Proteomics

Proteomics can be broadly defined as the large-scale study of proteins whose ultimate goal is to understand the function of each protein and how the cell works.

Much effort is currently put on:

• Determination of protein interactions ("cell-mapping proteomics"), using e.g. Y2H or protein chips, in order to build a picture of the complex network that constitute intracellular signaling pathways.
• "Protein expression proteomics": monitors global expression of large numbers of proteins within a cell type or tissue, and quantitatively identifies how patterns of expression change in deifferent circumstances.

Technologies

2D-PAGE, Two-dimensional polyacrylamide gel electrophoresis

It is a technics used to separate a set of proteins in two dimensions based on their charge and their mass. Widely used to monitor the protein expression profiles.

Limitations:

• inability to detect proteins of medium or low abundance

Y2H, yeast 2-hybrid system

The goal is to identify protein-protein interactions in vivo, without handling any protein molecules at all. It has been used to build interaction maps between all ORFs of the yeast.

Two groups published interaction maps (Ito group at Kanazawa University, 841 interactions, and Curagen, New Haven, CT, USA, 691 interactions). Unfortunately the results barely overlap... (141 interactions are shared).

The technics is based on the molecular architecture transcription factors (TF), split into two parts:

• a DNA-binding domain,
• a trans-activation domain.

Limitations:

• many false positives (because the reporter can be expressed in some cases without a real interactions between the proteins)
• membrane proteins missed
• transcription factors cannot be tested
• post-translational modifications missed
• some proteins don't fold correctly as hybrids