution to journalArticle

Toll-Like Receptor 4
Lipopolysaccharides
Yeasts
Proteins
Immune System

Substrate control in stereoselective lanthionine biosynthesis

Tang, W., Jiménez-Osés, G., Houk, K. N. & van der Donk, W. A., Jan 1 2015, In : Nature Chemistry. 7, 1, p. 57-64 8 p.

Research output: Contribution to journalArticle

Biosynthesis
Enzymes
Substrates
Stereoselectivity
Cyclization

Synergistic binding of the leader and core peptides by the lantibiotic synthetase HalM2

Thibodeaux, G. N., McClerren, A. L., Ma, Y., Gancayco, M. R. & van der Donk, W. A., Apr 17 2015, In : ACS chemical biology. 10, 4, p. 970-977 8 p.

Research output: Contribution to journalArticle

Peptide Synthases
Bacteriocins
Ligases
Protein Sorting Signals
Peptides

Synthesis of many different types of organic small molecules using one automated process

Li, J., Ballmer, S. G., Gillis, E. P., Fujii, S., Schmidt, M. J., Palazzolo, A. M. E., Lehmann, J. W., Morehouse, G. F. & Burke, M. D., Mar 13 2015, In : Science. 347, 6227, p. 1221-1226 6 p.

Research output: Contribution to journalArticle

Biological Products

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

Li, W., You, B., Hoque, M., Zheng, D., Luo, W., Ji, Z., Park, J. Y., Gunderson, S. I., Kalsotra, A., Manley, J. L. & Tian, B., Apr 1 2015, In : PLoS genetics. 11, 4, e1005166.

Research output: Contribution to journalArticle

Polyadenylation
Poly A
3' untranslated regions
cleavage
introns

Task-related differential expression of four cytochrome P450 genes in honeybee appendages

Mao, W., Schuler, M. A. & Berenbaum, M. R., Oct 1 2015, In : Insect Molecular Biology. 24, 5, p. 582-588 7 p.

Research output: Contribution to journalArticle

appendages
cytochrome P-450
Cytochrome P-450 Enzyme System
honey bees
Leg

TCR affinity for p/MHC formed by tumor antigens that are self-proteins: Impact on efficacy and toxicity

Stone, J. D., Harris, D. T. & Kranz, D. M., Apr 1 2015, In : Current Opinion in Immunology. 33, p. 16-22 7 p.

Research output: Contribution to journalReview article

Neoplasm Antigens
T-Cell Antigen Receptor
Peptides
Proteins
T-Lymphocytes

The atypical occurrence of two biotin protein ligases in Francisella novicida is due to distinct roles in virulence and biotin metabolism

Feng, Y., Chin, C. Y., Chakravartty, V., Gao, R., Crispell, E. K., Weiss, D. S. & Cronan, J. E., Jun 9 2015, In : mBio. 6, 3

Research output: Contribution to journalArticle

Francisella
Ligases
Biotin
Virulence
Proteins

The conserved modular elements of the acyl carrier proteins of lipid synthesis are only partially interchangeable

Zhu, L. & Cronan, J. E., May 29 2015, In : Journal of Biological Chemistry. 290, 22, p. 13791-13799 9 p.

Research output: Contribution to journalArticle

Acyl Carrier Protein
Lactococcus lactis
Escherichia coli
Lipids
Proteins

The Dual Characteristics of Light-Induced Cryptochrome 2, Homo-oligomerization and Heterodimerization, for Optogenetic Manipulation in Mammalian Cells

Che, D. L., Duan, L., Zhang, K. & Cui, B., Oct 16 2015, In : ACS synthetic biology. 4, 10, p. 1124-1135 12 p.

Research output: Contribution to journalArticle

Cryptochromes
Optogenetics
Oligomerization
Hominidae
Cells

The enterococcal cytolysin synthetase has an unanticipated lipid kinase fold

Dong, S. H., Tang, W., Lukk, T., Yu, Y., Nair, S. K. & van der Donk, W. A., Jul 30 2015, In : eLife. 4, JULY2015, e07607.

Research output: Contribution to journalArticle

Perforin
Ligases
Dehydration
Phosphotransferases
Lipids

The phosphoenolpyruvate: Sugar phosphotransferase system is involved in sensitivity to the glucosylated bacteriocin sublancin

Garcia De Gonzalo, C. V., Denham, E. L., Mars, R. A. T., Stülke, J., Van Der Donk, W. A. & Van Dijl, J. M., Nov 1 2015, In : Antimicrobial Agents and Chemotherapy. 59, 11, p. 6844-6854 11 p.

Research output: Contribution to journalArticle

Phosphoenolpyruvate Sugar Phosphotransferase System
Bacteriocins
Bacillus
Phosphotransferases
Gram-Positive Bacteria
Streptomyces coelicolor
Escherichia coli
Ligases
Enzymes
Adenosine Monophosphate

The two transmembrane helices of CcoP are sufficient for assembly of the cbb3-type heme-copper oxygen reductase from Vibrio cholerae

Ahn, Y. O., Lee, H. J., Kaluka, D., Yeh, S. R., Rousseau, D. L., Ädelroth, P. & Gennis, R. B., Jul 13 2015, In : Biochimica et Biophysica Acta - Bioenergetics. 1847, 10, p. 1231-1239 9 p.

Research output: Contribution to journalArticle

Vibrio cholerae
Heme
Copper
Oxidoreductases
Oxygen

Tissue Factor Residues That Modulate Magnesium-Dependent Rate Enhancements of the Tissue Factor/Factor VIIa Complex

Gajsiewicz, J. M., Nuzzio, K. M., Rienstra, C. M. & Morrissey, J. H., Aug 4 2015, In : Biochemistry. 54, 30, p. 4665-4671 7 p.

Research output: Contribution to journalArticle

Factor VIIa
Factor X
Thromboplastin
Magnesium
Ions