Research Output 1967 2020

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Review article
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

Cytochrome c oxidase: Exciting progress and remaining mysteries

Brzezinski, P. & Gennis, R. B., Oct 1 2008, In : Journal of Bioenergetics and Biomembranes. 40, 5, p. 521-531 11 p.

Research output: Contribution to journalReview article

Proton Pumps
Electron Transport Complex IV
Proton-Motive Force
Protons
Observation

Tissue factor and factor VIIa: Understanding the molecular mechanism

Morrissey, J. & Mackman, N., 2008, In : Thrombosis Research. 122, SUPPL.1, p. S1-S2

Research output: Contribution to journalReview article

Factor VIIa
Thromboplastin
Blood Coagulation
2007

Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins

Nath, A., Atkins, W. M. & Sligar, S. G., Feb 27 2007, In : Biochemistry. 46, 8, p. 2059-2069 11 p.

Research output: Contribution to journalReview article

Phospholipids
Membrane Proteins
Membranes
Lipid bilayers
Lipid Bilayers

Display, engineering, and applications of antigen-specific T cell receptors

Richman, S. A. & Kranz, D. M., Oct 1 2007, In : Biomolecular Engineering. 24, 4, p. 361-373 13 p.

Research output: Contribution to journalReview article

T-cells
Antigens
T-Cell Antigen Receptor
Display devices
Monoclonal Antibodies

Encryption remains cryptic

Morrissey, J. H., Dec 1 2007, In : Blood. 110, 12, p. 3822-3823 2 p.

Research output: Contribution to journalReview article

Thromboplastin
Isomerization
Disulfides
Cryptography
Switches

Lantibiotics: Peptides of diverse structure and function

Willey, J. M. & van der Donk, W. A., Nov 14 2007, In : Annual review of microbiology. 61, p. 477-501 25 p.

Research output: Contribution to journalReview article

Bacteriocins
Peptides
Anti-Bacterial Agents
Protein Engineering
Gram-Positive Bacteria

Understanding cooperativity in human P450 mediated drug-drug interactions

Sligar, S. G. & Denisov, I. G., Apr 1 2007, In : Drug Metabolism Reviews. 39, 2-3, p. 567-579 13 p.

Research output: Contribution to journalReview article

Drug Interactions
Pharmaceutical Preparations
Metabolome
Thermodynamics
Cytochrome P-450 Enzyme System
2006

A bacterium that has three pathways to regulate membrane lipid fluidity

Cronan, J. E., Apr 1 2006, In : Molecular Microbiology. 60, 2, p. 256-259 4 p.

Research output: Contribution to journalReview article

Membrane Fluidity
Membrane Lipids
Unsaturated Fatty Acids
Bacteria
Bacillus subtilis

Arabidopsis cytochrome P450s through the looking glass: A window on plant biochemistry

Schuler, M. A., Duan, H., Bilgin, M. & Ali, S., Jun 1 2006, In : Phytochemistry Reviews. 5, 2-3, p. 205-237 33 p.

Research output: Contribution to journalReview article

plant biochemistry
Cytochromes
cytochromes
Arabidopsis
Biochemistry

Evolution of enzyme superfamilies

Glasner, M. E., Gerlt, J. A. & Babbitt, P. C., Oct 1 2006, In : Current Opinion in Chemical Biology. 10, 5, p. 492-497 6 p.

Research output: Contribution to journalReview article

Catalysis
Amidohydrolases
Molecular Sequence Annotation
Protein Engineering
Phosphopyruvate Hydratase

Heterologous expression and strategies for encapsulation of membrane-localized plant P450s

Duan, H. & Schuler, M. A., Jun 1 2006, In : Phytochemistry Reviews. 5, 2-3, p. 507-523 17 p.

Research output: Contribution to journalReview article

encapsulation
Membrane Proteins
membrane proteins
Plant Proteins
Membranes

Homology modeling of plant cytochrome P450s

Rupasinghe, S. & Schuler, M. A., Jun 1 2006, In : Phytochemistry Reviews. 5, 2-3, p. 473-505 33 p.

Research output: Contribution to journalReview article

Cytochromes
cytochromes
Mixed Function Oxygenases
Plant Proteins
structure-activity relationships

Lighting up the nascent cell wall.

van der Donk, W. A., Aug 22 2006, In : ACS chemical biology. 1, 7, p. 425-428 4 p.

Research output: Contribution to journalReview article

Lighting
Cell Wall
Cells
Peptidoglycan
Anti-Bacterial Agents

Rings, radicals, and regeneration: The early years of a bioorganic laboratory

van der Donk, W. A., Dec 22 2006, In : Journal of Organic Chemistry. 71, 26, p. 9561-9571 11 p.

Research output: Contribution to journalReview article

Nisin
Fosfomycin
Biosynthesis
Anti-Bacterial Agents
lacticin 481

Structural aspects of interactions within the Myc/Max/Mad network

Nair, S. K. & Burley, S. K., Feb 27 2006, In : Current Topics in Microbiology and Immunology. 302, p. 123-143 21 p.

Research output: Contribution to journalReview article

Nucleoproteins
DNA
Proteins

The status of high-valent metal oxo complexes in the P450 cytochromes

Makris, T. M., Koenig, K. V., Schlichting, I. & Sligar, S. G., Apr 1 2006, In : Journal of Inorganic Biochemistry. 100, 4, p. 507-518 12 p.

Research output: Contribution to journalReview article

Coordination Complexes
Manganese
Heme
Cytochrome P-450 Enzyme System
Iron

Transmembrane proton translocation by cytochrome c oxidase

Brändén, G., Gennis, R. B. & Brzezinski, P., Aug 1 2006, In : Biochimica et Biophysica Acta - Bioenergetics. 1757, 8, p. 1052-1063 12 p.

Research output: Contribution to journalReview article

Electron Transport Complex IV
Protons
Proton transfer
Heme
Electrons

Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin

Maeda, A., Morgan, J. E., Gennis, R. B. & Ebrey, T. G., Nov 1 2006, In : Photochemistry and Photobiology. 82, 6, p. 1398-1405 8 p.

Research output: Contribution to journalReview article

Bacteriorhodopsins
Proton transfer
Protons
Schiff Bases
Light
2005

Biosynthesis and mode of action of lantibiotics

Chatterjee, C., Paul, M., Xie, L. & van der Donk, W. A., Feb 1 2005, In : Chemical reviews. 105, 2, p. 633-683 51 p.

Research output: Contribution to journalReview article

Bacteriocins
Biosynthesis
Nisin
Bioactivity
Genes

Chemical and enzymatic synthesis of lanthionines

Paul, M. & van der Donk, W. A., Jan 1 2005, In : Mini-Reviews in Organic Chemistry. 2, 1, p. 23-37 15 p.

Research output: Contribution to journalReview article

Bacteriocins
Nisin
Peptides
Food Preservatives
Sulfides

Function, attachment and synthesis of lipoic acid in Escherichia coli

Cronan, J. E., Zhao, X. & Jiang, Y., Oct 17 2005, In : Advances in Microbial Physiology. 50, p. 103-146 44 p.

Research output: Contribution to journalReview article

Thioctic Acid
Escherichia coli
Archaea
Enzymes
Biotin

Mechanism and applications of phosphite dehydrogenase

Relyea, H. A. & Van Der Donk, W. A., Jun 2005, In : Bioorganic Chemistry. 33, 3, p. 171-189 19 p.

Research output: Contribution to journalReview article

NAD
Phosphites
Organophosphonates
Enzymes
Metabolism

Molecular dynamics simulations of proteins in lipid bilayers

Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E. & Schulten, K., Aug 1 2005, In : Current Opinion in Structural Biology. 15, 4, p. 423-431 9 p.

Research output: Contribution to journalReview article

Lipid Bilayers
Molecular Dynamics Simulation
Membrane Proteins
Proteins
Aquaporins

New developments in lantibiotic biosynthesis and mode of action

Patton, G. C. & Van Der Donk, W. A., Oct 1 2005, In : Current Opinion in Microbiology. 8, 5, p. 543-551 9 p.

Research output: Contribution to journalReview article

Bacteriocins
Peptides
Peptidoglycan
Threonine
Post Translational Protein Processing

Scalable molecular dynamics with NAMD

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L. & Schulten, K., Dec 2005, In : Journal of Computational Chemistry. 26, 16, p. 1781-1802 22 p.

Research output: Contribution to journalReview article

Molecular Dynamics
Molecular dynamics
Molecular graphics
Laptop computers
Pressure control

Structure and chemistry of cytochrome P450

Denisov, I. G., Makris, T. M., Sligar, S. G. & Schlichting, I., Jun 1 2005, In : Chemical reviews. 105, 6, p. 2253-2277 25 p.

Research output: Contribution to journalReview article

Cytochrome P-450 Enzyme System
Cytochromes
Oxygen
Reaction intermediates
Proton transfer

Thirty years of microbial P450 monooxygenase research: Peroxo-heme intermediates - The central bus station in heme oxygenase catalysis

Sligar, S. G., Makris, T. M. & Denisov, I. G., Dec 9 2005, In : Biochemical and Biophysical Research Communications. 338, 1, p. 346-354 9 p.

Research output: Contribution to journalReview article

Heme Oxygenase (Decyclizing)
Motor Vehicles
Mixed Function Oxygenases
Catalysis
Heme
2004

Coupled proton and electron transfer reactions in cytochrome oxidase

Gennis, R. B., Jan 1 2004, In : Frontiers in Bioscience. 9, p. 581-591 11 p.

Research output: Contribution to journalReview article

Electron Transport Complex IV
Protons
Electrons
Membranes
Proton Pumps

Diversity in chemotaxis mechanisms among the bacteria and archaea

Szurmant, H. & Ordal, G. W., Jun 1 2004, In : Microbiology and Molecular Biology Reviews. 68, 2, p. 301-319 19 p.

Research output: Contribution to journalReview article

Archaea
Chemotaxis
Bacillus subtilis
Escherichia coli
Bacteria

Effect of loss of CheC and other adaptational proteins on chemotactic behaviour in Bacillus subtilis

Saulmon, M. M., Karatan, E. & Ordal, G. W., Mar 2004, In : Microbiology. 150, 3, p. 581-589 9 p.

Research output: Contribution to journalReview article

Chemotaxis
Bacillus subtilis
Asparagine
Methylation
Proteins

FTIR studies of internal proton transfer reactions linked to inter-heme electron transfer in bovine cytochrome c oxidase

McMahon, B. H., Fabian, M., Tomson, F., Causgrove, T. P., Bailey, J. A., Rein, F. N., Dyer, R. B., Palmer, G., Gennis, R. B. & Woodruff, W. H., Apr 12 2004, In : Biochimica et Biophysica Acta - Bioenergetics. 1655, 1-3, p. 321-331 11 p.

Research output: Contribution to journalReview article

Proton transfer
Electron Transport Complex IV
Fourier Transform Infrared Spectroscopy
Carbon Monoxide
Heme

Post-translational modifications during lantibiotic biosynthesis

Xie, L. & Van Der Donk, W. A., Oct 1 2004, In : Current Opinion in Chemical Biology. 8, 5, p. 498-507 10 p.

Research output: Contribution to journalReview article

Bacteriocins
Biosynthesis
Post Translational Protein Processing
Threonine
Substrate Specificity

Tissue Factor: A Key Molecule in Hemostatic and Nonhemostatic Systems

Morrissey, J. H., Feb 2004, In : International Journal of Hematology. 79, 2, p. 103-108 6 p.

Research output: Contribution to journalReview article

Thromboplastin
Hemostatics
Hemostasis
Thrombosis
Factor VIIa
2003

A model T-cell receptor system for studying memory T-cell development

Chen, J., Eisen, H. N. & Kranz, D. M., Mar 1 2003, In : Microbes and Infection. 5, 3, p. 233-240 8 p.

Research output: Contribution to journalReview article

T-Cell Antigen Receptor
T-Lymphocytes
Clone Cells
Peptides
Antigen Receptors

Bacterial Membrane Lipids: Where Do We Stand?

Cronan, J. E., Nov 20 2003, In : Annual review of microbiology. 57, p. 203-224 22 p.

Research output: Contribution to journalReview article

Membrane Lipids
Phospholipids
Protein Precursors
DNA Replication
Permeability

Comparison of the properties of prostaglandin H synthase-1 and -2

Kulmacz, R. J., Van Der Donk, W. A. & Tsai, A. L., Sep 2003, In : Progress in Lipid Research. 42, 5, p. 377-404 28 p.

Research output: Contribution to journalReview article

Cyclooxygenase 1
Cyclooxygenase 2
Protein Isoforms
Prostaglandin-Endoperoxide Synthases
Biosynthesis

Evolution of function in (β/α)8-barrel enzymes

Gerlt, J. A. & Raushel, F. M., Apr 2003, In : Current Opinion in Chemical Biology. 7, 2, p. 252-264 13 p.

Research output: Contribution to journalReview article

Enzymes
Databases

Functional Genomics of P450s

Schuler, M. A. & Werck-Reichhart, D., Nov 24 2003, In : Annual Review of Plant Biology. 54, p. 629-667 39 p.

Research output: Contribution to journalReview article

Biosynthetic Pathways
Genomics
Mixed Function Oxygenases
biochemical pathways
Physiological Phenomena

How to Find "missing" Genes

Gerlt, J. A., Dec 2003, In : Chemistry and Biology. 10, 12, p. 1141-1142 2 p.

Research output: Contribution to journalReview article

Microbial Genome
Metabolic Networks and Pathways
Genes
Proteins

Recent developments in pyridine nucleotide regeneration

van der Donk, W. A. & Zhao, H., Aug 2003, In : Current Opinion in Biotechnology. 14, 4, p. 421-426 6 p.

Research output: Contribution to journalReview article

Nucleotides
Pyridine
Regeneration
Oxidoreductases
Enzymes

Regeneration of cofactors for use in biocatalysis

Zhao, H. & van der Donk, W. A., Dec 2003, In : Current Opinion in Biotechnology. 14, 6, p. 583-589 7 p.

Research output: Contribution to journalReview article

Biocatalysis
Regeneration
Enzymes
Phosphoadenosine Phosphosulfate
Adenosinetriphosphate

RNA Gel Shift Assays for Analysis of Hormone Control of mRNA Stability

Dodson, R. E., Goolsby, K. M., Acena-Nagel, M., Mao, C. & Shapiro, D. J., Jan 1 2003, In : Methods in enzymology. 364, p. 350-361 12 p.

Research output: Contribution to journalReview article

RNA Stability
Electrophoretic Mobility Shift Assay
Hormones
RNA

TCRs with high affinity for foreign pMHC show self-reactivity

Holler, P. D., Chlewicki, L. K. & Kranz, D. M., Jan 1 2003, In : Nature Immunology. 4, 1, p. 55-62 8 p.

Research output: Contribution to journalReview article

T-Cell Antigen Receptor
Major Histocompatibility Complex
Peptides
T-Lymphocytes
Complementarity Determining Regions
2002
Nucleic Acids
Pressure
Proteins
DNA
Hydrostatic Pressure

High pressure, a tool for exploring heme protein active sites

Hui Bon Hoa, G., McLean, M. A. & Sligar, S. G., Mar 25 2002, In : Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology. 1595, 1-2, p. 297-308 12 p.

Research output: Contribution to journalReview article

Hemeproteins
Cytochromes
Catalytic Domain
Pressure
Camphor 5-Monooxygenase

Mechanistic enzymology of oxygen activation by the cytochromes P450

Makris, T. M., Davydov, R., Denisov, I. G., Hoffman, B. M. & Sligar, S. G., Jan 1 2002, In : Drug Metabolism Reviews. 34, 4, p. 691-708 18 p.

Research output: Contribution to journalReview article

Cytochrome P-450 Enzyme System
Camphor 5-Monooxygenase
Oxygen
Camphor
Xenobiotics

Multi-subunit acetyl-CoA carboxylases

Cronan, J. E. & Waldrop, G. L., Jul 11 2002, In : Progress in Lipid Research. 41, 5, p. 407-435 29 p.

Research output: Contribution to journalReview article

Acetyl-CoA Carboxylase
Carboxylation
Malonyl Coenzyme A
Acetyl Coenzyme A
Mammals

Phospholipid modifications in bacteria

Cronan, J. E., Jan 1 2002, In : Current Opinion in Microbiology. 5, 2, p. 202-205 4 p.

Research output: Contribution to journalReview article

Periplasmic Proteins
Heme
Mycobacterium tuberculosis
Phospholipids
Escherichia coli

The cyclooxygenase reaction mechanism

van der Donk, W. A., Tsai, A. L. & Kulmacz, R. J., Dec 31 2002, In : Biochemistry. 41, 52, p. 15451-15458 8 p.

Research output: Contribution to journalReview article

Prostaglandins G
Molecular Conformation
Cyclooxygenase 1
Cyclooxygenase 2
Prostaglandin-Endoperoxide Synthases