Systems Biology


    Protocols in Current Issue
    Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics
    Authors:  Vidyasiri Vemulapalli, Stephen C. Blacklow, Steven P. Gygi and Alison Erickson, date: 02/05/2022, view: 1199, Q&A: 0

    Cells sense and respond to mitogens by activating a cascade of signaling events, primarily mediated by tyrosine phosphorylation (pY). Because of its key roles in cellular homeostasis, deregulation of this signaling is often linked to oncogenesis. To understand the mechanisms underlying these signaling pathway aberrations, it is necessary to

    Differential Analysis of N-glycopeptide Abundance and N-glycosylation Site Occupancy for Studying Protein N-glycosylation Dysregulation in Human Disease
    Authors:  Qi Zhang, Cheng Ma, Lian Li and Lih-Shen Chin, date: 06/20/2021, view: 1992, Q&A: 0

    Protein N-glycosylation plays a vital role in diverse cellular processes, and dysregulated N-glycosylation is implicated in a variety of human diseases including neurodegenerative disorders and cancer. With recent advances in high-resolution mass spectrometry-based glycoproteomics technologies enabling large-scale N-glycoproteome profiling of

    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 6358, Q&A: 3
    [Abstract] Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a ...
    A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae
    Authors:  Daniel J. H. Nightingale, Kathryn S. Lilley and Stephen G. Oliver, date: 07/20/2019, view: 4483, Q&A: 0
    [Abstract] The correct subcellular localization of proteins is vital for cellular function and the study of this process at the systems level will therefore enrich our understanding of the roles of proteins within the cell. Multiple methods are available for the study of protein subcellular localization, including fluorescence microscopy, organelle ...
    Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila
    [Abstract] Advanced mass spectrometry technology has pushed proteomic analyses to the forefront of biological and biomedical research. Limitations of proteomic approaches now often remain with sample preparations rather than with the sensitivity of protein detection. However, deciphering proteomes and their context-dependent dynamics in subgroups of ...
    Character-State Reconstruction to Infer Ancestral Protein-Protein Interaction Patterns
    Authors:  Florian Rümpler, Günter Theißen and Rainer Melzer, date: 08/20/2015, view: 11804, Q&A: 0
    [Abstract] Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal ...
    A Phosphopeptide Purification Protocol for the Moss Physcomitrella paten
    Authors:  Xiaoqin Wang and Yikun He, date: 07/20/2015, view: 8466, Q&A: 0
    [Abstract] Protein phosphorylation is one of the most common post-translational modifications in eukaryotic cells and plays a critical role in a vast array of cellular processes. Efficient methods of protein extraction and phosphopeptide purification are required to ensure the detection of high quality of proteins. In our hands, phenol extraction of proteins ...
    Protocol for Preparation of Nuclear Protein from Mouse Lungs
    Authors:  Zuoxiang Xiao and Qun Jiang, date: 06/05/2014, view: 12937, Q&A: 0
    [Abstract] This protocol describes how to extract nuclear protein from mouse lungs, including tissue preparation, stepwise lysis of cells and centrifugal isolation of nuclear protein fraction. This is an efficient method to get comparable nuclear protein extracts from lung tissues.
    Protein Sample Preparation for Proteomic Analysis in Leishmania donovani
    Authors:  Alexandros Alexandratos and Despina Smirlis, date: 03/05/2014, view: 9940, Q&A: 0
    [Abstract] Leishmania is a genus of trypanosomatid protozoa and is the parasite responsible for the disease leishmaniasis. These protozoa, regulate their gene expression in an atypical way, compared to other higher eukaryotes. The regulation of gene expression is characterized by a predominance of post-transcriptional over pre-transcriptional ...
    Isolation of the Secretome from Bacillus subtilis
    Authors:  Juri Niño Bach and Marc Bramkamp, date: 01/20/2014, view: 10028, Q&A: 2
    [Abstract] Bacteria are commonly known to secret proteins in large amounts into the surrounding environment in high concentrations via various pathways. These proteins can be involved in numerous processes like cell-cell communication, exopolymer formation but also metabolic active enzymes are secreted that are interesting for industrial production of ...

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