Open main menu

Biolecture.org β

Proteomics-OG

What is proteome? the entire set of proteins expressed by a genome, cell tissue, or organism at a certain time.

Type

  • cellular proteome : the collection of proteins found in a particular cell type 
  • complete proteome : whole set of proteins 

 

proteomics : study of proteome

 

 

How to study the proteome

 

  • separation >> gel electrophoresis
    • isoelectric focusing (charge) + SDS-PAGE (molecular weight) --> gel dyed with comassie blue to visualization
  • How to know their identity (their component, amino acids sequence ) >> mass spectroscopy
    • Peptide mass fingerprinting : cleave the protein into short peptides --> deduce the protein's identity based on sequence database
    • Tandem mass spectrometry : isolate individual peptides --> collide them with non-reactive gas --> cataloguing the [fragment ion] produced (by detecting ion, they can deduce the identity of peptides)

 

methods

  • cryo-electron microscopy 
    • what ? TEM studied at cryogenic temperature
    • advantage : do not require crystallization / relatively easy
    • disadvantage : low resolution
  • microscopy
    • source: reflection , diffraction of electromagnetic radiation beams interacting with the specimen
    • Types : TEM  / SEM
    • disadvantage : limitation of resolution    / show specimen by only dark or light color
  • NMR 
    • source : nuclear magnetic resonance. It means that electromagnetic radiation that nuclei absorb and re-emit. this radiaction is in the state of specific resonance frequency 
    • frequency is directly proportional to the strength of the magnetic field
    • type 
      • Solid-state NMR spectroscopy
      • Multi-dimensional NMR spectroscopy
      • Fourier-transform spectroscopy
      • CW spectroscopy

 

 

protein structure

  • a-helix
  • b-strand
  • coil (irregular, antibody for binding)

 

 

Post translational modifications

  • Glocosylation
  • Phosphorylation
  • SUMOylation

 

experimental methods >> identifying proteins

 

  • way 
    • One-dimensional SDS-PAGE
    • two-dimensional SDS-PAGE

 

Interaction proteomics

  • application
    • signal transduction / trafficking / cell cycle/ gene regulation
  • detection
    • Chips / Microarray

 


reference

1) https://en.wikipedia.org/wiki/Proteomics

2) http://www.slideshare.net/COST-events/proteomics-analysis-basics-and-applications