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Introduction to Proteomics

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Introduction to Proteomics – PowerPoint PPT presentation

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Date added: 9 October 2019
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Title: Introduction to Proteomics


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Introduction to Proteomics
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  • First issue of Proteomics- Jan. 1, 2001

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  • abcNEWS.com- April 27 Genes may be the stuff
    of life, but they're not the whole story.
    Scientists wrapping up the mammoth task of
    decoding the human genome say the next step will
    be understanding the "proteome" the proteins
    that genes help make.

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Search the Database for a protein match?
  • How? Explain.

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Peptide Mass Fingerprinting
  • Developed 1993
  • Today- automated (including Database Searches)
    ? 500 proteins/day analyzed (one lab)
  • Goal- annotated 2D gel map.

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MS-MS
  • Peptide fingerprints are sufficient ot identify
    proteins only in cases where the sequence of a
    protein is already in a database. MS-MS can
    obtain partial sequence info. from each peptide
    in the fingerprint. Within the mass
    spectrometer, each peptide can then be further
    broken down in to ionized fragments. The goals
    is to produce a ladder of fragments each
    differing in length by one aa. Because each aa
    has different MW, the sequence of each peptide
    can be deduced.

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  • What is DiGE?
  • labeling two protein samples to be compared with
    different fluorescent dyes, and then mixing the
    samples before application onto the same 2D gel.
    The same isoform of a given protein from each
    sample will thus migrate to same position on the
    2D gel. The relative abundance of each protein in
    each sample can then be obtained by scanning the
    gel using excitation and emission wavelengths
    unique to each dye used. This technique known as
    DiGE or differential gel electrophoresis has been
    pioneered by the Minden group at Carnegie Mellon
    University in Pittsburg and relies on the use of
    the NHS esters of Cy3 and Cy5 binding to a small
    fraction of lysine residues within a protein
    sample.

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  • ExPASy Molecular Biology Server

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The primary objective of KEGG is to computerize
the current knowledge of molecular interactions
namely, metabolic pathways, regulatory pathways,
and molecular assemblies.
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Current Questions?
  • Are pathways identical across species?
  • Do some speciez have alternative pathways to
    generic ones?
  • Are certain enzymes in pathway more important
    than other ones?

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  • Kyoto Encyclopedia of Genes and Genomes

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The Future is Looking Very Small
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BIOCHEMISTRY Protein Arrays Step Out of DNA's
Shadow
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Protein arrays
  • Early progress has been slow proteins are harder
    to synthesize than DNA, and plunking them down on
    solid surfaces tends to cause them to unfold and
    thereby lose their activity. Now, however, those
    barriers appear to be crumbling. On page 1760 of
    this issue, researchers at Harvard University
    report creating arrays of over 10,000 proteins on
    a piece of glass just half the size of a
    microscope slide. They then used their arrays to
    study a variety of protein functions, work that
    included identifying members of the array that
    bind to other free-floating proteins and to
    small, druglike molecules.

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  • Once protein microarrays are perfected,
    researchers will be able to measure the functions
    of thousands upon thousands of proteins
    simultaneously, and rapidly screening them all
    for new drug targets. It also will be
    (relatively) easy to take a potential drug
    candidate and screen all the metabolic pathways
    to check for unwanted reactions. But that's the
    future -- and it's barely begun.

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The End
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