Research Output 1971 2019

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2019

Bacterial expression of membrane-associated cytochrome P450s and their activity assay in nanodiscs

Maroutsos, D., Huff, H. & Das, A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 47-72 26 p. (Methods in Molecular Biology; vol. 1927).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytochromes
Membranes
Cytochrome P-450 Enzyme System
Bacteria
Paclitaxel

Determination of sec18-lipid interactions by liposome-binding assay

Starr, M. L. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 211-220 10 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Liposomes
Lipids
Proteins
SNARE Proteins
Unilamellar Liposomes

Nanodiscs as a New Tool to Examine Lipid–Protein Interactions

Denisov, I. G., Schuler, M. A. & Sligar, S., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 645-671 27 p. (Methods in Molecular Biology; vol. 2003).

Research output: Chapter in Book/Report/Conference proceedingChapter

Thromboplastin
Cytochrome P-450 Enzyme System
Lipoproteins
Lipids
Proteins

Real-time fluorescence detection of calcium efflux during vacuolar membrane fusion

Miner, G. E. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 323-331 9 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Fusion
Vacuoles
Fluorescence
Calcium
Organelles

Use of microscale thermophoresis (MST) to measure binding affinities of components of the fusion machinery

Sparks, R. P. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 191-198 8 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

SNARE Proteins
Proteins
Aromatic Amino Acids
Tryptophan
Ligands

Use of surface plasmon resonance (SPR) to determine binding affinities and kinetic parameters between components important in fusion machinery

Sparks, R. P., Jenkins, J. L. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 199-210 12 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Surface Plasmon Resonance
Ligands
SNARE Proteins
Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins
Carrier Proteins
2018

Deregulation of RNA metabolism in microsatellite expansion diseases

Misra, C., Lin, F. & Kalsotra, A., Jan 1 2018, Advances in Neurobiology. Springer New York LLC, p. 213-238 26 p. (Advances in Neurobiology; vol. 20).

Research output: Chapter in Book/Report/Conference proceedingChapter

Deregulation
Metabolism
Microsatellite Repeats
Trinucleotide Repeat Expansion
RNA

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

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 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
2017

Chapter 7: Computational Characterization of Molecular Mechanisms of Membrane Transporter Function

Trebesch, N., Vermaas, J. V. & Tajkhorshid, E., Jan 1 2017, Computational Biophysics of Membrane Proteins. Hirst, J. & Domene, C. (eds.). 10 ed. Royal Society of Chemistry, p. 197-236 40 p. (RSC Theoretical and Computational Chemistry Series; vol. 2017-January, no. 10).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Membranes
Computational methods
Free energy
Adenosinetriphosphate

Simultaneous removal of multiple DNA segments by polymerase chain reactions

Krishnamurthy, V. & Zhang, K., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 193-203 11 p. (Methods in Molecular Biology; vol. 1472).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed DNA Polymerase
Synthetic Biology
Polymerase Chain Reaction
DNA
Organism Cloning
2016

Inorganic polyphosphate in blood coagulation

Smith, S. A. & Morrissey, J. H., Jan 1 2016, Inorganic Polyphosphates in Eukaryotic Cells. Springer International Publishing, p. 159-176 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyphosphates
Blood Coagulation
Coagulation
Blood
Chemical activation

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

Vermaas, J. V., Trebesch, N., Mayne, C. G., Thangapandian, S., Shekhar, M., Mahinthichaichan, P., Baylon, J. L., Jiang, T., Wang, Y., Muller, M. P., Shinn, E., Zhao, Z., Wen, P. C. & Tajkhorshid, E., Jan 1 2016, Methods in Enzymology. Academic Press Inc., p. 373-428 56 p. (Methods in Enzymology; vol. 578).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Computer Simulation
Biological membranes
Membranes
Chemical Phenomena

Motif-driven design of protein–protein interfaces

Silva, D. A., Correia, B. E. & Procko, E., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 285-304 20 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Synthetic Biology
Aptitude
Learning Curve
2015

Activation of molecular oxygen in cytochromes P450

Denisov, I. G. & Sligar, S., 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

Escherichia coli Auxotroph Host Strains for Amino Acid-Selective Isotope Labeling of Recombinant Proteins

Lin, M. T., Fukazawa, R., Miyajima-Nakano, Y., Matsushita, S., Choi, S. K., Iwasaki, T. & Gennis, R. B., Jan 1 2015, Methods in Enzymology. Academic Press Inc., p. 45-66 22 p. (Methods in Enzymology; vol. 565).

Research output: Chapter in Book/Report/Conference proceedingChapter

Isotope Labeling
Recombinant Proteins
Isotopes
Labeling
Escherichia coli

P450s in plants, insects, and their fungal pathogens

Schuler, M. A., Jan 1 2015, Cytochrome P450: Structure, Mechanism, and Biochemistry, Fourth Edition. Springer International Publishing, p. 409-449 41 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Pathogens
Insects
Genes
Mixed Function Oxygenases
Biosynthetic Pathways
2014

RiPPs: Ribosomally Synthesized and Posttranslationally Modified Peptides

Bindman, N. A. & van der Donk, W. A., May 5 2014, Natural Products: Discourse, Diversity, and Design. Wiley Blackwell, p. 195-217 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Oxazoles
Thiazoles
Cyanobacteria
Peptides
Depsipeptides
2013

Coagulation Factor VIIa

Morrissey, J. H., Aug 29 2013, Handbook of Proteolytic Enzymes. Elsevier Ltd, Vol. 3. p. 2905-2908 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Factor VIIa

Nanodiscs in the studies of membrane-bound cytochrome P450 enzymes

Luthra, A., Gregory, M., Grinkova, Y. V., Denisov, I. G. & Sligar, S., Jan 1 2013, Cytochrome P450 Protocols. Humana Press Inc., p. 115-127 13 p. (Methods in Molecular Biology; vol. 987).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytochrome P-450 Enzyme System
NADPH-Ferrihemoprotein Reductase
Membranes
Cytochrome P-450 CYP3A
Lipid Bilayers
2012

Cryoradiolysis and cryospectroscopy for studies of heme-oxygen intermediates in cytochromes P450

Denisov, I. G., Grinkova, Y. V. & Sligar, S., Jan 1 2012, Spectroscopic Methods of Analysis: Methods and Protocols. Humana Press Inc., p. 375-391 17 p. (Methods in Molecular Biology; vol. 875).

Research output: Chapter in Book/Report/Conference proceedingChapter

Heme
Cytochrome P-450 Enzyme System
Oxygen
Peroxidases
Heme Oxygenase (Decyclizing)

Discovery and biosynthesis of phosphonate and phosphinate natural products

Peck, S. C., Gao, J. & van der Donk, W. A., Jan 1 2012, Methods in Enzymology. Academic Press Inc., p. 101-123 23 p. (Methods in Enzymology; vol. 516).

Research output: Chapter in Book/Report/Conference proceedingChapter

Organophosphonates
Biosynthesis
Biosynthetic Pathways
Biological Products
Esters

T cell receptor engineering

Stone, J. D., Chervin, A. S., Aggen, D. H. & Kranz, D. M., Jan 1 2012, Methods in Enzymology. Academic Press Inc., p. 189-222 34 p. (Methods in Enzymology; vol. 503).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Engineering
T-cells
T-Cell Antigen Receptor
T-Lymphocytes
Major Histocompatibility Complex
2011

Coagulation factor VIIa as an agent

Morrissey, J. H., Dec 1 2011, xPharm: The Comprehensive Pharmacology Reference. Elsevier Inc., p. 1 1 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Factor VIIa

Membrane transporters: Molecular machines coupling cellular energy to vectorial transport across the membrane

Huang, Z., Shaikh, S. A., Wen, P. C., Enkavi, G., Li, J. & Tajkhorshid, E., Jan 1 2011, Molecular Machines. World Scientific Publishing Co., p. 151-182 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Membranes

Molecular and structural perspectives on cytochrome P450s in plants

Schuler, M. A. & Rupasinghe, S. G., Jan 1 2011, Advances in Botanical Research. Academic Press Inc., p. 263-307 45 p. (Advances in Botanical Research; vol. 60).

Research output: Chapter in Book/Report/Conference proceedingChapter

cytochromes
biopharmaceuticals
genome
decarboxylation
carbon

Probing protein dynamics in vivo using backbone cyclization: Bacterial acyl carrier protein as a case study

Volkmann, G., Murphy, P. W., Rowland, E. E., Cronan, J. E. & Byers, D. M., Dec 23 2011, Methods in Protein Biochemistry. Walter de Gruyter GmbH and Co. KG, p. 271-293 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Acyl Carrier Protein
acyl carrier protein
Cyclization
case studies
Proteins
2010

Biosynthesis and mode of action of lantibiotics

Cooper, L. E., Li, B. & van der Donk, W. A., Mar 1 2010, Comprehensive Natural Products II: Chemistry and Biology. Elsevier Ltd, Vol. 5. p. 217-256 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacteriocins
Biosynthesis
2009

Chapter 17 Bacterial Fatty Acid Synthesis and its Relationships with Polyketide Synthetic Pathways

Cronan, J. E. & Thomas, J., Apr 14 2009, Complex Enzymes in Microbial Natural Product Biosynthesis, Part B: Polyketides, Aminocoumarins and Carbohydrates. Hopwood, D. (ed.). B ed. p. 395-433 39 p. (Methods in Enzymology; vol. 459, no. B).

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyketides
Fatty Acids
Escherichia coli
Bacteria
Streptomyces

Chapter 21 In Vitro Studies of Lantibiotic Biosynthesis

Li, B., Cooper, L. E. & van der Donk, W. A., Apr 16 2009, Complex Enzymes in Microbial Natural Product Biosynthesis, Part A: Overview Articles and Peptides. Hopwood, D. (ed.). A ed. p. 533-558 26 p. (Methods in Enzymology; vol. 458, no. A).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacteriocins
Biosynthesis
Sulfides
Dehydration
Anti-Bacterial Agents

Chapter 6 Using Expressed Protein Ligation to Probe the Substrate Specificity of Lantibiotic Synthetases

Zhang, X. & van der Donk, W. A., Jul 24 2009, Methods in Enzymology. Muir, T. & Abelson, J. (eds.). p. 117-134 18 p. (Methods in Enzymology; vol. 462).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bacteriocins
Sulfides
Ligases
Substrate Specificity
Ligation
2008

Chapter 12 Gas Conduction of Lipid Bilayers and Membrane Channels

Wang, Y., Ohkubo, Y. Z. & Tajkhorshid, E., Jul 2 2008, Computational Modeling of Membrane Bilayers. Feller, S. (ed.). p. 343-367 25 p. (Current Topics in Membranes; vol. 60).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lipid Bilayers
Ion Channels
Gases
Membranes
Ligands

Diversity of the Heme-Copper superfamily in archaea: Insights from genomics and structural modeling

Hemp, J. & Gennis, R. B., Jun 5 2008, Bioenergetics: Energy Conservation and Conversion. Schäfer, G. & Penefsky, H. (eds.). p. 1-31 31 p. (Results and Problems in Cell Differentiation; vol. 45).

Research output: Chapter in Book/Report/Conference proceedingChapter

Archaea
Genomics
Heme
Copper
Oxidoreductases

Splice site requirements and switches in plants

Schuler, M. A., Dec 1 2008, Human Cytomegalovirus. Vol. 326. p. 39-59 21 p. (Current Topics in Microbiology and Immunology; vol. 326).

Research output: Chapter in Book/Report/Conference proceedingChapter

Introns
RNA Splice Sites
Consensus Sequence
RNA Precursors
Nucleotides

Transgenic models of uterine biology

Bagchi, I. C. & Bagchi, M. K., Jan 1 2008, The Endometrium: Molecular, Cellular and Clinical Perspectives, Second Edition. CRC Press, p. 154-161 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Pregnancy
Epithelium
Myometrium
Endometrium
Uterus
2007

Coagulation factor VIIa as a target

Morrissey, J. H., Jan 1 2007, xPharm: The Comprehensive Pharmacology Reference. Elsevier Inc., p. 1-18 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Factor VIIa
Serine Proteases
Blood Coagulation
Hemostasis
Enzymes

Enzymatic Catalysis of Proton Transfer at Carbon Atoms

Gerlt, J. A., Jul 17 2007, Hydrogen-Transfer Reactions. John Wiley and Sons, Vol. 3. p. 1107-1137 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Proton transfer
Catalysis
Carbon
Atoms

Mechanisms of protein evolution and their application to protein engineering

Glasner, M. E., Gerlt, J. A. & Babbitt, P. C., Jan 11 2007, Protein Evolution. Toone, E. (ed.). p. 193-239 47 p. (Advances in Enzymology and Related Areas of Molecular Biology; vol. 75).

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein Engineering
Proteins
Environmental Biodegradation
Biosensing Techniques
Catalysis

Mechanisms of protein evolution and their application to protein engineering

Glasner, M. E., Gerlt, J. A. & Babbitt, P. C., Jan 11 2007, Protein Evolution. Toone, E. (ed.). p. 193-239 47 p. (Advances in Enzymology and Related Areas of Molecular Biology; vol. 75).

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein Engineering
Proteins
Environmental Biodegradation
Biosensing Techniques
Catalysis

Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics

Li, X., Schuler, M. A. & Berenbaum, M. R., Jan 26 2007, Annual Review of Entomology. Berenbaum, Carde & Robinson (eds.). p. 231-253 23 p. (Annual Review of Entomology; vol. 52).

Research output: Chapter in Book/Report/Conference proceedingChapter

xenobiotics
insecticide resistance
allelochemicals
insecticides
genes
2006

Oxygen Reduction by the P450 Monoxygenase Systems

Gunsalus, I. C. & Sligar, S., Nov 27 2006, Advances in Enzymology and Related Areas of Molecular Biology. Wiley Blackwell, Vol. 47. p. 1-44 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Flavins
Iron-Sulfur Proteins
Electron Transport
Mixed Function Oxygenases
Heme
2005

Activation of molecular oxygen by cytochrome P450

Makris, T. M., Denisov, I., Schlichting, I. & Sligar, S., Dec 1 2005, Cytochrome P450: Structure, Mechanism, and Biochemistry: Third edition. Springer US, p. 149-182 34 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytochrome P-450 Enzyme System
Physiological Phenomena
Oxygen
Metabolome
Hydrogen Bonding
2002

Regulation of pathways of mRNA destabilization and stabilization

Dodson, R. E. & Shapiro, D. J., Dec 1 2002, Progress in Nucleic Acid Research and Molecular Biology. p. 129-164 36 p. (Progress in Nucleic Acid Research and Molecular Biology; vol. 72).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Stability
Messenger RNA
Endonucleases
Carrier Proteins
Vitellogenins
1996

Chapter 2 Lipid metabolism in prokaryotes

Rock, C. O., Jackowski, S. & Cronan, J. E., Jan 1 1996, New Comprehensive Biochemistry. C ed. Elsevier, p. 35-74 40 p. (New Comprehensive Biochemistry; vol. 31, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lipid Metabolism