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