Anaerobic methods for the transient-state study of flavoproteins: The use of specialized glassware to define the concentration of dioxygen.

Abstract:

:The methods described here concern the use specialized glassware to achieve accurate sub-micromolar to low-millimolar dioxygen concentrations specifically for the study of flavoproteins. Since the early 1960s, these methods have been passed through the lineage of flavin enzymologists almost exclusively as an oral tradition. Given that these methods have been used to systematically reveal a multitude of natural phenomena, it is a curiosity that they have not been comprehensively committed to print prior to this entry. It should be noted that the author is describing these methods with scant added modernity and should not be attributed with their invention. The investigators to whom such ingenuity should be accredited include David P. Ballou, Quentin H. Gibson, Vincent Massey, Charles H. Williams, and Graham Palmer (Foust, Burleigh, & Mayhew, 1969; Gibson, Massey, & Atherton, 1962; Massey, Brumby, Komai, & Palmer, 1969; Massey, Gibson, & Veeger, 1960), who, out of necessity, developed the vessel design and approach over a period of two decades.

journal_name

Methods Enzymol

journal_title

Methods in enzymology

authors

Moran GR

doi

10.1016/bs.mie.2019.03.005

subject

Has Abstract

pub_date

2019-01-01 00:00:00

pages

27-49

eissn

0076-6879

issn

1557-7988

pii

S0076-6879(19)30086-2

journal_volume

620

pub_type

杂志文章
  • Identification of human cytochrome P450s as autoantigens.

    abstract::Antimicrosomal antibodies in inflammatory liver diseases all seem to be directed against members of the cytochrome P450 family of proteins. These autoantigens seem to be genetically polymorphic, the autoantibodies are inhibitory, and the autoepitopes are generally conserved among species. Anti-P450 autoantibodies shar...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/0076-6879(91)06092-h

    authors: Manns MP,Johnson EF

    更新日期:1991-01-01 00:00:00

  • Nitrite and nitrate measurement by Griess reagent in human plasma: evaluation of interferences and standardization.

    abstract::Nitrite and nitrate represent the final products of nitric oxide (NO) oxidation pathways, and their hematic concentrations are frequently assessed as an index of systemic NO production. However, their intake with food can influence their levels. Nitrite and nitrate could have a role by producing NO, because nitrite ca...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(07)00823-3

    authors: Giustarini D,Rossi R,Milzani A,Dalle-Donne I

    更新日期:2008-01-01 00:00:00

  • Peroxiredoxin-6 and NADPH oxidase activity.

    abstract::Peroxiredoxins (Prdxs) are a family of proteins which catalyze the reduction of H2O2 through the interaction of active site cysteine residues. Conserved within all plant and animal kingdoms, the function of these proteins is related to protection from oxidation or participation of signaling through degradation of H2O2...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-405882-8.00008-8

    authors: Ambruso DR

    更新日期:2013-01-01 00:00:00

  • Reannotation of Genomes by Means of Proteomics Data.

    abstract::Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes ma...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2016.09.019

    authors: Armengaud J

    更新日期:2017-01-01 00:00:00

  • Physical methods for studying flavoprotein photoreceptors.

    abstract::Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-in...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2019.03.023

    authors: Yee EF,Chandrasekaran S,Lin C,Crane BR

    更新日期:2019-01-01 00:00:00

  • Characterizing and measuring endocytosis of lipid-binding effectors in mammalian cells.

    abstract::Pathogen-host interactions are mediated in part by secreted microbial proteins capable of exploiting host cells for their survival. Several of these manipulations involve, but are not limited to, suppression of defense responses, alterations in host vesicular trafficking, and manipulation of gene expression. The deliv...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-397925-4.00007-9

    authors: Clark HR,Hayes TA,Kale SD

    更新日期:2014-01-01 00:00:00

  • Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

    abstract::The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of bot...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/S0076-6879(06)11019-8

    authors: Barrett T,Edgar R

    更新日期:2006-01-01 00:00:00

  • Modern methods to investigate the oligomerization of glycoprotein hormone receptors (TSHR, LHR, FSHR).

    abstract::As for other GPCRs, the oligomerization of glycoprotein hormone receptors (GPHRs) appears as critical event for receptor function. By means of modern techniques based on the BRET or FRET principle, GPHR oligomerization has been reported to explain several physiological and pathological conditions. In particular, the p...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-391862-8.00020-X

    authors: Bonomi M,Persani L

    更新日期:2013-01-01 00:00:00

  • Combination of C(17) sphingoid base homologues and mass spectrometry analysis as a new approach to study sphingolipid metabolism.

    abstract::In recent years, sphingolipid metabolites ceramide, sphingosine, and sphingosine-1-phosphate have emerged as important second messengers in addition to their role as precursors of biomembrane components. The investigation of these sphingolipid metabolites requires the development of new, more sensitive methods for ass...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(07)34012-3

    authors: Spassieva S,Bielawski J,Anelli V,Obeid LM

    更新日期:2007-01-01 00:00:00

  • Developing novel lentiviral vectors into clinical products.

    abstract::Gene therapy vectors based on murine retroviruses have now been in clinical trials for over 20 years. During that time, a variety of novel vector pseudotypes were developed in an effort to improve gene transfer. Lentiviral vectors are now in clinical trials and a similar evolution of vector technology is anticipated. ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-386509-0.00005-3

    authors: Leath A,Cornetta K

    更新日期:2012-01-01 00:00:00

  • Bioluminescent imaging of ubiquitin ligase activity: measuring Cdk2 activity in vivo through changes in p27 turnover.

    abstract::Optical imaging of reporter molecules such as firefly luciferase has become a popular method of tracking and visualizing cells in living animals. Many biological processes involve ubiquitin ligases, which target specific proteins for destruction under specific sets of conditions. Importantly, the motifs recognized by ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(05)99036-8

    authors: Zhang GJ,Kaelin WG Jr

    更新日期:2005-01-01 00:00:00

  • Using Drosophila for Studies of Intermediate Filaments.

    abstract::Drosophila melanogaster is a useful organism for determining protein function and modeling human disease. Drosophila offers a rapid generation time and an abundance of genomic resources and genetic tools. Conservation in protein structure, signaling pathways, and developmental processes make studies performed in Droso...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2015.08.028

    authors: Bohnekamp J,Cryderman DE,Thiemann DA,Magin TM,Wallrath LL

    更新日期:2016-01-01 00:00:00

  • Detection and quantification of nitric oxide (NO) synthase-independent generation of NO.

    abstract::Nitric oxide formation in ischemia-reperfusion injury can be identified and measured directly using EPR of nitroso-heme complexes comprising NO bound to either Mb or Hb-Fe2+. This article described the successful use of this method to detect and quantify the generation of NO formed independently of nitric oxide syntha...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/s0076-6879(02)59182-5

    authors: Lepore DA

    更新日期:2002-01-01 00:00:00

  • Methods to monitor chaperone-mediated autophagy.

    abstract::Chaperone-mediated autophagy (CMA) is a selective type of autophagy responsible for the lysosomal degradation of soluble cytosolic proteins. In contrast to other forms of autophagy where cargo is sequestered and delivered to lysosomes through membrane fusion/excision, CMA substrates reach the lysosomal lumen after dir...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(08)03619-7

    authors: Kaushik S,Cuervo AM

    更新日期:2009-01-01 00:00:00

  • Fluorescent FYVE Chimeras to Quantify PtdIns3P Synthesis During Autophagy.

    abstract::Autophagy is the major cellular process of degradation and is modulated by several signaling pathways. Phosphatidylinositol 3-kinase (PtdIns3K) class III (Vps34) and PtdIns3K class I regulate the autophagy pathway positively and negatively, respectively. Both classes of PtdIns3K participate in the synthesis of phospha...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2016.09.060

    authors: Yakhine-Diop SM,Martínez-Chacón G,González-Polo RA,Fuentes JM,Niso-Santano M

    更新日期:2017-01-01 00:00:00

  • Study of Chemotaxis and Cell-Cell Interactions in Cancer with Microfluidic Devices.

    abstract::Microfluidic devices have very broad applications in biological assays from simple chemotaxis assays to much more complicated 3D bioreactors. In this chapter, we describe the design and methods for performing chemotaxis assays using simple microfluidic chemotaxis chambers. With these devices, using real-time video mic...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2015.09.023

    authors: Sai J,Rogers M,Hockemeyer K,Wikswo JP,Richmond A

    更新日期:2016-01-01 00:00:00

  • On-pot and cell-free biocatalysis using coimmobilized enzymes on advanced materials.

    abstract::Complex synthetic schemes catalyzed by multienzyme systems immobilized on solid materials are gaining momentum in chemical biomanufacturing. These systems harness the high chemo-, regio-, and stereoselectivity of the enzymes and the recyclability of the heterogeneous catalysts. Moreover, when the enzymes become part o...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.12.013

    authors: López-Gallego F

    更新日期:2019-01-01 00:00:00

  • Multistate protein design using CLEVER and CLASSY.

    abstract::Structure-based protein design is a powerful technique with great potential. Challenges in two areas limit performance: structure scoring and sequence-structure searching. Many of the functions used to describe the relationship between protein sequence and energy are computationally expensive to evaluate, and the spac...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/B978-0-12-394292-0.00008-4

    authors: Negron C,Keating AE

    更新日期:2013-01-01 00:00:00

  • Redox clamp model for study of extracellular thiols and disulfides in redox signaling.

    abstract::Extracellular thiol/disulfide redox environments are highly regulated in healthy individuals and become oxidized in disease. This oxidation affects the function of cell surface receptors, ion channels, and structural proteins. Downstream signaling due to changes in extracellular redox potential can be studied using a ...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(10)74010-6

    authors: Go YM,Jones DP

    更新日期:2010-01-01 00:00:00

  • High Content, Phenotypic Assays and Screens for Compounds Modulating Cellular Processes in Primary Neurons.

    abstract::High content, phenotypic screens offer a powerful approach to systems biology at the cellular level. The approach employs cells carrying fluorescently labeled molecules or organelles in 384- or 1536-well microplates, and an automated confocal screening microscope for capturing images from each well. Although some spec...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.09.021

    authors: Kepiro M,Varkuti BH,Davis RL

    更新日期:2018-01-01 00:00:00

  • A Networks Approach to Modeling Enzymatic Reactions.

    abstract::Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is benefic...

    journal_title:Methods in enzymology

    pub_type: 杂志文章,评审

    doi:10.1016/bs.mie.2016.05.025

    authors: Imhof P

    更新日期:2016-01-01 00:00:00

  • GTPases and the control of neuronal polarity.

    abstract::Neurons are probably the most highly polarized cell type and typically develop a single axon and several dendrites. The establishment of a polarized morphology and the functional specialization of axonal and dendritic compartments are essential steps in the differentiation of neurons. Primary cultures of dissociated h...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(06)06056-3

    authors: Schwamborn JC,Li Y,Püschel AW

    更新日期:2006-01-01 00:00:00

  • Multifragment DNA Assembly of Biochemical Pathways via Automated Ligase Cycling Reaction.

    abstract::The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designe...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.04.011

    authors: Robinson CJ,Dunstan MS,Swainston N,Titchmarsh J,Takano E,Scrutton NS,Jervis AJ

    更新日期:2018-01-01 00:00:00

  • Design of modular "plug-and-play" expression platforms derived from natural riboswitches for engineering novel genetically encodable RNA regulatory devices.

    abstract::Genetically encodable RNA devices that directly detect small molecules in the cellular environment are of increasing interest for a variety of applications including live cell imaging and synthetic biology. Riboswitches are naturally occurring sensors of intracellular metabolites, primarily found in the bacterial mRNA...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2014.10.031

    authors: Trausch JJ,Batey RT

    更新日期:2015-01-01 00:00:00

  • Manipulation of PKC isozymes by RNA interference and inducible expression of PKC constructs.

    abstract::Protein kinase C (PKC), a family of serine/threonine kinases, plays an important role in apoptosis. Several members of the PKC family act as substrates for caspases. In addition, PKCs can also regulate caspase activation and cell death by apoptosis. The cleavage of PKCs separates the regulatory domain from the catalyt...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(08)01608-X

    authors: Basu A,Persaud SD,Sivaprasad U

    更新日期:2008-01-01 00:00:00

  • Liposome-mediated therapy of neuroblastoma.

    abstract::Neuroblastoma (NB) is the most common extracranial solid tumor in childhood and the most frequently diagnosed neoplasm during infancy. Despite of aggressive treatment strategies, the 5-year survival rate for metastatic disease is still less than 60% and, consequently, novel therapeutic approaches are needed. For incre...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(09)65012-6

    authors: Di Paolo D,Loi M,Pastorino F,Brignole C,Marimpietri D,Becherini P,Caffa I,Zorzoli A,Longhi R,Gagliani C,Tacchetti C,Corti A,Allen TM,Ponzoni M,Pagnan G

    更新日期:2009-01-01 00:00:00

  • Analysis of cell migration and its regulation by Rho GTPases and p53 in a three-dimensional environment.

    abstract::Cell migration plays a key role both in physiological conditions, such as tissue repair or embryonic development, and in pathological processes, including tumor metastasis. Understanding the mechanisms that allow cancer cells to invade tissues during metastasis requires studying their ability to migrate. While spectac...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/S0076-6879(07)00429-6

    authors: Vinot S,Anguille C,de Toledo M,Gadea G,Roux P

    更新日期:2008-01-01 00:00:00

  • A Tethered Vesicle Assay for High-Throughput Quantification of Membrane Fission.

    abstract::Membrane fission, which divides membrane surfaces into separate compartments, is essential to diverse cellular processes including membrane trafficking and cell division. Quantitative assays are needed to elucidate the physical mechanisms by which proteins drive membrane fission. Toward this goal, several experimental...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2018.08.014

    authors: Snead WT,Stachowiak JC

    更新日期:2018-01-01 00:00:00

  • Competitive binding assay for biotin and biotin derivatives, based on avidin and biotin-4-fluorescein.

    abstract::Biotinylated molecules are extensively employed in bioanalytics and biotechnology. The currently available assays for quantification of biotin groups suffer from low sensitivity, low accuracy, or provide highly variable responses for different biotin derivatives. We developed a competitive binding assay in which avidi...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2019.10.028

    authors: Oberbichler E,Wiesauer M,Schlögl E,Stangl J,Faschinger F,Knör G,Gruber HJ,Hytönen VP

    更新日期:2020-01-01 00:00:00

  • Chemical biology of glycoproteins: From chemical synthesis to biological impact.

    abstract::Recent advances have demonstrated the feasibility and robustness of chemical synthesis for the production of homogeneously glycosylated protein forms (glycoforms). By taking advantage of the unmatchable flexibility and precision provided by chemical synthesis, the quantitative effects of glycosylation were obtained us...

    journal_title:Methods in enzymology

    pub_type: 杂志文章

    doi:10.1016/bs.mie.2019.02.030

    authors: Li Y,Tran AH,Danishefsky SJ,Tan Z

    更新日期:2019-01-01 00:00:00