A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

Abstract:

:New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a new fluorescent peptide reporter substrate for each target kinase. These kinase chemosensors were readily phosphorylated by recombinant target enzyme and underwent a several-fold fluorescence increase upon phosphorylation. Then, using unfractionated cell lysates, a homogeneous kinase assay was developed that was reproducible, linear and highly preferential for monitoring changes in cellular activity of the target kinase. The general protocol was developed for the kinase Akt and then easily extended to measure protein kinase A (PKA) and mitogen-activated protein kinase-associated protein kinase 2 (MK2) activities. This assay platform is immediately useful for studying protein kinase signaling in crude cellular extracts.

journal_name

Nat Methods

journal_title

Nature methods

authors

Shults MD,Janes KA,Lauffenburger DA,Imperiali B

doi

10.1038/nmeth747

keywords:

subject

Has Abstract

pub_date

2005-04-01 00:00:00

pages

277-83

issue

4

eissn

1548-7091

issn

1548-7105

pii

nmeth747

journal_volume

2

pub_type

杂志文章
  • Nanoscopy with more than 100,000 'doughnuts'.

    abstract::We show that nanoscopy based on the principle called RESOLFT (reversible saturable optical fluorescence transitions) or nonlinear structured illumination can be effectively parallelized using two incoherently superimposed orthogonal standing light waves. The intensity minima of the resulting pattern act as 'doughnuts'...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2556

    authors: Chmyrov A,Keller J,Grotjohann T,Ratz M,d'Este E,Jakobs S,Eggeling C,Hell SW

    更新日期:2013-08-01 00:00:00

  • Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots.

    abstract::The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth791

    authors: Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MH

    更新日期:2005-10-01 00:00:00

  • Cell-type specific sequencing of microRNAs from complex animal tissues.

    abstract::MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4610

    authors: Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

    更新日期:2018-04-01 00:00:00

  • Localization-based super-resolution imaging meets high-content screening.

    abstract::Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcomi...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4486

    authors: Beghin A,Kechkar A,Butler C,Levet F,Cabillic M,Rossier O,Giannone G,Galland R,Choquet D,Sibarita JB

    更新日期:2017-12-01 00:00:00

  • Imaging dynamics of endogenous mitochondrial RNA in single living cells.

    abstract::We developed genetically encoded RNA probes for characterizing localization and dynamics of mitochondrial RNA (mtRNA) in single living cells. The probes consist of two RNA-binding domains of PUMILIO1, each connected with split fragments of a fluorescent protein capable of reconstituting upon binding to a target RNA. W...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth1030

    authors: Ozawa T,Natori Y,Sato M,Umezawa Y

    更新日期:2007-05-01 00:00:00

  • High-speed volumetric imaging of neuronal activity in freely moving rodents.

    abstract::Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0008-0

    authors: Skocek O,Nöbauer T,Weilguny L,Martínez Traub F,Xia CN,Molodtsov MI,Grama A,Yamagata M,Aharoni D,Cox DD,Golshani P,Vaziri A

    更新日期:2018-06-01 00:00:00

  • NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites.

    abstract::The reconstruction of neuronal populations, a key step in understanding neural circuits, remains a challenge in the presence of densely packed neurites. Here we achieved automatic reconstruction of neuronal populations by partially mimicking human strategies to separate individual neurons. For populations not resolvab...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3662

    authors: Quan T,Zhou H,Li J,Li S,Li A,Li Y,Lv X,Luo Q,Gong H,Zeng S

    更新日期:2016-01-01 00:00:00

  • Meltome atlas-thermal proteome stability across the tree of life.

    abstract::We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic protein...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-0801-4

    authors: Jarzab A,Kurzawa N,Hopf T,Moerch M,Zecha J,Leijten N,Bian Y,Musiol E,Maschberger M,Stoehr G,Becher I,Daly C,Samaras P,Mergner J,Spanier B,Angelov A,Werner T,Bantscheff M,Wilhelm M,Klingenspor M,Lemeer S,Liebl W

    更新日期:2020-05-01 00:00:00

  • Virtual microfluidics for digital quantification and single-cell sequencing.

    abstract::We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3955

    authors: Xu L,Brito IL,Alm EJ,Blainey PC

    更新日期:2016-09-01 00:00:00

  • Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.

    abstract::Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related off-target sequences. To better understand TALEN specificity, we profiled 30 unique TALENs with different target sites, array length and domain sequences for their abil...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2845

    authors: Guilinger JP,Pattanayak V,Reyon D,Tsai SQ,Sander JD,Joung JK,Liu DR

    更新日期:2014-04-01 00:00:00

  • On the art of identifying effective and specific siRNAs.

    abstract::Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth911

    authors: Pei Y,Tuschl T

    更新日期:2006-09-01 00:00:00

  • Tracking the wily transcription factor.

    abstract::A 'paired-end ditag' (PET) strategy for pinpointing protein binding sites can reveal a wealth of information about transcription factors and other DNA-binding proteins. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0506-341

    authors: Eisenstein M

    更新日期:2006-05-01 00:00:00

  • Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms.

    abstract::Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization....

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0114-z

    authors: Gruber AJ,Gypas F,Riba A,Schmidt R,Zavolan M

    更新日期:2018-10-01 00:00:00

  • CRISPR off-target analysis in genetically engineered rats and mice.

    abstract::Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that hig...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0011-5

    authors: Anderson KR,Haeussler M,Watanabe C,Janakiraman V,Lund J,Modrusan Z,Stinson J,Bei Q,Buechler A,Yu C,Thamminana SR,Tam L,Sowick MA,Alcantar T,O'Neil N,Li J,Ta L,Lima L,Roose-Girma M,Rairdan X,Durinck S,Warming S

    更新日期:2018-07-01 00:00:00

  • Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase.

    abstract::We introduce a method for sequencing peptides by mass spectrometry using a metalloendopeptidase that cleaves proteins at the amino side of lysine (Lys-N). When analyzed by electron transfer dissociation (ETD)-based mass spectrometric sequencing, Lys-N-digested peptides that contain a single lysine residue produce spec...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1204

    authors: Taouatas N,Drugan MM,Heck AJ,Mohammed S

    更新日期:2008-05-01 00:00:00

  • Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

    abstract::Generation of complex libraries of defined nucleic acid sequences can greatly aid the functional analysis of protein and gene function. Previously, such studies relied either on individually synthesized oligonucleotides or on cellular nucleic acids as the starting material. As each method has disadvantages, we have de...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth724

    authors: Cleary MA,Kilian K,Wang Y,Bradshaw J,Cavet G,Ge W,Kulkarni A,Paddison PJ,Chang K,Sheth N,Leproust E,Coffey EM,Burchard J,McCombie WR,Linsley P,Hannon GJ

    更新日期:2004-12-01 00:00:00

  • Identification of differentially methylated cell types in epigenome-wide association studies.

    abstract::An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CellDMC ( https://github.com/sjczheng/EpiDISH ), which can ide...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0213-x

    authors: Zheng SC,Breeze CE,Beck S,Teschendorff AE

    更新日期:2018-12-01 00:00:00

  • Improved specificity of TALE-based genome editing using an expanded RVD repertoire.

    abstract::Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3330

    authors: Miller JC,Zhang L,Xia DF,Campo JJ,Ankoudinova IV,Guschin DY,Babiarz JE,Meng X,Hinkley SJ,Lam SC,Paschon DE,Vincent AI,Dulay GP,Barlow KA,Shivak DA,Leung E,Kim JD,Amora R,Urnov FD,Gregory PD,Rebar EJ

    更新日期:2015-05-01 00:00:00

  • The Caenorhabditis elegans Lifespan Machine.

    abstract::The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The actions of molecular mechanisms on lifespan are therefore visible only through their statistical effects o...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2475

    authors: Stroustrup N,Ulmschneider BE,Nash ZM,López-Moyado IF,Apfeld J,Fontana W

    更新日期:2013-07-01 00:00:00

  • Measurement of mechanical tractions exerted by cells in three-dimensional matrices.

    abstract::Quantitative measurements of cell-generated forces have heretofore required that cells be cultured on two-dimensional substrates. We describe a technique to quantitatively measure three-dimensional traction forces exerted by cells fully encapsulated in well-defined elastic hydrogel matrices. Using this approach we mea...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1531

    authors: Legant WR,Miller JS,Blakely BL,Cohen DM,Genin GM,Chen CS

    更新日期:2010-12-01 00:00:00

  • Glycomics: an integrated systems approach to structure-function relationships of glycans.

    abstract::In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information dens...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth807

    authors: Raman R,Raguram S,Venkataraman G,Paulson JC,Sasisekharan R

    更新日期:2005-11-01 00:00:00

  • Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging.

    abstract::Circuit mapping requires knowledge of both structural and functional connectivity between cells. Although optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactiv...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3480

    authors: Berlin S,Carroll EC,Newman ZL,Okada HO,Quinn CM,Kallman B,Rockwell NC,Martin SS,Lagarias JC,Isacoff EY

    更新日期:2015-09-01 00:00:00

  • Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.

    abstract::Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to lar...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0529-1

    authors: Zhang AW,O'Flanagan C,Chavez EA,Lim JLP,Ceglia N,McPherson A,Wiens M,Walters P,Chan T,Hewitson B,Lai D,Mottok A,Sarkozy C,Chong L,Aoki T,Wang X,Weng AP,McAlpine JN,Aparicio S,Steidl C,Campbell KR,Shah SP

    更新日期:2019-10-01 00:00:00

  • Unitary permeability of gap junction channels to second messengers measured by FRET microscopy.

    abstract::Gap junction channels assembled from connexin protein subunits mediate intercellular transfer of ions and metabolites. Impaired channel function is implicated in several hereditary human diseases. In particular, defective permeation of cAMP or inositol-1,4,5-trisphosphate (InsP(3)) through connexin channels is associa...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth1031

    authors: Hernandez VH,Bortolozzi M,Pertegato V,Beltramello M,Giarin M,Zaccolo M,Pantano S,Mammano F

    更新日期:2007-04-01 00:00:00

  • Nanoscale resolution in GFP-based microscopy.

    abstract::We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth922

    authors: Willig KI,Kellner RR,Medda R,Hein B,Jakobs S,Hell SW

    更新日期:2006-09-01 00:00:00

  • High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases.

    abstract::Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point mutation, (ii) targeted g...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1653

    authors: Chen F,Pruett-Miller SM,Huang Y,Gjoka M,Duda K,Taunton J,Collingwood TN,Frodin M,Davis GD

    更新日期:2011-07-17 00:00:00

  • Use of microRNA sponges to explore tissue-specific microRNA functions in vivo.

    abstract::MicroRNA depletion by sequestration produces flexible hypomorphs that mimic mutants obtained by microRNA gene targeting. ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/nmeth1209-873

    authors: Cohen SM

    更新日期:2009-12-01 00:00:00

  • Whole-genome genotyping with the single-base extension assay.

    abstract::We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth842

    authors: Steemers FJ,Chang W,Lee G,Barker DL,Shen R,Gunderson KL

    更新日期:2006-01-01 00:00:00

  • Structural biology: 'seeing' crystals the XFEL way.

    abstract::X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3070

    authors: Marx V

    更新日期:2014-09-01 00:00:00

  • Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering.

    abstract::We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1255

    authors: Cammarata M,Levantino M,Schotte F,Anfinrud PA,Ewald F,Choi J,Cupane A,Wulff M,Ihee H

    更新日期:2008-10-01 00:00:00