Research Output 1968 2019

2016

Nanodiscs for structural and functional studies of membrane proteins

Denisov, I. G. & Sligar, S., Jun 7 2016, In : Nature Structural and Molecular Biology. 23, 6, p. 481-486 6 p.

Research output: Contribution to journalReview article

Membrane Proteins
Multiprotein Complexes
Technology
Membranes

New insights into the biosynthesis of fosfazinomycin

Huang, Z., Wang, K. K. A. & van der Donk, W. A., Jan 1 2016, In : Chemical Science. 7, 8, p. 5219-5223 5 p.

Research output: Contribution to journalArticle

Biosynthesis
Adenylosuccinate Lyase
RNA, Transfer, Val
Nitrous Acid
Acetylation

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

Ortega, M. A. & van der Donk, W. A., Jan 21 2016, In : Cell chemical biology. 23, 1, p. 31-44 14 p.

Research output: Contribution to journalReview article

Biosynthesis
Biological Products
Synthetic Biology
Peptides
Biosynthetic Pathways

Orthogonal Assays Clarify the Oxidative Biochemistry of Taxol P450 CYP725A4

Biggs, B. W., Rouck, J. E., Kambalyal, A., Arnold, W., Lim, C. G., De Mey, M., Oneil-Johnson, M., Starks, C. M., Das, A. & Ajikumar, P. K., May 20 2016, In : ACS chemical biology. 11, 5, p. 1445-1451 7 p.

Research output: Contribution to journalArticle

Biochemistry
Paclitaxel
Metabolic Engineering
Assays
Metabolic engineering

Our Path to Less Toxic Amphotericins

Endo, M. M., Cioffi, A. G. & Burke, M. D., Feb 12 2016, In : Synlett. 27, 3, p. 337-354 18 p.

Research output: Contribution to journalArticle

Poisons
Amphotericin B
Ergosterol
Biological Products
Ion Channels

PBR322 vectors having tetracycline-dependent replication

Cronan, J. E., Mar 1 2016, In : Plasmid. 84-85, p. 20-26 7 p.

Research output: Contribution to journalArticle

Tetracycline
Plasmids
Lac Repressors
Tetracycline Resistance
Genetic Vectors

Peptide release promoted by methylated RF2 and ArfA in nonstop translation is achieved by an induced-fit mechanism

Zeng, F. & Jin, H., Jan 2016, In : RNA. 22, 1, p. 49-60 12 p.

Research output: Contribution to journalArticle

Messenger RNA
Peptides
Ribosomes
Methylation
Recycling

Phosphatidic Acid Sequesters Sec18p from cis-SNARE Complexes to Inhibit Priming

Starr, M. L., Hurst, L. R. & Fratti, R., Oct 1 2016, In : Traffic. 17, 10, p. 1091-1109 19 p.

Research output: Contribution to journalArticle

SNARE Proteins
Phosphatidic Acids
Phosphatidate Phosphatase
Diglycerides
Vacuoles

Phosphatidylinositol (3,4,5)-trisphosphate binds to sortilin and competes with neurotensin: Implications for very low density lipoprotein binding

Sparks, R. P., Jenkins, J. L., Miner, G. E., Wang, Y., Guida, W. C., Sparks, C. E., Fratti, R. & Sparks, J. D., Oct 21 2016, In : Biochemical and Biophysical Research Communications. 479, 3, p. 551-556 6 p.

Research output: Contribution to journalArticle

Neurotensin
VLDL Lipoproteins
Liposomes
Surface Plasmon Resonance
Surface plasmon resonance

Phosphatidylinositol 4,5-Bisphosphate Modulates the Affinity of Talin-1 for Phospholipid Bilayers and Activates Its Autoinhibited Form

Ye, X., McLean, M. A. & Sligar, S., Sep 13 2016, In : Biochemistry. 55, 36, p. 5038-5048 11 p.

Research output: Contribution to journalArticle

Talin
Phosphatidylinositols
Phospholipids
Integrins
Lipid bilayers

Platelet-derived short-chain polyphosphates enhance the inactivation of tissue factor pathway inhibitor by activated coagulation factor XI

Puy, C., Tucker, E. I., Ivanov, I. S., Gailani, D., Smith, S. A., Morrissey, J. H., Gruber, A. & McCarty, O. J. T., Oct 2016, In : PloS one. 11, 10, e0165172.

Research output: Contribution to journalArticle

Factor XIa
Factor XI
Polyphosphates
polyphosphates
Platelets

Polyphosphate is a novel cofactor for regulation of complement by a serpin, C1 inhibitor

Wijeyewickrema, L. C., Lameignere, E., Hor, L., Duncan, R. C., Shiba, T., Travers, R. J., Kapopara, P. R., Lei, V., Smith, S. A., Kim, H., Morrissey, J. H., Pike, R. N. & Conway, E. M., Sep 29 2016, In : Blood. 128, 13, p. 1766-1776 11 p.

Research output: Contribution to journalArticle

Complement C1 Inhibitor Protein
Polyphosphates
Antithrombin III
Heparin
Serine Proteases

Proton Dynamics at the Membrane Surface

Gennis, R. B., May 10 2016, In : Biophysical journal. 110, 9, p. 1909-1911 3 p.

Research output: Contribution to journalShort survey

Protons
Membranes
Agrobacterium tumefaciens
Lactones
Crystallization
purification
Purification

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo 3 from Escherichia coli

Sun, C., Taguchi, A. T., Vermaas, J. V., Beal, N. J., O'Malley, P. J., Tajkhorshid, E., Gennis, R. B. & Dikanov, S. A., Oct 11 2016, In : Biochemistry. 55, 40, p. 5714-5725 12 p.

Research output: Contribution to journalArticle

coenzyme Q10
Electron Spin Resonance Spectroscopy
Cytochromes
Escherichia coli
Ubiquinone

Revealing an outward-facing open conformational state in a CLC CL-/H+ exchange transporter

Khantwal, C. M., Abraham, S. J., Han, W., Jiang, T., Chavan, T. S., Cheng, R. C., Elvington, S. M., Liu, C. W., Mathews, I. I., Stein, R. A., McHaourab, H. S., Tajkhorshid, E. & Maduke, M., Jan 22 2016, In : eLife. 5, JANUARY2016, e11189.

Research output: Contribution to journalArticle

Facings
Molecular Dynamics Simulation
Constriction
Glutamic Acid
Protonation

Reversible optogenetic control of kinase activity during differentiation and embryonic development

Krishnamurthy, V. V., Khamo, J. S., Mei, W., Turgeon, A. J., Ashraf, H. M., Mondal, P., Patel, D. B., Risner, N., Cho, E. E., Yang, J. & Zhang, K., Nov 1 2016, In : Development (Cambridge). 143, 21, p. 4085-4094 10 p.

Research output: Contribution to journalArticle

Optogenetics
embryonic development
Embryonic Development
Phosphotransferases
Cryptochromes

Sortilin facilitates VLDL-B100 secretion by insulin sensitive McArdle RH7777 cells

Sparks, R. P., Guida, W. C., Sowden, M. P., Jenkins, J. L., Starr, M. L., Fratti, R., Sparks, C. E. & Sparks, J. D., Sep 16 2016, In : Biochemical and Biophysical Research Communications. 478, 2, p. 546-552 7 p.

Research output: Contribution to journalArticle

Insulin
Insulin Resistance
Neurotensin
Apolipoproteins B
sortilin

Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction

Speltz, T. E., Fanning, S. W., Mayne, C. G., Fowler, C., Tajkhorshid, E., Greene, G. L. & Moore, T. W., Mar 18 2016, In : Angewandte Chemie - International Edition. 55, 13, p. 4252-4255 4 p.

Research output: Contribution to journalArticle

Hydrocarbons
Estrogen Receptors
Peptides
Amino acids
Amino Acids
Bacteriocins
Ruminants
Bioactivity
Bacteria
Peptides

Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity

Adams, J. J., Narayanan, S., Birnbaum, M. E., Sidhu, S. S., Blevins, S. J., Gee, M. H., Sibener, L. V., Baker, B. M., Kranz, D. M. & Garcia, K. C., Jan 1 2016, In : Nature Immunology. 17, 1, p. 87-94 8 p.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor
Major Histocompatibility Complex
Peptides
T-Lymphocytes
Antigens

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

Ortega, M. A., Hao, Y., Walker, M. C., Donadio, S., Sosio, M., Nair, S. K. & van der Donk, W., Mar 17 2016, In : Cell chemical biology. 23, 3, p. 370-380 11 p.

Research output: Contribution to journalArticle

RNA, Transfer, Glu
Hydro-Lyases
Bacteriocins
Actinobacteria
Biosynthesis

Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine

Yadava, U., Vetting, M. W., Al Obaidi, N., Carter, M. S., Gerlt, J. A. & Almo, S. C., Jan 1 2016, In : Acta Crystallographica Section:F Structural Biology Communications. 72, p. 467-472 6 p.

Research output: Contribution to journalArticle

Amino Sugars
transporter
Galactosamine
ATP-Binding Cassette Transporters
Glucosamine

Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates

Chekan, J. R., Koos, J. D., Zong, C., Maksimov, M. O., Link, A. J. & Nair, S. K., Dec 21 2016, In : Journal of the American Chemical Society. 138, 50, p. 16452-16458 7 p.

Research output: Contribution to journalArticle

peptide
Peptides
topology
Topology
substrate

Substrate binding to cytochrome P450-2J2 in Nanodiscs detected by nanoplasmonic Lycurgus cup arrays

Plucinski, L., Ranjan Gartia, M., Arnold, W. R., Ameen, A., Chang, T. W., Hsiao, A., Liu, G. L. & Das, A., Jan 15 2016, In : Biosensors and Bioelectronics. 75, p. 337-346 10 p.

Research output: Contribution to journalArticle

Cytochrome P-450 Enzyme System
Sensor arrays
Proteins
Substrates
Preclinical Drug Evaluations

Synthesis and Bioactivity of Diastereomers of the Virulence Lanthipeptide Cytolysin

Mukherjee, S., Huo, L., Thibodeaux, G. N. & van der Donk, W. A., Dec 2 2016, In : Organic Letters. 18, 23, p. 6188-6191 4 p.

Research output: Contribution to journalArticle

virulence
Perforin
Stereochemistry
Bioactivity
Virulence

The cellular membrane as a mediator for small molecule interaction with membrane proteins

Mayne, C. G., Arcario, M. J., Mahinthichaichan, P., Baylon, J. L., Vermaas, J. V., Navidpour, L., Wen, P. C., Thangapandian, S. & Tajkhorshid, E., Oct 1 2016, In : Biochimica et Biophysica Acta - Biomembranes. 1858, 10, p. 2290-2304 15 p.

Research output: Contribution to journalArticle

Membrane Proteins
Membranes
Molecules
Pharmaceutical Preparations
Signal transduction

The central polybasic region of the soluble snare (soluble n-ethylmaleimide-sensitive factor attachment protein receptor) Vam7 affects binding to phosphatidylinositol 3-phosphate by the PX (Phox Homology) domain

Miner, G. E., Starr, M. L., Hurst, L. R., Sparks, R. P., Padolina, M. & Fratti, R., Aug 19 2016, In : Journal of Biological Chemistry. 291, 34, p. 17651-17663 13 p.

Research output: Contribution to journalArticle

Ethylmaleimide
SNARE Proteins
Vacuoles
Fusion reactions
Proteins

The Charge Properties of Phospholipid Nanodiscs

Her, C., Filoti, D. I., McLean, M. A., Sligar, S., Alexander Ross, J. B., Steele, H. & Laue, T. M., Sep 6 2016, In : Biophysical journal. 111, 5, p. 989-998 10 p.

Research output: Contribution to journalArticle

Phospholipids
Lipids
Anions
Membranes
Membrane Proteins

The CO Photodissociation and Recombination Dynamics of the W172Y/F282T Ligand Channel Mutant of Rhodobacter sphaeroides aa3 Cytochrome c Oxidase

Cassano, J. A., Choi, S. K., McDonald, W., Szundi, I., Villa Gawboy, T. R., Gennis, R. B. & Einarsdóttir, Ó., May 1 2016, In : Photochemistry and Photobiology. 92, 3, p. 410-419 10 p.

Research output: Contribution to journalArticle

Photodissociation
Rhodobacter sphaeroides
oxidase
cytochromes
Electron Transport Complex IV

The Enterococcal Cytolysin Synthetase Coevolves with Substrate for Stereoselective Lanthionine Synthesis

Tang, W., Thibodeaux, G. N. & van der Donk, W. A., Sep 16 2016, In : ACS chemical biology. 11, 9, p. 2438-2446 9 p.

Research output: Contribution to journalArticle

Perforin
Ligases
Stereoselectivity
Substrates
Peptides

The many roles of glutamate in metabolism

Walker, M. C. & van der Donk, W. A., Mar 1 2016, In : Journal of Industrial Microbiology and Biotechnology. 43, 2-3, p. 419-430 12 p.

Research output: Contribution to journalReview article

Metabolism
Amino acids
Glutamic Acid
Bioremediation
Biosynthesis
Operon
Ligases
Biotin
Staphylococcus aureus
DNA

The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins

Stadtmueller, B. M., Huey-Tubman, K. E., López, C. J., Yang, Z., Hubbell, W. L. & Bjorkman, P. J., Mar 4 2016, In : eLife. 5, MARCH2016, e10640.

Research output: Contribution to journalArticle

Polymeric Immunoglobulin Receptors
Secretory Component
Immunoglobulins
Ligands
Mammals

The Timing of Raf/ERK and AKT Activation in Protecting PC12 Cells against Oxidative Stress

Ong, Q., Guo, S., Duan, L., Zhang, K., Collier, E. A. & Cui, B., Jan 1 2016, In : PloS one. 11, 4, p. e0153487

Research output: Contribution to journalArticle

Oxidative stress
MAP Kinase Signaling System
PC12 Cells
Optogenetics
protective effect

The unusual redox properties of C-type oxidases

Melin, F., Xie, H., Meyer, T., Ahn, Y. O., Gennis, R. B., Michel, H. & Hellwig, P., Dec 1 2016, In : Biochimica et Biophysica Acta - Bioenergetics. 1857, 12, p. 1892-1899 8 p.

Research output: Contribution to journalArticle

Heme
Oxidation-Reduction
Oxidoreductases
Protons
Pseudomonas stutzeri

The use of isomeric testosterone dimers to explore allosteric effects in substrate binding to cytochrome P450 CYP3A4

Denisov, I. G., Mak, P. J., Grinkova, Y. V., Bastien, D., Bérubé, G., Sligar, S. & Kincaid, J. R., May 1 2016, In : Journal of Inorganic Biochemistry. 158, p. 77-85 9 p.

Research output: Contribution to journalArticle

Cytochrome P-450 CYP3A
Dimers
Cytochrome P-450 Enzyme System
Testosterone
Substrates

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

Vermaas, J. V., Hardy, D. J., Stone, J. E., Tajkhorshid, E. & Kohlmeyer, A., Jun 27 2016, In : Journal of Chemical Information and Modeling. 56, 6, p. 1112-1116 5 p.

Research output: Contribution to journalArticle

Topology
Molecular dynamics
simulation
Engines
energy

Trimerization of the HIV Transmembrane Domain in Lipid Bilayers Modulates Broadly Neutralizing Antibody Binding

Reichart, T. M., Baksh, M. M., Rhee, J. K., Fiedler, J. D., Sligar, S. G., Finn, M. G., Zwick, M. B. & Dawson, P. E., Feb 18 2016, In : Angewandte Chemie - International Edition. 55, 8, p. 2688-2692 5 p.

Research output: Contribution to journalArticle

Lipid bilayers
Neutralizing Antibodies
Antibodies
Peptides
Membranes

Unsaturated Fatty Acid Synthesis in the Gastric Pathogen Helicobacter pylori Proceeds via a Backtracking Mechanism

Bi, H., Zhu, L., Jia, J., Zeng, L. & Cronan, J. E., Dec 22 2016, In : Cell chemical biology. 23, 12, p. 1480-1489 10 p.

Research output: Contribution to journalArticle

Pathogens
Unsaturated Fatty Acids
Helicobacter pylori
Acyl Carrier Protein
Stomach

X-ray structures define human P2X 3 receptor gating cycle and antagonist action

Mansoor, S. E., Lü, W., Oosterheert, W., Shekhar, M., Tajkhorshid, E. & Gouaux, E., Sep 14 2016, In : Nature. 538, 7623, p. 66-71 6 p.

Research output: Contribution to journalArticle

X-Rays
Receptors, Tumor Necrosis Factor, Member 25
Ions
Cardiovascular System
Ion Channels
2015

2013 Scientific Sessions Sol Sherry Distinguished Lecture in Thrombosis Polyphosphate: A Novel Modulator of Hemostasis and Thrombosis

Smith, S. A. & Morrissey, J. H., Jun 27 2015, In : Arteriosclerosis, Thrombosis, and Vascular Biology. 35, 6, p. 1298-1305 8 p.

Research output: Contribution to journalReview article

Polyphosphates
Polymethyl Methacrylate
Hemostasis
Thrombosis
Blood Coagulation

A common late-stage intermediate in catalysis by 2-hydroxyethyl-phosphonate dioxygenase and methylphosphonate synthase

Peck, S. C., Chekan, J. R., Ulrich, E. C., Nair, S. K. & van der Donk, W. A., Feb 2015, In : Journal of the American Chemical Society. 137, 9, p. 3217-3220 4 p.

Research output: Contribution to journalArticle

Dioxygenases
catalysis
Catalysis
Isotopes
Iron

Activation of molecular oxygen in cytochromes P450

Denisov, I. G. & Sligar, S. G., Jan 1 2015, Cytochrome P450: Structure, Mechanism, and Biochemistry, Fourth Edition. Springer International Publishing, p. 69-109 41 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular oxygen
Cytochrome P-450 Enzyme System
Chemical activation
Oxygen
Protonation

A dietary phytochemical alters caste-associated gene expression in honey bees

Mao, W., Schuler, M. A. & Berenbaum, M. R., Aug 2015, In : Science Advances. 1, 7, e1500795.

Research output: Contribution to journalArticle

Honey
Bees
Phytochemicals
Social Class
Larva

A dysregulated acetyl/SUMO switch of FXR promotes hepatic inflammation in obesity

Kim, D. H., Xiao, Z., Kwon, S., Sun, X., Ryerson, D., Tkac, D., Ma, P., Wu, S. Y., Chiang, C. M., Zhou, E., Xu, H. E., Palvimo, J. J., Chen, L-F., Kemper, B. & Kemper, K. J., Jan 14 2015, In : EMBO Journal. 34, 2, p. 184-199 16 p.

Research output: Contribution to journalArticle

Acetylation
Obesity
Switches
Inflammation
Liver

A General Strategy for the Discovery of Metabolic Pathways: D -Threitol, l -Threitol, and Erythritol Utilization in Mycobacterium smegmatis

Huang, H., Carter, M. S., Vetting, M. W., Al-Obaidi, N., Patskovsky, Y., Almo, S. C. & Gerlt, J. A., Nov 25 2015, In : Journal of the American Chemical Society. 137, 46, p. 14570-14573 4 p.

Research output: Contribution to journalArticle

Erythritol
Mycobacterium smegmatis
Metabolic Networks and Pathways
ATP-Binding Cassette Transporters
genome

A multiplex assay for detection of staphylococcal and streptococcal exotoxins

Sharma, P., Wang, N., Chervin, A. S., Quinn, C. L., Stone, J. D. & Kranz, D. M., Aug 25 2015, In : PloS one. 10, 8, e0135986.

Research output: Contribution to journalArticle

exotoxins
Exotoxins
Assays
toxins
Food

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

Zhao, H., Palencia, A., Seiradake, E., Ghaemi, Z., Cusack, S., Luthey-Schulten, Z. & Martinis, S., Oct 16 2015, In : ACS chemical biology. 10, 10, p. 2277-2285 9 p.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
Transfer RNA
Tyrosine
Catalytic Domain
RNA, Transfer, Leu

Anticipatory estrogen activation of the unfolded protein response is linked to cell proliferation and poor survival in estrogen receptor α-positive breast cancer

Andruska, N., Zheng, X., Yang, X., Helferich, W. G. & Shapiro, D. J., Jul 21 2015, In : Oncogene. 34, 29, p. 3760-3769 10 p.

Research output: Contribution to journalArticle

Unfolded Protein Response
Estrogen Receptors
Estrogens
Cell Proliferation
Breast Neoplasms