1Department of Pharmacology, University of Illinois at Chicago
Flow cytometric analysis of Bimolecular Fluorescence Complementation provides a high throughput quantitative method to study protein-protein interaction. This methodology can be applied to mapping protein binding sites and for screening factors that regulate protein-protein interaction.
Published August 15, 2013. Keywords: Molecular Biology, Biochemistry, Cellular Biology, Genetics, Pharmacology, Proteins, Flow Cytometry, Bimolecular Fluorescence Complementation, BiFC, quantative analysis, protein-protein interaction, Förster resonance energy transfer, FRET, Bioluminescence Resonance Energy Transfer, BRET, protein, cell, transfection, fluorescence, microscopy
1Division of Virology, Department of Pathology, University of Cambridge
SILAC immunoprecipitation experiments represent a powerful means for discovering novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants, and low affinity interactions preserved through use of less-stringent buffer conditions.
Published July 6, 2014. Keywords: Biochemistry, mass spectrometry, tissue culture techniques, isotope labeling, SILAC, Stable Isotope Labeling of Amino Acids in Cell Culture, proteomics, Interactomics, immunoprecipitation, pulldown, eIF4A, GFP, nanotrap, orbitrap
1Institute of Chemistry, The Hebrew University of Jerusalem
Peptide array screening is a high throughput assay for identifying protein-protein interaction sites. This allows mapping multiple interactions of a target protein and can serve as a method for identifying sites for inhibitors that target a protein. Here we describe a protocol for screening and analyzing peptide arrays.
Published November 18, 2014. Keywords: Molecular Biology, peptides, peptide arrays, protein-protein interactions, binding sites, peptide synthesis, micro-arrays
1Neuroscience Center of Excellence, Louisiana State University Health Sciences Center
Drosophila is famous for its powerful genetic manipulation, but not for its suitability of in-depth biochemical analysis. Here we present a TAP-based procedure to identify interacting partners of any protein of interest from the fly brain. This procedure can potentially lead to new avenues of research.
Published December 5, 2013. Keywords: Biochemistry, Drosophila, GAL4/UAS system, transgenic, Tandem Affinity Purification, protein-protein interaction, proteomics
1Department of Pharmaceutical Biotechnology and Molecular Biology, Centre for Pharmaceutical Research, Vrije Universiteit Brussel
In this article, a simple, quantitative, liquid phase affinity capture assay is presented. It is a reliable technique based on the interaction between magnetic beads and tagged proteins (e.g. nanobodies) on one hand and the affinity between the tagged protein and a second, labeled protein (e.g. poliovirus) on the other.
Published May 29, 2012. Keywords: Molecular Biology, Virology, Poliovirus, VHH, nanobody, magnetic beads, affinity capture, liquid phase based assay, protein interaction
1Dept. Of Cell Biology and Molecular Genetics, University of Maryland
This article illustrates how to properly use the BioRad Helios Gene Gun to introduce plasmid DNA into onion epidermal cells and how to test for protein-protein interactions in onion cells based on the principle of Bimolecular Fluorescence Complementation (BiFC)
Published June 12, 2010. Keywords: Plant Biology, Bimolecular Fluorescence Complementation (BiFC), particle bombardment, protein-protein interaction, onion cells, Helios Gene Gun
1Language and Genetics Department, Max Planck Institute for Psycholinguistics, 2Donders Institute for Brain, Cognition and Behaviour
Interactions between proteins are fundamental to all cellular processes. Using Bioluminescence Resonance Energy Transfer, the interaction between a pair of proteins can be monitored in live cells and in real time. Furthermore, the effects of potentially pathogenic mutations can be assessed.
Published May 26, 2014. Keywords: Cellular Biology, Protein-protein interactions, Bioluminescence Resonance Energy Transfer, Live cell, Transfection, Luciferase, Yellow Fluorescent Protein, Mutations
1Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology
Surface Plasmon Resonance (SPR) is a label-free method for detecting bio-molecular interactions in real time. Herein, a protocol for a membrane protein:receptor interaction experiment is described, while discussing the pros and cons of the technique.
Published November 29, 2014. Keywords: Structural Biology, ABC transporter, substrate binding protein, bio-molecular interaction kinetics, label-free, protein-protein interaction, Surface plasmon resonance (SPR), Biacore
JoVE Immunology and Infection
1Unité de Génétique, Papillomavirus et Cancer Humain (GPCH), Institut Pasteur, 2Cellule Pasteur, Université Sorbonne Paris Cité, 3Center for Cancer Systems Biology (CCSB), Harvard Medical School, Department of Cancer Biology, Dana Farber Cancer Institute
This article focuses on the identification of high-confident interaction datasets between host and pathogen proteins using a combination of two orthogonal methods: yeast two-hybrid followed by a high-throughput interaction assay in mammalian cells called HT-GPCA.
Published July 18, 2013. Keywords: Immunology, Genetics, Microbiology, Biochemistry, Molecular Biology, Cellular Biology, Biomedical Engineering, Infection, Cancer Biology, Virology, Medicine, Host-Pathogen Interactions, Host-Pathogen Interactions, Protein-protein interaction, High-throughput screening, Luminescence, Yeast two-hybrid, HT-GPCA, Network, protein, yeast, cell, culture
1Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg
Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.
Published November 29, 2013. Keywords: Chemistry, Molecular Chaperones, mass spectrometers, Amino Acids, Peptides, Proteins, Enzymes, Coenzymes, Protein dynamics, conformational changes, allostery, protein folding, secondary structure, mass spectrometry
1Department of Molecular Biology and Biochemistry, Simon Fraser University, 2Department of Biomedical Physiology and Kinesiology, Simon Fraser University
This protocol demonstrates how Proximity Ligation Assay can be used to detect in situ protein-protein interactions at the Drosophila larval neuromuscular junction. With this technique, Discs large and Hu-li tai shao are shown to form a complex at the postsynaptic region, an association previously identified through co-immunoprecipitation.
Published January 20, 2015. Keywords: Neuroscience, adducin, body wall dissection, developmental biology, Discs large, Drosophila, Hu-li tai shao, immunohistochemistry, neuromuscular junction, neuroscience, protein-protein interaction, Proximity Ligation Assay, third instar larvae
1Molekulare Mikrobiologie, Universität Osnabrück
A biochemical approach is described to identify in vivo protein-protein interactions (PPI) of membrane proteins. The method combines protein cross-linking, affinity purification and mass spectrometry, and is adaptable to almost any cell type or organism. With this approach, even the identification of transient PPIs becomes possible.
Published November 7, 2013. Keywords: Bioengineering, Membrane Proteins, in vivo protein-protein interaction, formaldehyde cross-linking, MS-analysis, Strep-tag
1Department of Cell Biology, University of Texas Southwestern Medical Center at Dallas
Procedures for complete reconstitution of a prototype voltage-gated potassium channel into lipid membranes are described. The reconstituted channels are suitable for biochemical assays, electrical recordings, ligand screening and electron crystallographic studies. These methods may have general applications to the structural and functional studies of other membrane proteins.
Published July 13, 2013. Keywords: Molecular Biology, Biochemistry, Genetics, Cellular Biology, Structural Biology, Biophysics, Membrane Lipids, Phospholipids, Carrier Proteins, Membrane Proteins, Micelles, Molecular Motor Proteins, life sciences, biochemistry, Amino Acids, Peptides, and Proteins, lipid-protein interaction, channel reconstitution, lipid-dependent gating, voltage-gated ion channel, conformation-specific ligands, lipids
1Department Biologie I, Botanik, Ludwig-Maximilians-Universität, München
Formation of protein complexes in vivo can be visualized by bimolecular fluorescence complementation. Interaction partners are fused to complementary parts of fluorescent tags and transiently expressed in tobacco leaves, resulting in a reconstituted fluorescent signal upon close proximity of the two proteins.
Published March 9, 2014. Keywords: Plant Biology, Tetratricopeptide repeat domain, chaperone, chloroplasts, endoplasmic reticulum, HSP90, Toc complex, Sec translocon, BiFC
1Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute
AVEXIS is a high throughput protein interaction assay developed to systematically screen for novel extracellular receptor-ligand pairs involved in cellular recognition processes. It is specifically designed to detect transient protein interactions that are difficult to identify using other high throughput approaches.
Published March 5, 2012. Keywords: Molecular Biology, Receptor-ligand pairs, Extracellular protein interactions, AVEXIS, Adhesion receptors, Transient/weak interactions, High throughput screening
1GE Healthcare Bio-Sciences AB
We apply label-free protein interaction analysis using Biacore X100 for structure-function analysis of the binding of several cystatin B mutants to papain through kinetic characterization. Calibration-free concentration analysis (CFCA) measures the concentration of protein with retained binding activity without the need for a standard curve. We show that confirmation of concentrations using CFCA increases the reliability of the kinetic analysis and that kinetic constants can reliably be determined even if the activity of a recombinant protein is reduced.
Published March 17, 2010. Keywords: Cellular Biology, Protein interaction, Surface Plasmon Resonance, Biacore X100, CFCA, Cystatin B, Papain
JoVE Immunology and Infection
1Biological Sciences Division, Pacific Northwest National Laboratory, 2Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, 3Structural Proteomics Group, Ontario Center for Structural Proteomics, University of Toronto, 4Center for Bioproducts and Bioenergy, Washington State University
Electroporation was used to insert purified bacterial virulence effector proteins directly into living eukaryotic cells. Protein localization was monitored by confocal immunofluorescence microscopy. This method allows for studies on trafficking, function, and protein-protein interactions using active exogenous proteins, avoiding the need for heterologous expression in eukaryotic cells.
Published January 19, 2015. Keywords: Immunology, electroporation, protein, transfection, expression, localization, confocal microscopy, Salmonella, effector
JoVE Immunology and Infection
1Department of Microbiology, Biochemistry, & Immunology, Morehouse School of Medicine, 2Institute for Systems Biology, 3Advanced Medical & Dental Institute, Universiti Sains Malaysia
Techniques to dissect the mechanisms underlying the secretion of HIV-1 Nef in exosomes are described. Specific short peptides derived from Nef and protein transfection were exploited to determine the structure, function, and binding partners of Nef’s Secretion Modification Region. These procedures have general relevance in many mechanistic studies.
Published June 30, 2013. Keywords: Virology, Biochemistry, Immunology, Infection, Infectious Diseases, Molecular Biology, Medicine, Genetics, Microbiology, Genomics, Proteins, Exosomes, HIV, Peptides, Exocytosis, protein trafficking, secretion, HIV-1, Nef, Secretion Modification Region, SMR, peptide, AIDS, assay
1Department of Biochemistry, University of Toronto, 2Department of Molecular Genetics, University of Toronto, 3Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto
MYTH allows the sensitive detection of transient and stable interactions between proteins that are expressed in the model organism Saccharomyces cerevisiae. It has been successfully applied to study exogenous and yeast integral membrane proteins in order to identify their interacting partners in a high throughput manner.
Published February 1, 2010. Keywords: Cellular Biology, protein-protein interaction, membrane, split-ubiquitin, yeast, library screening, Y2H, yeast two-hybrid, MYTH
1Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 2Deparment of Biochemistry, Research and Innovation Centre, University of Regina, 3Department of Medical Genetics and Microbiology, University of Toronto
Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.
Published November 12, 2012. Keywords: Genetics, Molecular Biology, Medicine, Biochemistry, Microbiology, affinity purification, Escherichia coli, gram-negative bacteria, cytosolic proteins, SPA-tagging, homologous recombination, mass spectrometry, protein interaction, protein complex
1Max Planck Institute of Molecular Plant Physiology, 2University of Kaiserslautern
We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.
Published September 24, 2012. Keywords: Genetics, Molecular Biology, Physiology, Plant Biology, 15N metabolic labeling, QUICK, protein cross-linking, Chlamydomonas, co-immunoprecipitation, molecular chaperones, HSP70
1Lawrence Berkeley National Laboratory, The Molecular Foundry
More than half of proteins are small proteins (molecular mass <200 kDa) that are challenging for both electron microscope imaging and three-dimensional reconstructions. Optimized negative staining is a robust and high-throughput protocol to obtain high contrast and relatively high resolution (~1 nm) images of small asymmetric proteins or complexes under different physiological conditions.
Published August 15, 2014. Keywords: Environmental Sciences, small and asymmetric protein structure, electron microscopy, optimized negative staining
1Promega Corporation, 2MS Bioworks LLC
HaloTag technology is a multifunctional technology which has shown significant success in isolation of both small and large protein complexes from mammalian cells. Here we highlight the advantages of this technology compared to existing alternatives and demonstrate its utility to study numerous aspects of protein function inside eukaryotic cells.
Published July 12, 2014. Keywords: Cellular Biology, proteomics, HaloTag, protein interactions, mass spectrometry, bromodomain proteins, BRD4, histone deacetylase (HDAC), HDAC cellular assays, and confocal imaging
1Department of Genetics, Albert Einstein College of Medicine, 2Shanghai Key Laboratory of Complex Prescription and MOE Key Laboratory for Standardization of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine
Ketoconazole binds to and antagonizes Pregnane X Receptor (PXR) activation. Yeast high throughput screens of PXR mutants define a unique region for ketoconazole binding. This yeast-based genetic method discovers novel nuclear receptor interactions with ligands that associate with surface binding sites.
Published November 15, 2013. Keywords: Biochemistry, Orphan nuclear receptor, ketoconazole, yeast two-hybrid, Pregnane X Receptor, ligand, antatogist, coactivators SRC-1 (steroid receptor coactivator 1), drug-receptor interaction
1Department of Biochemistry and Cell Biology, State University of New York
Testing protein-protein interaction is indispensable for dissection of protein functionality. Here, we introduce an in vitro protein-protein binding assay to probe a membrane-immobilized protein with a soluble protein. This assay provides a reliable method to test interaction between an insoluble protein and a protein in solution.
Published August 14, 2011. Keywords: Molecular Biology, protein-protein interactions, overlay, in vitro, western blotting, nitrocellulose membrane, insoluble protein
1Institute of Biochemistry, Stuttgart University
Peptide arrays synthesized by the SPOT method can be used to analyze the substrate specificity of Protein lysine methyltransferases (PKMTs) and to define the substrate spectrum of PKMTs to understand their biological role. This protocol describes how to synthesize peptide arrays, methylate them with PKMTs, and analyze the results.
Published November 29, 2014. Keywords: Biochemistry, Peptide arrays, solid phase peptide synthesis, SPOT synthesis, protein lysine methyltransferases, substrate specificity profile analysis, lysine methylation
1Department of Horticulture, University of Kentucky
Phage display is a powerful technique to capture proteins or protein moieties that interact with an immobilized molecule of interest. Once a decision of the type of phage cDNA library to create and screen has been made, the protocol described here permits efficient affinity selection leading to identification of interactors.
Published February 16, 2014. Keywords: Biochemistry, Affinity selection, Phage display, protein-protein interaction
1Department of Pharmacy and Biotechnology, University of Bologna, 2CSGI, Department of Chemistry, University of Firenze
Protein co-expression is a powerful alternative to the reconstitution in vitro of protein complexes, and is of help in performing biochemical and genetic tests in vivo. Here we report on the use of protein co-expression in Escherichia coli to obtain protein complexes, and to tune the mutation frequency of cells.
Published February 5, 2015. Keywords: Biochemistry, Escherichia coli, protein co-expression, compatible plasmids, complementation test, DNA polymerase III, mutator strains
JoVE Immunology and Infection
1Genetics and Biochemistry Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
This article illustrates the use of pulse-chase radio labeling in combination with site-specific photocrosslinking to monitor interactions between a protein of interest and other factors in E. coli. Unlike traditional chemical cross-linking methods, this approach generates high resolution “snapshots” of an ordered assembly pathway in a living cell.
Published December 17, 2013. Keywords: Immunology, Autotransporters, Bam complex, Molecular chaperones, protein-protein interactions, Site-specific photocrosslinking
1Department of Physics and Astronomy, Rowan University, 2Department of Biomedical and Translational Sciences, Rowan University, 3Department of Biomedical Sciences, Cooper Medical School of Rowan University, 4Department of Chemistry and Biochemistry, Rowan University
Blending is an efficient approach to generate biomaterials with a broad range of properties and combined features. By predicting the molecular interactions between different natural silk proteins, new silk-silk protein alloy platforms with tunable mechanical resiliency, electrical response, optical transparency, chemical processability, biodegradability, or thermal stability can be designed.
Published August 13, 2014. Keywords: Bioengineering, protein alloys, biomaterials, biomedical, silk blends, computational simulation, implantable electronic devices
1Lady Davis Institute for Medical Research, Jewish General Hospital, 2Department of Medicine, McGill University
Here we present a protocol to analyze RNA/protein interactions. The electrophoretic mobility shift assay (EMSA) is based on the differential migration of RNA/protein complexes and free RNA during native gel electrophoresis. By using a radiolabeled RNA probe, RNA/protein complexes can be visualized by autoradiography.
Published December 3, 2014. Keywords: Biochemistry, RNA metabolism, mRNA translation, post-transcriptional gene regulation, mRNA stability, IRE, IRP1, IRP2, iron metabolism, ferritin, transferrin receptor
1Department of Neuroscience, Tufts University, 2Neuroscience Program, Tufts Sackler School of Graduate Biomedical Sciences
This study describes the procedures of setting up a novel neuronal axon and (astro)glia co-culture platform. In this co-culture system, manipulation of direct interaction between a single axon (and single glial cell) becomes feasible, allowing mechanistic analysis of the mutual neuron to glial signaling.
Published October 14, 2012. Keywords: Neuroscience, Molecular Biology, Cellular Biology, Biophysics, Microfluidics, Microfluidic culture platform, Compartmented culture, Neuron to glia signaling, neurons, glia, cell culture
1Institute of Molecular Medicine and Genetics, Georgia Health Sciences University
To test the interaction of a protein with its target lipid we used MACS and Annexin V-conjugated magnetic beads and lipid vesicles synthesized from the target lipid and Annexin V-binding phosphatidylserine. Proteins bound to the target lipid are co-purified and analyzed after elution from the beads.
Published April 26, 2011. Keywords: Cellular Biology, ceramide, phosphatidylserine, lipid-protein interaction, atypical PKC
1Department of Biochemistry / Analytics, caprotec bioanalytics GmbH, 2Institute of Organic Chemistry, RWTH Aachen University
Capture Compounds are trifunctional small molecules to reduce the complexity of the proteome by functional reversible small molecule-protein interaction followed by photo-crosslinking and purification. Here we use a Capture Compound with S-adenosyl-L-homocysteine-binding as selectivity function to isolate methyltransferases from an Escherichia coli whole cell lysate and identify them by MS.
Published December 20, 2010. Keywords: Biochemistry, Capture Compound, photo-crosslink, small molecule-protein interaction, methyltransferase, S-adenosyl-l-homocysteine, SAH, S-adenosyl-l-methionine, SAM, functional proteomics, LC-MS/MS
1Institute for Clinical Neurobiology, University of Wuerzburg, 2Department of Synapses - Circuits - Plasticity, Max Planck Institute of Neurobiology, Martinsried, 3Walter Brendel Centre of Experimental Medicine, Ludwig-Maximilians University of Munich
Targeted-esterase induced dye loading (TED) supports the analysis of intracellular calcium store dynamics by fluorescence imaging. The method bases on targeting of a recombinant Carboxylesterase to the endoplasmic reticulum (ER), where it improves the local unmasking of synthetic low-affinity Ca2+ indicator dyes in the ER lumen.
Published May 7, 2013. Keywords: Cellular Biology, Neurobiology, Neuroscience, Molecular Biology, Biochemistry, Biomedical Engineering, Bioengineering, Virology, Medicine, Anatomy, Physiology, Surgery, Endoplasmic Reticulum, ER, Calcium Signaling, calcium store, calcium imaging, calcium indicator, metabotropic signaling, Ca2+, neurons, cells, mouse, animal model, cell culture, targeted esterase induced dye loading, imaging
1Greenebaum Cancer Center, University of Maryland School of Medicine, 2Program in Molecular Medicine, University of Maryland School of Medicine, 3Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 4Department of Pharmacology & Experimental Therapeutics, University of Maryland School of Medicine, 5Department of Pathology and Biochemistry & Molecular Biology, University of Maryland School of Medicine
We developed a quantitative DNA-binding, ELISA-based assay to measure transcription factor interactions with DNA. High specificity for the RUNX2 protein was achieved with a consensus DNA-recognition oligonucleotide and specific monoclonal antibody. Colorimetric detection with an enzyme-coupled antibody substrate reaction was monitored in real time.
Published August 31, 2013. Keywords: Cellular Biology, Transcription Factors, Vitamin D, Drug Discovery, Enzyme-Linked Immunosorbent Assay (ELISA), DNA-binding, transcription factor, drug screening, antibody
1Department of Physics, University of Wisconsin - Milwaukee, 2Department of Biological Sciences, University of Wisconsin - Milwaukee
By employing a spectrally resolved two-photon microscopy imaging system, pixel-level maps of Förster Resonance Energy Transfer (FRET) efficiencies are obtained for cells expressing membrane receptors hypothesized to form homo-oligomeric complexes. From the FRET efficiency maps, we are able to estimate stoichiometric information about the oligomer complex under study.
Published January 19, 2011. Keywords: Cellular Biology, Forster (Fluorescence) Resonance Energy Transfer (FRET), protein-protein interactions, protein complex, in vivo determinations, spectral resolution, two-photon microscopy, G protein-coupled receptor (GPCR), sterile 2 alpha-factor protein (Ste2p)
1Department of Orthopaedic Surgery, NYU Hospital for Joint Diseases, 2Department of Cell Biology, New York University School of Medicine
We have modified the conventional yeast two-hybrid screening, an effective genetic tool in identifying protein interaction. This modification markedly shortens the process, reduces the workload, and most importantly, reduces the number of false positives. In addition, this approach is reproducible and reliable.
Published January 17, 2012. Keywords: Molecular Biology, Modified yeast two-hybrid screen, PGRN, TNFR2, inflammation, autoimmune diseases
1Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, 2iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Saclay, France
A protocol for the quantitative, high throughput expression screening and analytical purification of fusion proteins from small-scale Escherichia coli cultures is described and applied to the expression of disulfide-rich animal venom protein targets.
Published July 30, 2014. Keywords: Bioengineering, E. coli, expression, recombinant, high throughput (HTP), purification, auto-induction, immobilized metal affinity chromatography (IMAC), tobacco etch virus protease (TEV) cleavage, disulfide bond isomerase C (DsbC) fusion, disulfide bonds, animal venom proteins/peptides
1Department of Biochemistry & Molecular Biology, Wayne State University School of Medicine, 2Cardiovascular Research Institute, Wayne State University School of Medicine, 3Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine
Cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial chloride channel, has been reported to interact with various proteins and regulate important cellular processes; among them the CFTR PDZ motif-mediated interactions have been well documented. This protocol describes methods we developed to assemble a PDZ-dependent CFTR macromolecular signaling complex in vitro.
Published August 13, 2012. Keywords: Biochemistry, Molecular Biology, Chemistry, CFTR, macromolecular complex, protein interaction, PDZ scaffold protein, epithelial cell, cystic fibrosis
1Department of Physics and Astronomy, VU University Amsterdam
This protocol details the reconstitution of light-harvesting complexes in vitro. These integral membrane proteins coordinate chlorophylls and carotenoids and are responsible for harvesting light in higher plants and green algae.
Published October 10, 2014. Keywords: Biochemistry, Reconstitution, Photosynthesis, Chlorophyll, Carotenoids, Light Harvesting Protein, Chlamydomonas reinhardtii, Arabidopsis thaliana
1Department of Biochemistry, University of Oxford
Exonucleases play critical roles in ensuring genome stability. Loss of WRN exonuclease function results in premature aging. Studying substrates and other requirements of the nuclease in vitro can help elucidate its role in vivo. Here we demonstrate a rapid and reproducible fluorescence-based assay to measure its nuclease activity.
Published December 23, 2013. Keywords: Biochemistry, Aging, Premature, Exonucleases, Enzyme Assays, biochemistry, WRN, exonuclease, nuclease, RecQ, progeroid disease, aging, DmWRNexo
1Department of Biological Sciences, Murray State University
Multi-component protein complexes play crucial roles during cellular function and development. Here we describe a method used to isolate native protein complexes from Drosophila embryos after in vivo crosslinking followed by purification of the crosslinked complexes for subsequent structure-function analysis.
Published April 23, 2014. Keywords: Developmental Biology, Drosophila, Germ cells, embryonic development, RNA-protein complexes, in vivo crosslinking, Tudor domain
1MRC LMCB, University College London, 2Center for Computational and Integrative Biology, Massachusetts General Hospital
A high-content screening method for the identification of novel signaling competent transmembrane receptors is described. This method is amenable to large-scale automation and allows predictions about in vivo protein binding and the sub-cellular localization of protein complexes in mammalian cells.
Published October 30, 2012. Keywords: Molecular Biology, Grb2, cDNA preparation, high-throughput, high-content screening, signal transduction, expression cloning, 96-well
1The Mina & Everard Goodman Faculty of Life Sciences, The Nanotechnology Institute, Bar-Ilan University
We present a microfluidic approach for the expression of protein arrays. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for experimental use.
Published August 23, 2012. Keywords: Bioengineering, Genetics, Chemistry, Molecular Biology, In vitro protein expression, microfluidics, protein microarray, systems biology, high-throughput, screening
1Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University Medical Center, 2Division of Gastroenterology, Hepatology & Nutrition and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine
A method is described for analyzing protein degradation using radiolabeled and luciferase-fusion proteins in Xenopus egg extract and its adaptation for high-throughput screening for small molecule modulators of protein degradation.
Published June 17, 2014. Keywords: Molecular Biology, Xenopus laevis, Xenopus egg extracts, protein degradation, radiolabel, luciferase, autoradiography, high-throughput screening
1Department of Biology, University of Western Ontario, 2Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada
We have developed a technique to test protein-protein interactions in plant. A yellow fluorescent protein (YFP) is split into two non-overlapping fragments. Each fragment is cloned in-frame to a gene of interest via Gateway system, enabling expression of fusion proteins. Reconstitution of YFP signal only occurs when the inquest proteins interact.
Published September 16, 2011. Keywords: Plant Biology, protein interaction, Gateway, Bimolecular fluorescence complementation, Confocal microscope, Agrobacterium, Nicotiana benthamiana, Arabidopsis
1Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University
We genetically-encode the unnatural amino acid, p-azido-L-phenylalanine at various targeted positions in GPCRs and show the versatility of the azido group in different applications. These include a targeted photocrosslinking technology to identify residues in the ligand-binding pocket of a GPCR, and site-specific bioorthogonal modification of GPCRs with a peptide-epitope tag or fluorescent probe.
Published September 13, 2013. Keywords: Genetics, Receptors, G-Protein-Coupled, Protein Engineering, Signal Transduction, Biochemistry, Unnatural amino acid, site-directed mutagenesis, G protein-coupled receptor, targeted photocrosslinking, bioorthogonal labeling, targeted epitope tagging
1Medical Research Council, Clinical Sciences Centre, Imperial College, Hammersmith Hospital
Here we show how to use Proximity Ligation Assay (PLA), with a combination of antibodies to visualize Bone Morphogenetic Protein (BMP) signaling in fixed cells. This technique allowed us to follow the nuclear accumulation of endogenous BMP activated effector-complexes and quantify their levels over time under BMP4 stimulation.
Published March 3, 2011. Keywords: Cellular Biology, Proximity Ligation Assay, BMP, signaling, Smad4, Smad1/5, HEK293T, signaling effectors, phospho-Smads, immunocytochemistry, Antibody
1Department of Biological Chemistry, Weizmann Institute of Science
Mass spectrometry has proven to be a valuable tool for analyzing large protein complexes. This method enables insights into the composition, stoichiometry and overall architecture of multi-subunit assemblies. Here, we describe, step-by-step, how to perform a structural mass spectrometry analysis, and characterize macromolecular structures.
Published June 19, 2010. Keywords: Cellular Biology, mass spectrometry, protein complexes, non-covalent interactions, structural biology, nanoElectrospray, QToF