Research Output 1967 2020

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Review article
2015

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
2014

Multitarget drug discovery for tuberculosis and other infectious diseases

Li, K., Schurig-Briccio, L. A., Feng, X., Upadhyay, A., Pujari, V., Lechartier, B., Fontes, F. L., Yang, H., Rao, G., Zhu, W., Gulati, A., No, J. H., Cintra, G., Bogue, S., Liu, Y. L., Molohon, K., Orlean, P., Mitchell, D. A., Freitas-Junior, L., Ren, F. & 8 others, Sun, H., Jiang, T., Li, Y., Guo, R. T., Cole, S. T., Gennis, R. B., Crick, D. C. & Oldfield, E., Apr 10 2014, In : Journal of Medicinal Chemistry. 57, 7, p. 3126-3129 4 p.

Research output: Contribution to journalReview article

Drug Discovery
Malaria
Communicable Diseases
Parasites
Tuberculosis

Soluble T cell receptor Vβ domains engineered for high-affinity binding to staphylococcal or streptococcal superantigens

Sharma, P., Wang, N. & Kranz, D. M., Feb 13 2014, In : Toxins. 6, 2, p. 556-574 19 p.

Research output: Contribution to journalReview article

Superantigens
T-Cell Antigen Receptor
T-cells
T-Lymphocytes
Staphylococcus aureus

Structure and mechanism of lanthipeptide biosynthetic enzymes

van der Donk, W. A. & Nair, S. K., Dec 1 2014, In : Current Opinion in Structural Biology. 29, p. 58-66 9 p.

Research output: Contribution to journalReview article

Peptides
Sulfides
Enzymes
Post Translational Protein Processing
Biological Products

The chain-flipping mechanism of ACP (acyl carrier protein)-dependent enzymes appears universal

Cronan, J. E., Jun 1 2014, In : Biochemical Journal. 460, 2, p. 157-163 7 p.

Research output: Contribution to journalReview article

Acyl Carrier Protein
Enzymes
Fatty Acids
Polyketides
Proteins
Biosynthetic Pathways
Sulfur
Thioctic Acid
Fatty Acid Synthases
Enzymes
2013

Insights into the evolution of lanthipeptide biosynthesis

Yu, Y., Zhang, Q. & Van Der Donk, W. A., Nov 1 2013, In : Protein Science. 22, 11, p. 1478-1489 12 p.

Research output: Contribution to journalReview article

Biosynthesis
Post Translational Protein Processing
Biological Products
Peptides
Sulfides

Optimizations to achieve high-level expression of cytochrome P450 proteins using Escherichia coli expression systems

Zelasko, S., Palaria, A. & Das, A., Nov 1 2013, In : Protein Expression and Purification. 92, 1, p. 77-87 11 p.

Research output: Contribution to journalReview article

Escherichia coli Proteins
Cytochrome P-450 Enzyme System
Cytochromes
Proteins
Bacterial Structures

Phosphonate biosynthesis and catabolism: A treasure trove of unusual enzymology

Peck, S. C. & van der Donk, W. A., Aug 1 2013, In : Current Opinion in Chemical Biology. 17, 4, p. 580-588 9 p.

Research output: Contribution to journalReview article

Organophosphonates
Biosynthesis
Biochemistry
Phosphates
Biological Products

Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature

Arnison, P. G., Bibb, M. J., Bierbaum, G., Bowers, A. A., Bugni, T. S., Bulaj, G., Camarero, J. A., Campopiano, D. J., Challis, G. L., Clardy, J., Cotter, P. D., Craik, D. J., Dawson, M., Dittmann, E., Donadio, S., Dorrestein, P. C., Entian, K. D., Fischbach, M. A., Garavelli, J. S., Göransson, U. & 45 others, Gruber, C. W., Haft, D. H., Hemscheidt, T. K., Hertweck, C., Hill, C., Horswill, A. R., Jaspars, M., Kelly, W. L., Klinman, J. P., Kuipers, O. P., Link, A. J., Liu, W., Marahiel, M. A., Mitchell, D. A., Moll, G. N., Moore, B. S., Müller, R., Nair, S. K., Nes, I. F., Norris, G. E., Olivera, B. M., Onaka, H., Patchett, M. L., Piel, J., Reaney, M. J. T., Rebuffat, S., Ross, R. P., Sahl, H. G., Schmidt, E. W., Selsted, M. E., Severinov, K., Shen, B., Sivonen, K., Smith, L., Stein, T., Süssmuth, R. D., Tagg, J. R., Tang, G. L., Truman, A. W., Vederas, J. C., Walsh, C. T., Walton, J. D., Wenzel, S. C., Willey, J. M. & Van Der Donk, W. A., Jan 2013, In : Natural Product Reports. 30, 1, p. 108-160 53 p.

Research output: Contribution to journalReview article

Biosynthesis
Terminology
Biological Products
Peptides
compound 20

Role of T cell receptor affinity in the efficacy and specificity of adoptive T cell therapies

Stone, J. D. & Kranz, D. M., Sep 16 2013, In : Frontiers in immunology. 4, AUG, Article 244.

Research output: Contribution to journalReview article

Cell- and Tissue-Based Therapy
T-Cell Antigen Receptor
T-Lymphocytes
Antigens
Single-Chain Antibodies

Role of the Helicobacter pylori-Induced inflammatory response in the development of gastric cancer

Lamb, A. & Chen, L. F., Mar 1 2013, In : Journal of Cellular Biochemistry. 114, 3, p. 491-497 7 p.

Research output: Contribution to journalReview article

Virulence Factors
Pathogens
Helicobacter pylori
Stomach Neoplasms
Transcription Factors
2012

A novel type of allosteric regulation: Functional cooperativity in monomeric proteins

Denisov, I. G. & Sligar, S., Mar 15 2012, In : Archives of Biochemistry and Biophysics. 519, 2, p. 91-102 12 p.

Research output: Contribution to journalReview article

Allosteric Regulation
Cytochrome P-450 Enzyme System
Drug interactions
Xenobiotics
Heme

Discovery, biosynthesis, and engineering of lantipeptides

Knerr, P. J. & van der Donk, W. A., Jul 1 2012, In : Annual review of biochemistry. 81, p. 479-505 27 p.

Research output: Contribution to journalReview article

Bacterial Genomes
Biosynthesis
Gram-Positive Bacteria
Sulfides
Post Translational Protein Processing

Genome of papaya, a fast growing tropical fruit tree

Ming, R., Yu, Q., Moore, P. H., Paull, R. E., Chen, N. J., Wang, M. L., Zhu, Y. J., Schuler, M. A., Jiang, J. & Paterson, A. H., Jun 1 2012, In : Tree Genetics and Genomes. 8, 3, p. 445-462 18 p.

Research output: Contribution to journalReview article

Carica
tropical and subtropical fruits
papayas
fruit trees
Fruit

Insect P450s: Mounted for battle in their war against toxins

Schuler, M. A., Sep 1 2012, In : Molecular ecology. 21, 17, p. 4157-4159 3 p.

Research output: Contribution to journalReview article

Insecticides
toxin
insecticide
Insects
deltamethrin

Microcin C: Biosynthesis and mechanisms of bacterial resistance

Severinov, K. & Nair, S. K., Feb 1 2012, In : Future Microbiology. 7, 2, p. 281-289 9 p.

Research output: Contribution to journalReview article

Aspartate-tRNA Ligase
Bacterial Drug Resistance
Anti-Bacterial Agents
Amino Acyl-tRNA Synthetases
Bacteria

Polyphosphate: An ancient molecule that links platelets, coagulation, and inflammation

Morrissey, J. H., Choi, S. H. & Smith, S. A., Jun 21 2012, In : Blood. 119, 25, p. 5972-5979 8 p.

Research output: Contribution to journalReview article

Polyphosphates
Platelets
Coagulation
Blood Platelets
Inflammation

Proton transfer in ba 3 cytochrome c oxidase from Thermus thermophilus

Von Ballmoos, C., Ädelroth, P., Gennis, R. B. & Brzezinski, P., Apr 1 2012, In : Biochimica et Biophysica Acta - Bioenergetics. 1817, 4, p. 650-657 8 p.

Research output: Contribution to journalReview article

Thermus thermophilus
Proton transfer
Electron Transport Complex IV
Protons
Oxidoreductases

Quorum sensing: How bacteria can coordinate activity and synchronize their response to external signals?

Li, Z. & Nair, S. K., Oct 1 2012, In : Protein Science. 21, 10, p. 1403-1417 15 p.

Research output: Contribution to journalReview article

Acyl-Butyrolactones
Quorum Sensing
Bacteria
Gene expression
Bioluminescence

Reconstitution of respiratory oxidases in membrane nanodiscs for investigation of proton-coupled electron transfer

Näsvik Öjemyr, L., Von Ballmoos, C., Gennis, R. B., Sligar, S. & Brzezinski, P., Mar 9 2012, In : FEBS Letters. 586, 5, p. 640-645 6 p.

Research output: Contribution to journalReview article

Liposomes
Protons
Oxidoreductases
Electrons
Membranes
2011

Closing in on complete pathways of biotin biosynthesis

Lin, S. & Cronan, J. E., Jun 1 2011, In : Molecular BioSystems. 7, 6, p. 1811-1821 11 p.

Research output: Contribution to journalReview article

Biotin
Bacillus subtilis
Escherichia coli
Coenzymes
Biosynthetic Pathways

Cytochromes P450 in nanodiscs

Denisov, I. G. & Sligar, S., Jan 1 2011, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1814, 1, p. 223-229 7 p.

Research output: Contribution to journalReview article

Cytochrome P-450 Enzyme System
Membranes
Kinetics
Viral Antigens
Biosynthesis

Genome mining for ribosomally synthesized natural products

Velásquez, J. E. & van der Donk, W. A., Feb 1 2011, In : Current Opinion in Chemical Biology. 15, 1, p. 11-21 11 p.

Research output: Contribution to journalReview article

Biological Products
Genes
Genome
Peptides
Cyclotides

Nanoscale studies of protein-membrane interactions in blood clotting

Morrissey, J. H., Tajkhorshid, E. & Rienstra, C. M., Jul 1 2011, In : Journal of Thrombosis and Haemostasis. 9, 1 S, p. 162-167 6 p.

Research output: Contribution to journalReview article

Blood Coagulation
Membrane Proteins
Membranes
Phosphatidylserines
Catalysis

P450s in plant-insect interactions

Schuler, M. A., Jan 1 2011, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1814, 1, p. 36-45 10 p.

Research output: Contribution to journalReview article

Mixed Function Oxygenases
Insects
Metabolites
Poisons
Wages

Spectroscopic features of cytochrome P450 reaction intermediates

Luthra, A., Denisov, I. G. & Sligar, S., Mar 1 2011, In : Archives of Biochemistry and Biophysics. 507, 1, p. 26-35 10 p.

Research output: Contribution to journalReview article

Reaction intermediates
Heme
Cytochrome P-450 Enzyme System
Enzymes
Isoenzymes
Fosfomycin
Organophosphonates
Biosynthesis
Enzymes
Proteins

Synthesis of the α,ω-dicarboxylic acid precursor of biotin by the canonical fatty acid biosynthetic pathway

Cronan, J. E. & Lin, S., Jun 1 2011, In : Current Opinion in Chemical Biology. 15, 3, p. 407-413 7 p.

Research output: Contribution to journalReview article

Dicarboxylic Acids
Pimelic Acids
Biosynthetic Pathways
Biotin
Fatty Acids

The cytochrome bd respiratory oxygen reductases

Borisov, V. B., Gennis, R. B., Hemp, J. & Verkhovsky, M. I., Nov 1 2011, In : Biochimica et Biophysica Acta - Bioenergetics. 1807, 11, p. 1398-1413 16 p.

Research output: Contribution to journalReview article

Cytochromes
Oxidoreductases
Oxygen
Cyanides
Protons

The enzyme function initiative

Gerlt, J. A., Allen, K. N., Almo, S. C., Armstrong, R. N., Babbitt, P. C., Cronan, J. E., Dunaway-Mariano, D., Imker, H. J., Jacobson, M. P., Minor, W., Poulter, C. D., Raushel, F. M., Sali, A., Shoichet, B. K. & Sweedler, J. V., Nov 22 2011, In : Biochemistry. 50, 46, p. 9950-9962 13 p.

Research output: Contribution to journalReview article

Enzymes
Microbiology
Genes
Amidohydrolases
Genome
2010

Capturing functional motions of membrane channels and transporters with molecular dynamics simulation

Shaikh, S. A., Wen, P. C., Enkavi, G., Huang, Z. & Tajkhorshid, E., Dec 1 2010, In : Journal of Computational and Theoretical Nanoscience. 7, 12, p. 2481-2500 20 p.

Research output: Contribution to journalReview article

transporter
Membrane Transport Proteins
Ion Channels
Molecular Dynamics Simulation
Molecular dynamics

Exploring transmembrane diffusion pathways with molecular dynamics

Wang, Y., Shaikh, S. A. & Tajkhorshid, E., Jun 2010, In : Physiology. 25, 3, p. 142-154 13 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Gases
Lipids
Membranes
Water

Follow the leader: The use of leader peptides to guide natural product biosynthesis

Oman, T. J. & Van Der Donk, W. A., Jan 2010, In : Nature chemical biology. 6, 1, p. 9-18 10 p.

Research output: Contribution to journalReview article

Protein Sorting Signals
Biological Products
Avalanches
Peptides
Post Translational Protein Processing

Membrane protein assembly into Nanodiscs

Bayburt, T. H. & Sligar, S. G., May 1 2010, In : FEBS Letters. 584, 9, p. 1721-1727 7 p.

Research output: Contribution to journalReview article

Membrane Proteins
Phospholipids
Micelles
Liposomes
Detergents

Posttranslational modifications of NF-κB: Another layer of regulation for NF-κB signaling pathway

Huang, B., Yang, X. D., Lamb, A. & Chen, L-F., Sep 1 2010, In : Cellular Signalling. 22, 9, p. 1282-1290 9 p.

Research output: Contribution to journalReview article

Post Translational Protein Processing
Cell Differentiation
Cytoplasm
Cell Death
Transcription Factors

Protein-Phospholipid interactions in blood clotting

Morrissey, J. H., Davis-Harrison, R. L., Tavoosi, N., Ke, K., Pureza, V., Boettcher, J. M., Clay, M. C., Rienstra, C., Ohkubo, Y. Z., Pogorelov, T. V. & Tajkhorshid, E., Apr 1 2010, In : Thrombosis Research. 125, SUPPL. 1

Research output: Contribution to journalReview article

Blood Coagulation
Phospholipids
Membrane Proteins
Membranes
Serine Proteases

Substrate activation by iron superoxo intermediates

van der Donk, W. A., Krebs, C. & Bollinger, J. M., Dec 1 2010, In : Current Opinion in Structural Biology. 20, 6, p. 673-683 11 p.

Research output: Contribution to journalReview article

Iron
Oxygenases
Superoxides
Hydrogen
Oxidoreductases

The balance between pre- and post-transfer editing in tRNA synthetases

Martinis, S. A. & Boniecki, M. T., Jan 21 2010, In : FEBS Letters. 584, 2, p. 455-459 5 p.

Research output: Contribution to journalReview article

Amino Acyl-tRNA Synthetases
Transfer RNA
Catalytic Domain
Transfer RNA Aminoacylation
Aminoacylation
2009

Biosynthesis of phosphonic and phosphinic acid natural products

Metcalf, W. W. & van der Donk, W. A., Jul 27 2009, In : Annual review of biochemistry. 78, p. 65-94 30 p.

Research output: Contribution to journalReview article

Phosphinic Acids
Biosynthesis
Biological Products
Biochemistry
Phosphorous Acids

Chapter 11 Reconstitution of Membrane Proteins in Phospholipid Bilayer Nanodiscs

Ritchie, T. K., Grinkova, Y. V., Bayburt, T. H., Denisov, I. G., Zolnerciks, J. K., Atkins, W. M. & Sligar, S. G., Dec 14 2009, In : Methods in enzymology. 464, C, p. 211-231 21 p.

Research output: Contribution to journalReview article

Phospholipids
Membrane Proteins
Membranes
Bacteriorhodopsins
Lipids

Cooperative properties of cytochromes P450

Denisov, I. G., Frank, D. J. & Sligar, S., Nov 1 2009, In : Pharmacology and Therapeutics. 124, 2, p. 151-167 17 p.

Research output: Contribution to journalReview article

Cytochrome P-450 Enzyme System
Xenobiotics
Aptitude
Enzymes
Mixed Function Oxygenases

Diversity in enoyl-acyl carrier protein reductases

Massengo-Tiassé, R. P. & Cronan, J. E., Jan 1 2009, In : Cellular and Molecular Life Sciences. 66, 9, p. 1507-1517 11 p.

Research output: Contribution to journalReview article

Acyl Carrier Protein
Oxidoreductases
Triclosan
Isoniazid
Enzymes

Enzyme (re)design: lessons from natural evolution and computation

Gerlt, J. A. & Babbitt, P. C., Feb 1 2009, In : Current Opinion in Chemical Biology. 13, 1, p. 10-18 9 p.

Research output: Contribution to journalReview article

Mutagenesis
Enzymes
Screening

Methylation, a new epigenetic mark for protein stability

Yang, X. D., Lamb, A. & Chen, L-F., Oct 1 2009, In : Epigenetics. 4, 7, p. 429-433 5 p.

Research output: Contribution to journalReview article

Protein Stability
Epigenomics
Methylation
Lysine
Histones

Molecular dynamics simulations of membrane channels and transporters

Khalili-Araghi, F., Gumbart, J., Wen, P. C., Sotomayor, M., Tajkhorshid, E. & Schulten, K., Apr 1 2009, In : Current Opinion in Structural Biology. 19, 2, p. 128-137 10 p.

Research output: Contribution to journalReview article

Membrane Transport Proteins
Molecular Dynamics Simulation
Ion Channels
Aquaporins
Proteins

Polyphosphate and omptins: Novel bacterial procoagulant agents

Yun, T. H. & Morrissey, J. H., Oct 1 2009, In : Journal of Cellular and Molecular Medicine. 13, 10, p. 4146-4153 8 p.

Research output: Contribution to journalReview article

Polyphosphates
Yersinia pestis
Blood Coagulation
Plague
Plasminogen

Protein-membrane interactions: Blood clotting on nanoscale bilayers

Morrissey, J. H., Pureza, V., Davis-Harrison, R. L., Sligar, S. G., Rienstra, C. M., Kijac, A. Z., Ohkubo, Y. Z. & Tajkhorshid, E., Aug 4 2009, In : Journal of Thrombosis and Haemostasis. 7, SUPPL. 1, p. 169-172 4 p.

Research output: Contribution to journalReview article

Blood Coagulation
Phospholipids
Membrane Proteins
Peptide Hydrolases
Membrane Microdomains

T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity

Stone, J. D., Chervin, A. S. & Kranz, D. M., Feb 1 2009, In : Immunology. 126, 2, p. 165-176 12 p.

Research output: Contribution to journalReview article

T-Cell Antigen Receptor Specificity
T-Cell Antigen Receptor
Major Histocompatibility Complex
Peptides
T-Lymphocytes
2008

Blood clotting reactions on nanoscale phospholipid bilayers

Morrissey, J. H., Pureza, V., Davis-Harrison, R. L., Sligar, S. G., Ohkubo, Y. Z. & Tajkhorshid, E., Aug 6 2008, In : Thrombosis Research. 122, SUPPL.1, p. S23-S26

Research output: Contribution to journalReview article

Blood Coagulation
Phospholipids
Phosphatidylserines
Factor VIIa
Membranes