This document describes a study that used a yeast two-hybrid system to map protein-protein interactions (PPIs) in the human proteome. Over 5,500 human proteins were analyzed, revealing a network of over 3,000 high-confidence PPIs connecting 1,700 proteins. These PPIs were validated using biochemical methods like pull-down assays and bioinformatics analyses. The network provides new insights into human disease mechanisms and functions of previously uncharacterized proteins.

2. - molecular genetic tool to study protein-protein interactions
- if two proteins interact, then a reporter gene is transcriptionally activated
- Gal4 protein, transcriptional activator composed of two domains with distinct functions
1. DNA binding domain, interacts with promotor (bait) 2.
1. polymerase
2. Activating domain, interacts with polymerase (prey) promoter reporter gene
- the yeast Gal4 gene is split in two parts, each of which fused to one of the
interacting partners to be tested
- if proteins interact: reporter gene is transcribed
2.
- HIS3, URA3, lacZ reporters 1. polymerase
promoter reporter gene

3. - PPIs (protein-protein interactions) are crucial for all biological processes
- human PPIs: generic organisational principles, understanding disease
mechanisms and signalling cascades
- proteome-wide studies for model organisms, but not for human proteome
- human proteome: only more specific interaction maps, e.g. TGF- β
- other approaches: bioinformatic analyses, e.g. hypothesis-driven or based on
conserved orthologous interactions
- here: PPI map describing a representative part of human interactome
- > 5500 proteins analysed by high-throughput yeast-two hybrid sceens
- network connecting 1705 proteins via 3186 interactions
- validated biochemically (pull-down and co-immunoprecipitation) and by
bioinformatics analyses

4. 3510 bait and 3589 prey 2033 bait and 2051 prey
1. Creation of human protein
11,183 clones
Matrix in yeast
three different
reporter genes
2. High-throughput Y2H
3. Confirmation with individual
reaction partners
> 25 million protein pairs examined!

5. verification
- representative sample of interactions, randomly selected
- 116 protein pairs were tested by membrane coimmunoprecipitation:
success rate 62%
- 131 protein pairs were tested by pull-down assay:
success rate 66%
properties of the Y2H network
- mean shortest path length between any two proteins: 4.85 links
- average interaction partners per protein in network: 1.87
- 804 proteins with one partner, 24 hubs-proteins with > 30 partners
- hubs 3x more likely to be essential for cells

6. confidence scoring
1. PPI activates three reporter genes (HIS3, URA3, lacZ)
2. PPI is found in human interaction clusters
3. PPI is found in orthologous D. melanogaster clusters
4. PPI is found in orthologous C. elegans clusters
5. PPI is found in orthologous S. cerevisiae clusters
6. PPI is formed of two proteins sharing GO annotation
--> network of high-confidence interactions (3186 among 1706 proteins)
with >3 points

7. - >3000 PPIs
- 911 supported by ‘confidence scoring”
- 159 verified biochemically
- 195 disease proteins with previously unidentified partners
- interactions of 342 previously uncharacterised proteins
- new roles for known proteins

8. www.mdc/berlin.de/neuroprot/database.htm

10. … have fun!
the end.