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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Tagging and Fusion Proteins01:24

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Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Structure-based barcoding of proteins.

Rahul Metri1, Gaurav Jerath, Govind Kailas

  • 1Institute of Bioinformatics & Applied Biotechnology, Bangalore, 560100, India.

Protein Science : a Publication of the Protein Society
|October 31, 2013
PubMed
Summary
This summary is machine-generated.

A new barcode method simplifies protein structure analysis by converting 3D coordinates into a visual code. This tool aids in comparing protein topology, structural changes, and evolutionary modifications.

Keywords:
barcodefold classificationprotein structure comparison

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Understanding protein topology is crucial for molecular biology.
  • Existing methods for protein structure comparison can be complex.
  • A simplified representation is needed for efficient analysis.

Purpose of the Study:

  • To develop a novel method for representing protein 3D structures as barcodes.
  • To enable facile comparison of protein topology.
  • To illustrate structural changes upon ligand binding and evolution.

Main Methods:

  • Converting Protein Data Bank (PDB) files into an alpha-numero code.
  • Generating a barcode image from the alpha-numero code.
  • Applying the barcode method to compare proteins within and across fold families.

Main Results:

  • A reduced representation of protein topology was achieved via barcodes.
  • The barcode method effectively compares protein structures, including those within the same fold family and across different folds.
  • Illustrations of ligand-induced structural changes and evolutionary modifications were provided.

Conclusions:

  • The barcode representation offers a novel and efficient way to analyze and compare protein structures.
  • This method facilitates the study of protein dynamics and evolution.
  • The associated program is publicly available for download.