Research Output 1968 2019

2018

Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins

McLean, M. A., Gregory, M. C. & Sligar, S., May 20 2018, In : Annual Review of Biophysics. 47, p. 107-124 18 p.

Research output: Contribution to journalReview article

Membrane Proteins
Proteins
Membranes
Lipids
Multiprotein Complexes

Near-Infrared Photoactivatable Nitric Oxide Donors with Integrated Photoacoustic Monitoring

Zhou, E. Y., Knox, H. J., Reinhardt, C. J., Partipilo, G., Nilges, M. J. & Chan, J. K. F., Sep 19 2018, In : Journal of the American Chemical Society. 140, 37, p. 11686-11697 12 p.

Research output: Contribution to journalArticle

Nitric Oxide Donors
Photoacoustic effect
Nitric oxide
nitric oxide
near infrared

Novel Xanthomonas campestris long-chain-specific 3-oxoacyl- acyl carrier protein reductase involved in diffusible signal factor synthesis

Hu, Z., Dong, H., Ma, J. C., Yu, Y., Li, K. H., Guo, Q. Q., Zhang, C., Zhang, W. B., Cao, X., Cronan, J. E. & Wang, H., May 1 2018, In : mBio. 9, 3, e00596-18.

Research output: Contribution to journalArticle

3-Oxoacyl-(Acyl-Carrier-Protein) Reductase
Xanthomonas campestris
Fatty Acids
Growth
Oxidoreductases

Peridinin Is an Exceptionally Potent and Membrane-Embedded Inhibitor of Bilayer Lipid Peroxidation

Haley, H. M. S., Hill, A. G., Greenwood, A. I., Woerly, E. M., Rienstra, C. & Burke, M., Nov 14 2018, In : Journal of the American Chemical Society. 140, 45, p. 15227-15240 14 p.

Research output: Contribution to journalArticle

Lipid bilayers
Endothelial cells
inhibitor
lipid
Lipid Peroxidation

Photophysical Tuning of N-Oxide-Based Probes Enables Ratiometric Photoacoustic Imaging of Tumor Hypoxia

Knox, H. J., Kim, T. W., Zhu, Z. & Chan, J. K. F., Jul 20 2018, In : ACS chemical biology. 13, 7, p. 1838-1843 6 p.

Research output: Contribution to journalArticle

Photoacoustic effect
Oxides
Tumors
Tuning
Imaging techniques

Post-Translational Tyrosine Geranylation in Cyanobactin Biosynthesis

Morita, M., Hao, Y., Jokela, J. K., Sardar, D., Lin, Z., Sivonen, K., Nair, S. K. & Schmidt, E. W., May 16 2018, In : Journal of the American Chemical Society. 140, 19, p. 6044-6048 5 p.

Research output: Contribution to journalArticle

Biosynthesis
Cyanobacteria
Tyrosine
cyanobacterium
Geranyltranstransferase

Prediction of enzymatic pathways by integrative pathway mapping

Calhoun, S., Korczynska, M., Wichelecki, D. J., San Francisco, B., Zhao, S., Rodionov, D. A., Vetting, M. W., Al-Obaidi, N. F., Lin, H., O’Meara, M. J., Scott, D. A., Morris, J. H., Russel, D., Almo, S. C., Osterman, A. L., Gerlt, J. A., Jacobson, M. P., Shoichet, B. K. & Sali, A., Jan 29 2018, In : eLife. 7, e31097.

Research output: Contribution to journalArticle

Metabolic Networks and Pathways
Enzymes
Crystallography
Metabolomics
Systems Biology

Probing key elements of teixobactin-lipid II interactions in membranes

Wen, P. C., Vanegas, J. M., Rempe, S. B. & Tajkhorshid, E., Jan 1 2018, In : Chemical Science. 9, 34, p. 6997-7008 12 p.

Research output: Contribution to journalArticle

Membranes
Phosphates
Depsipeptides
Conformations
muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol
Thioctic Acid
Glycine Decarboxylase Complex H-Protein
Oxidoreductases
Enzymes
Keto Acids

P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II

Li, Y., Liu, M., Chen, L-F. & Chen, R., Mar 15 2018, In : Transcription. 9, 2, p. 88-94 7 p.

Research output: Contribution to journalReview article

Positive Transcriptional Elongation Factor B
RNA Polymerase II
Small Nuclear Ribonucleoproteins
Genetic Promoter Regions
Genes

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Scheurer, M., Rodenkirch, P., Siggel, M., Bernardi, R. C., Schulten, K., Tajkhorshid, E. & Rudack, T., Feb 6 2018, In : Biophysical journal. 114, 3, p. 577-583 7 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Purinergic P2X3 Receptors
Protein Interaction Maps
Biological Science Disciplines
Ions

Rapid Discovery of Glycocins through Pathway Refactoring in Escherichia coli

Ren, H., Biswas, S., Ho, S., van der Donk, W. A. & Zhao, H., Oct 19 2018, In : ACS chemical biology. 13, 10, p. 2966-2972 7 p.

Research output: Contribution to journalArticle

Bacteriocins
Escherichia coli
Genes
Anti-Bacterial Agents
Glycosylation

Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli

Si, T., Tian, Q., Min, Y., Zhang, L., Sweedler, J. V., van der Donk, W. A. & Zhao, H., Sep 26 2018, In : Journal of the American Chemical Society. 140, 38, p. 11884-11888 5 p.

Research output: Contribution to journalArticle

Protein Sorting Signals
peptide
Escherichia coli
Screening
Synthetic Biology

Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin

Chakravarti, A., Selvadurai, K., Shahoei, R., Lee, H., Fatma, S., Tajkhorshid, E. & Huang, R. H., Jan 1 2018, In : Journal of Biological Chemistry. 293, 36, p. 14122-14133 12 p.

Research output: Contribution to journalReview article

Substrate Specificity
Antiviral Agents
Substrates
Enzymes
Mevalonic Acid

Reduced axonal surface expression and phosphoinositide sensitivity in Kv7 channels disrupts their function to inhibit neuronal excitability in Kcnq2 epileptic encephalopathy

Kim, E. C., Zhang, J., Pang, W., Wang, S., Lee, K. Y., Cavaretta, J. P., Walters, J., Procko, E., Tsai, N-P. & Chung, H. J., Oct 2018, In : Neurobiology of Disease. 118, p. 76-93 18 p.

Research output: Contribution to journalArticle

Brain Diseases
Phosphatidylinositols
Calmodulin
Mutation
Voltage-Gated Potassium Channels

Role of the tightly bound quinone for the oxygen reaction of cytochrome bo3 oxidase from Escherichia coli

Melin, F., Sabuncu, S., Choi, S. K., Leprince, A., Gennis, R. B. & Hellwig, P., Oct 2018, In : FEBS Letters. 592, 20, p. 3380-3387 8 p.

Research output: Contribution to journalArticle

Electron Transport Complex IV
Escherichia coli
Oxygen
Quinones
Ubiquinone

Salt bridges gate ?-catenin activation at intercellular junctions

Barrick, S., Li, J., Kong, X., Ray, A., Tajkhorshid, E. & Leckband, D., Jan 15 2018, In : Molecular biology of the cell. 29, 2, p. 111-122 12 p.

Research output: Contribution to journalArticle

Catenins
Intercellular Junctions
Salts
Vinculin
Cadherins

Sbp1 modulates the translation of Pab1 mRNA in a poly(A)- and RGG-dependent manner

Brandariz-Núñez, A., Zeng, F., Ngoc Lam, Q. & Jin, H., Jan 2018, In : RNA. 24, 1, p. 43-55 13 p.

Research output: Contribution to journalArticle

Poly A
Protein Biosynthesis
Untranslated Regions
Messenger RNA
RNA-Binding Proteins

Selective Permeability of Carboxysome Shell Pores to Anionic Molecules

Mahinthichaichan, P., Morris, D. M., Wang, Y., Jensen, G. J. & Tajkhorshid, E., Oct 4 2018, In : Journal of Physical Chemistry B. 122, 39, p. 9110-9118 9 p.

Research output: Contribution to journalArticle

Anions
permeability
Negative ions
Nitrogen fixation
Proteins

Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins

Kerr, D., Tietjen, G. T., Gong, Z., Tajkhorshid, E., Adams, E. J. & Lee, K. Y. C., Oct 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 10, p. 2126-2133 8 p.

Research output: Contribution to journalReview article

T-cells
Phosphatidylserines
Mucins
Immunoglobulins
Membrane Proteins

SMPL synaptic membranes: Nanodisc-mediated synaptic membrane mimetics expand the toolkit for drug discovery and the molecular cell biology of synapses

Lo Bu, R., Clark, J., DiChiara, T., Sligar, S. & Klein, W. L., Jan 1 2018, Neuromethods. Humana Press Inc., p. 227-250 24 p. (Neuromethods; vol. 141).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytology
Synaptic Membranes
Molecular biology
Drug Discovery
Synapses

Solid-State NMR of highly 13 C-enriched cholesterol in lipid bilayers

Della Ripa, L. A., Petros, Z. A., Cioffi, A. G., Piehl, D. W., Courtney, J. M., Burke, M. D. & Rienstra, C. M., Apr 1 2018, In : Methods. 138-139, p. 47-53 7 p.

Research output: Contribution to journalArticle

Lipid bilayers
Lipid Bilayers
Sterols
Biophysical Phenomena
Biochemical Phenomena

Special Issue: Current Topics in Mechanistic Enzymology

Gerlt, J. A., Jun 5 2018, In : Biochemistry. 57, 22, p. 3085-3086 2 p.

Research output: Contribution to journalEditorial

Molecular Models
Biochemistry
Molecular Biology
Enzymes

Stereospecific Radical-Mediated B12-Dependent Methyl Transfer by the Fosfomycin Biosynthesis Enzyme Fom3

McLaughlin, M. I. & van der Donk, W. A., Aug 21 2018, In : Biochemistry. 57, 33, p. 4967-4971 5 p.

Research output: Contribution to journalArticle

Fosfomycin
Cytidine Monophosphate
Biosynthesis
Vitamin B 12
Enzymes

Strong and sustained activation of the anticipatory unfolded protein response induces necrotic cell death

Livezey, M., Huang, R., Hergenrother, P. & Shapiro, D. J., Oct 2018, In : Cell Death and Differentiation. 25, 10, p. 1796-1807 12 p.

Research output: Contribution to journalArticle

Unfolded Protein Response
Cell Death
Adenosine Triphosphate
Autophagy
Arachidonic Acid

Structural and Biochemical Studies of a Biocatalyst for the Enzymatic Production of Wax Esters

Petronikolou, N. & Nair, S. K., Jul 6 2018, In : ACS Catalysis. 8, 7, p. 6334-6344 11 p.

Research output: Contribution to journalArticle

Biocatalysts
Waxes
Diacylglycerol O-Acyltransferase
Esters
Enzymes

Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop “Out” Conformation for LasR

O'Reilly, M. C., Dong, S. H., Rossi, F. M., Karlen, K. M., Kumar, R. S., Nair, S. K. & Blackwell, H. E., Sep 20 2018, In : Cell chemical biology. 25, 9, p. 1128-1139.e3

Research output: Contribution to journalArticle

Quorum Sensing
Conformations
Ligands
Pseudomonas aeruginosa
Pathogens

Structural basis of transcriptional regulation by cour, a repressor of coumarate catabolism, in rhodopseudomonas palustris

Cogan, D. P., Baraquet, C., Harwood, C. S. & Nair, S. K., Jan 1 2018, In : Journal of Biological Chemistry. 293, 30, p. 11727-11735 9 p.

Research output: Contribution to journalArticle

Rhodopseudomonas
Ligands
Operon
DNA
Bearings (structural)

Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin

Kapoor, I. & Nair, S. K., Sep 11 2018, In : Biochemistry. 57, 36, p. 5282-5288 7 p.

Research output: Contribution to journalArticle

Flavin Mononucleotide
Biosynthesis
Catalytic Domain
Phosphates
Reaction intermediates

Structure of the alternative complex III in a supercomplex with cytochrome oxidase

Sun, C., Benlekbir, S., Venkatakrishnan, P., Wang, Y., Hong, S., Hosler, J., Tajkhorshid, E., Rubinstein, J. L. & Gennis, R. B., May 3 2018, In : Nature. 557, 7703, p. 123-126 4 p.

Research output: Contribution to journalArticle

Electron Transport Complex III
Electron Transport Complex IV
Electron Transport
Lipid Bilayers
Hydroquinones

Substrate-assisted enzymatic formation of lysinoalanine in duramycin

An, L., Cogan, D. P., Navo, C. D., Jiménez-Osés, G., Nair, S. K. & van der Donk, W. A., Oct 1 2018, In : Nature chemical biology. 14, 10, p. 928-933 6 p.

Research output: Contribution to journalArticle

Lysinoalanine
Viperidae
Catalysis
Cystic Fibrosis
duramycin

Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity

Sharma, P. & Kranz, D. M., Jan 1 2018, In : Journal of Biological Chemistry. 293, 5, p. 1820-1834 15 p.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor
Complementarity Determining Regions
varespladib methyl
Binding Sites
Substitution reactions

Surveillance of Cancer Stem Cell Plasticity Using an Isoform-Selective Fluorescent Probe for Aldehyde Dehydrogenase 1A1

Anorma, C., Hedhli, J., Bearrood, T. E., Pino, N. W., Gardner, S. H., Inaba, H., Zhang, P., Li, Y., Feng, D., Dibrell, S. E., Kilian, K. A., Dobrucki, W., Fan, T. M. & Chan, J. K. F., Aug 22 2018, In : ACS Central Science. 4, 8, p. 1045-1055 11 p.

Research output: Contribution to journalArticle

Aldehyde Dehydrogenase
Stem cells
Aldehydes
Fluorescent Dyes
Plasticity

Synthesis of Antibiotics and Related Molecules

Movassaghi, M. & van der Donk, W. A., Jul 6 2018, In : Journal of Organic Chemistry. 83, 13, p. 6826-6828 3 p.

Research output: Contribution to journalEditorial

Biological Products
Anti-Bacterial Agents

T63 inhibits osteoclast differentiation through regulating MAPKs and Akt signaling pathways

Zhao, X. L., Chen, J. J., SI, S. Y., Chen, L-F. & Wang, Z., Sep 5 2018, In : European Journal of Pharmacology. 834, p. 30-35 6 p.

Research output: Contribution to journalArticle

Osteoclasts
Osteogenesis
Osteoblasts
Osteoporosis
Bone and Bones

Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P., Nelson, E. & Shapiro, D. J., Jan 1 2018, In : Oncotarget. 9, 19, p. 14741-14753 13 p.

Research output: Contribution to journalArticle

Unfolded Protein Response
Estrogen Receptors
Ovarian Neoplasms
Paclitaxel
Adenosine Triphosphate

The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis

Gu, W., Dong, S. H., Sarkar, S., Nair, S. K. & Schmidt, E. W., Jan 1 2018, Methods in Enzymology. Moore, B. S. (ed.). Academic Press Inc., p. 113-163 51 p. (Methods in Enzymology; vol. 604).

Research output: Chapter in Book/Report/Conference proceedingChapter

Biochemistry
Biosynthesis
Enzymes
Dimethylallyltranstransferase
Methyltransferases

The electron distribution in the "activated" state of cytochrome c oxidase

Vilhjálmsdóttir, J., Gennis, R. B. & Brzezinski, P., Dec 1 2018, In : Scientific reports. 8, 1, 7502.

Research output: Contribution to journalArticle

Open Access
Electron Transport Complex IV
Electrons
Protons
Free energy
Membranes

The Enzymology of Prochlorosin Biosynthesis

Bobeica, S. C. & van der Donk, W. A., Jan 1 2018, Methods in Enzymology. Moore, B. S. (ed.). Academic Press Inc., p. 165-203 39 p. (Methods in Enzymology; vol. 604).

Research output: Chapter in Book/Report/Conference proceedingChapter

Prochlorococcus
Biosynthesis
Genes
Genome
Synechococcus

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules

Trobe, M. & Burke, M., Apr 9 2018, In : Angewandte Chemie - International Edition. 57, 16, p. 4192-4214 23 p.

Research output: Contribution to journalReview article

3D printers
Automation
Molecules
Innovation
Direction compound

The Need for Manuscripts to Include Database Identifiers for Proteins

Gerlt, J. A., Jul 24 2018, In : Biochemistry. 57, 29, p. 4239-4240 2 p.

Research output: Contribution to journalEditorial

Biochemistry
Animals
Internet
Proteins

The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells

Fanning, S. W., Jeselsohn, R., Dharmarajan, V., Mayne, C. G., Karimi, M., Buchwalter, G., Houtman, R., Toy, W., Fowler, C. E., Han, R., Lainé, M., Carlson, K. E., Martin, T. A., Nowak, J., Nwachukwu, J. C., Hosfield, D. J., Chandarlapaty, S., Tajkhorshid, E., Nettles, K. W., Griffin, P. R. & 4 others, Shen, Y., Katzenellenbogen, J. A., Brown, M. & Greene, G. L., Nov 1 2018, In : eLife. 7, e37161.

Research output: Contribution to journalArticle

Selective Estrogen Receptor Modulators
Estrogen Receptor Modulators
Estrogen Receptor alpha
Tamoxifen
Estrogen Receptors

Towards the generalized iterative synthesis of small molecules

Lehmann, J. W., Blair, D. J. & Burke, M., Jan 1 2018, In : Nature Reviews Chemistry. 2, 2, 0115.

Research output: Contribution to journalReview article

Molecules
Tall buildings
Biological Products
Macromolecules
Drug products

Type 2 NADH dehydrogenase is the only point of entry for electrons into the Streptococcus agalactiae respiratory chain and is a potential drug target

Lencina, A. M., Franza, T., Sullivan, M. J., Ulett, G. C., Ipe, D. S., Gaudu, P., Gennis, R. B. & Schurig-Briccio, L. A., Jul 1 2018, In : mBio. 9, 4, e01034-18.

Research output: Contribution to journalArticle

Open Access
NADH Dehydrogenase
Streptococcus agalactiae
Electron Transport
Electrons
Oxidoreductases

Unpaired Electron Spin Density Distribution across Reduced [2Fe-2S] Cluster Ligands by 13Cβ-Cysteine Labeling

Taguchi, A. T., Miyajima-Nakano, Y., Fukazawa, R., Lin, M. T., Baldansuren, A., Gennis, R. B., Hasegawa, K., Kumasaka, T., Dikanov, S. & Iwasaki, T., Jan 16 2018, In : Inorganic Chemistry. 57, 2, p. 741-746 6 p.

Research output: Contribution to journalArticle

cysteine
electron spin
Labeling
marking
Cysteine

X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds

Schieferstein, J. M., Pawate, A. S., Varel, M. J., Guha, S., Astrauskaite, I., Gennis, R. B. & Kenis, P. J. A., Jan 1 2018, In : Lab on a chip. 18, 6, p. 944-954 11 p.

Research output: Contribution to journalArticle

Microfluidics
Crystallization
Membrane Proteins
X-Rays
Proteins

‘Democratized’ genomic enzymology web tools for functional assignment

Zallot, R., Oberg, N. O. & Gerlt, J. A., Dec 2018, In : Current Opinion in Chemical Biology. 47, p. 77-85 9 p.

Research output: Contribution to journalReview article

Protein Databases
Genome
Genes
Proteins
Costs and Cost Analysis
2017

A bioreducible N-oxide-based probe for photoacoustic imaging of hypoxia

Knox, H. J., Hedhli, J., Kim, T. W., Khalili, K., Dobrucki, W. & Chan, J. K. F., Dec 1 2017, In : Nature communications. 8, 1, 1794.

Research output: Contribution to journalArticle

Photoacoustic effect
hypoxia
Oxides
Imaging techniques
oxides

Activation and Desensitization Mechanism of AMPA Receptor-TARP Complex by Cryo-EM

Chen, S., Zhao, Y., Wang, Y., Shekhar, M., Tajkhorshid, E. & Gouaux, E., Sep 7 2017, In : Cell. 170, 6, p. 1234-1246.e14

Research output: Contribution to journalArticle

AMPA Receptors
Chemical activation
Proteins
Quisqualic Acid
Kainic Acid
Esculin
Signal transduction
Metabolism
Osteogenesis
Signal Transduction