Research Output 1967 2020

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2015

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

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

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

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. L., 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

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

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

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. G. & 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 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

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 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
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

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