Biochemistry

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    Protocols in Current Issue
    Contemporaneous Measurement of Outer and Inner Membrane Permeability in Gram-negative Bacteria
    Authors:  Bo Ma, Chao Fang, Jing Zhang, Mingzhi Wang, Xiaoxing Luo and Zheng Hou, date: 03/05/2020, view: 236, Q&A: 0
    [Abstract] The emergence and rapid spread of multidrug resistance in bacteria have led to the urgent need for novel antibacterial agents. Membrane permeabilization is the mechanism for many antibacterial molecules that are being developed against gram-negative bacteria. Thus, to determine the efficacy of a potential antibacterial molecule, it is important to ...
    Assessing Self-interaction of Mammalian Nuclear Proteins by Co-immunoprecipitation
    Authors:  Claudia Cattoglio, Iryna Pustova, Xavier Darzacq, Robert Tjian and Anders S. Hansen, date: 02/20/2020, view: 619, Q&A: 0
    [Abstract] Protein-protein interactions constitute the molecular foundations of virtually all biological processes. Co-immunoprecipitation (CoIP) experiments are probably the most widely used method to probe both heterotypic and homotypic protein-protein interactions. Recent advances in super-resolution microscopy have revealed that several nuclear proteins ...
    Photoactivable Cholesterol as a Tool to Study Interaction of Influenza Virus Hemagglutinin with Cholesterol
    Authors:  Bodan Hu, Mohamed Rasheed Gadalla, Christoph Thiele and Michael Veit, date: 02/20/2020, view: 251, Q&A: 0
    [Abstract] Non-covalent binding of cholesterol to the transmembrane region of proteins affect their functionalities, but methods to prove such an interaction are rare. We describe our protocol to label the hemagglutinin (HA) of Influenza virus with a cholesterol derivative in living cells or with immunoprecipitated protein. We synthesized a “clickable” ...
    Proximity Ligation Assay for the Investigation of the Intramolecular Interaction of ELMO1
    Authors:  Wai Wa Ray Chan, Dik Long Dennis Chau, Wen Li and Kwok-Fai Lau, date: 12/05/2019, view: 593, Q&A: 0
    [Abstract] Intramolecular interaction is a common mechanism that regulates protein activities. Conventionally, such interactions are investigated by classical in vitro biochemical assays. Here, we describe a protocol for studying the intramolecular interaction of cell motility and engulfment 1 (ELMO1) in mammalian cells by using proximity ligation ...
    Detection of in vivo Protein Interactions in All Bacterial Compartments by Förster Resonance Energy Transfer with the Superfolder mTurquoise2 ox-mNeongreen FRET Pair
    Authors:  Nils Y. Meiresonne, Elisa Consoli, Laureen M.Y. Mertens and Tanneke den Blaauwen, date: 12/05/2019, view: 760, Q&A: 0
    [Abstract] This protocol was developed to qualitatively and quantitatively detect protein-protein interactions in all compartments of Escherichia coli by Förster Resonance Energy Transfer (FRET) using the Superfolder mTurquoise2 ox-mNeonGreen FRET pair (sfTq2ox-mNG). This FRET pair has more than twice the detection range for FRET ...
    Measuring Small-molecule Inhibition of Protein Interactions in Live Cells Using FLIM-FRET
    Authors:  James M. Pemberton, Qian Liu and David W. Andrews, date: 10/20/2019, view: 2159, Q&A: 0
    [Abstract] This protocol was designed to quantitatively measure small-molecule displacement of proteins in live mammalian cells using fluorescence lifetime imaging microscopy–Förster resonance energy transfer (FLIM-FRET). Tumour cell survival is often dependent on anti-apoptotic proteins, which bind to and inhibit pro-apoptotic proteins, thus preventing ...
    Supported Cell Membrane Sheets to Monitor Protein Assembly
    Authors:  Simon Erlendsson, Thor Seneca Thorsen and Kenneth Lindegaard Madsen, date: 09/20/2019, view: 781, Q&A: 0
    [Abstract] Studying protein-protein and protein-lipid interactions in their native environment is highly desirable, yet, the heterogeneity and complexity of cellular systems limits the repertoire of experimental methods available. In cells, interactions are often taking place in confined microenvironments where factors such as avidity, hindered diffusion, ...
    Cell-based Assay for Recruitment of DDR1 to Collagen-coated Beads
    Authors:  Victoria Juskaite and Birgit Leitinger, date: 08/20/2019, view: 745, Q&A: 0
    [Abstract] The discoidin domain receptors, DDR1 and DDR2, are key signaling receptors for the extracellular matrix protein collagen. The interactions of cells with collagen are difficult to study because of the difficulty to obtain native collagen fibers for in vitro studies. Thus, in vitro studies often use acid-soluble collagens in the ...
    Tryptophan Fluorescence Quenching Assays for Measuring Protein-ligand Binding Affinities: Principles and a Practical Guide
    Authors:  Anthony Yammine, Jinlong Gao and Ann H. Kwan, date: 06/05/2019, view: 4302, Q&A: 0
    [Abstract] Tryptophan fluorescence quenching is a type of fluorescence spectroscopy used for binding assays. The assay relies on the ability to quench the intrinsic fluorescence of tryptophan residues within a protein that results from changes in the local environment polarity experienced by the tryptophan(s) upon the addition of a binding partner or ligand. ...
    Cross-linking, Immunoprecipitation and Proteomic Analysis to Identify Interacting Proteins in Cultured Cells
    Authors:  Hao Wang, Meiling He, Belinda Willard and Qingyu Wu, date: 06/05/2019, view: 2815, Q&A: 0
    [Abstract] Extracellular expression is essential for the function of secreted and cell surface proteins. Proper intracellular trafficking depends on protein interactions in multiple subcellular compartments. Co-immunoprecipitation and the yeast two-hybrid system are commonly used to investigate protein-protein interactions. These methods, however, depend on ...



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