Biochemistry

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    Protocols in Current Issue
    Measurement of Ascorbic Acid and Glutathione Content in Cyanobacterium Synechocystis sp. PCC 6803
    Ascorbic acid (AsA) and gluthathione (GSH) are two key components of the antioxidant machinery of eukaryotic and prokaryotic cells. The cyanobacterium Synechocystis sp. PCC 6803 presents both compounds in different concentrations (AsA, ...
    Quantification of Salivary Charged Metabolites Using Capillary Electrophoresis Time-of-flight-mass Spectrometry
    Authors:  Masahiro Sugimoto, Sana Ota, Miku Kaneko, Ayame Enomoto and Tomoyoshi Soga, date: 10/20/2020, view: 79, Q&A: 0
    Salivary metabolomics have provided the potentials to detect both oral and systemic diseases. Capillary electrophoresis time-of-flight-mass spectrometry (CE-TOFMS) enables the identification and quantification of various charged metabolites. This ...
    Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations
    Authors:  Andrea Saponaro, Vincenzo Maione, Alexandre M. J. J. Bonvin and Francesca Cantini, date: 10/20/2020, view: 136, Q&A: 0
    This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ...
    Measurement of Ascorbic Acid and Glutathione Content in Cyanobacterium Synechocystis sp. PCC 6803
    [Abstract] Ascorbic acid (AsA) and gluthathione (GSH) are two key components of the antioxidant machinery of eukaryotic and prokaryotic cells. The cyanobacterium Synechocystis sp. PCC 6803 presents both compounds in different concentrations (AsA, 20-100 μM and GSH, 2-5 mM). Therefore, it is important to have precise and sensitive methods to ...
    Quantification of Salivary Charged Metabolites Using Capillary Electrophoresis Time-of-flight-mass Spectrometry
    Authors:  Masahiro Sugimoto, Sana Ota, Miku Kaneko, Ayame Enomoto and Tomoyoshi Soga, date: 10/20/2020, view: 79, Q&A: 0
    [Abstract] Salivary metabolomics have provided the potentials to detect both oral and systemic diseases. Capillary electrophoresis time-of-flight-mass spectrometry (CE-TOFMS) enables the identification and quantification of various charged metabolites. This method has been employed to biomarker discoveries using human saliva samples, especially for various ...
    Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations
    Authors:  Andrea Saponaro, Vincenzo Maione, Alexandre M. J. J. Bonvin and Francesca Cantini, date: 10/20/2020, view: 136, Q&A: 0
    [Abstract] This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical ...
    Radioactive Assay of in vitro Glutamylation Activity of the Legionella pneumophila Effector Protein SidJ
    Authors:  Alan G. Sulpizio, Jung-Ho Shin, Marena E. Minelli and Yuxin Mao, date: 10/05/2020, view: 266, Q&A: 0
    [Abstract] The Legionella effector protein SidJ has recently been identified to perform polyglutamylation on another Legionella effector, SdeA, ablating SdeA’s activity. SidJ is a kinase-like protein that requires the small eukaryotic protein calmodulin to perform glutamylation. Glutamylation is a relatively uncommon type of ...
    A Protocol for Flavonols, Kaempferol and Quercetin, Staining in Plant Root Tips
    Author:  Nguyen Hoai Nguyen, date: 10/05/2020, view: 316, Q&A: 0
    [Abstract] Flavonols are a subclass of flavonoids of the group of plant secondary metabolites. In planta, flavonols play various functions such as antioxidant and natural regulator of auxin polar transport. Many lines of evidence have shown that flavonols also contribute to human health in anti-oxidation, anti-inflammation, and even prevention some ...
    Expression and Purification of Arabidopsis Transmembrane Protein BCM1 in Saccharomyces cerevisiae
    Authors:  Peng Wang and Bernhard Grimm, date: 09/20/2020, view: 300, Q&A: 0
    [Abstract] Heterologous expression and purification of transmembrane proteins have remained a challenge for decades hampering detailed biochemical and structural characterization of key enzymes and their interacting regulators in multiple metabolic pathways. An in-depth study on the newly identified Arabidopsis thaliana integral membrane protein ...
    Novel Protein-oligonucleotide Conjugation Method Involving a High-affinity Capture HaloTag
    Author:  Junshi Yazaki, date: 09/20/2020, view: 390, Q&A: 0
    [Abstract] Highly sensitive quantitative protein profiling can play a key role in the early diagnosis of diseases, such as autoimmune diseases and cancer. We developed a modified protein-oligonucleotide conjugation method termed HaloTag-mediated barcoding, for quantifying protein molecules at a higher sensitivity than conventional protein quantification ...
    In vitro AMPylation/Adenylylation of Alpha-synuclein by HYPE/FICD
    Authors:  Ali Camara, Anwesha Sanyal, Sayan Dutta, Jean-Christophe Rochet and Seema Mattoo, date: 09/20/2020, view: 349, Q&A: 0
    [Abstract] One of the major histopathological hallmarks of Parkinson’s disease are Lewy bodies (LBs) –cytoplasmic inclusions, enriched with fibrillar forms of the presynaptic protein alpha-synuclein (α-syn). Progressive deposition of α-syn into LBs is enabled by its propensity to fibrillize into insoluble aggregates. We recently described a marked reduction ...
    A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry
    Authors:  Natarajan V. Bhanu, Simone Sidoli and Benjamin A Garcia, date: 09/20/2020, view: 479, Q&A: 0
    [Abstract] Chromatin modifications, like histone post translational modifications (PTMs), are critical for tuning gene expression and many other aspects of cell phenotype. Liquid chromatography coupled to mass spectrometry (LC-MS) has become the most suitable method to analyze histones and histone PTMs in a large-scale manner. Selected histone PTMs have ...
    Fluorescent Polysome Profiling in Caenorhabditis elegans
    Authors:  Dan Shaffer and Jarod A Rollins, date: 09/05/2020, view: 713, Q&A: 0
    [Abstract] An important but often overlooked aspect of gene regulation occurs at the level of protein translation. Many genes are regulated not only by transcription but by their propensity to be recruited to actively translating ribosomes (polysomes). Polysome profiling allows for the separation of unbound 40S and 60S subunits, 80S monosomes, and actively ...



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