1. Protein-protein interactions

2. Three types of interactions
Interactions between domains in multidomain proteins
Interactions between the domains in stable complexes
Interactions between proteins in transient interactions

3. Stable complexes
The proteins in stable complexes tend to be more closely co-expressed and more closely conserved compared to proteins in transient interactions and monomeric proteins

4. Yeast-two-hybrid screens
Uses the transcription of a reporter gene driven by the Gal4 transcription factor to monitor whether or not two proteins are interacting

5. Yeast-two-hybrid screens
RNApol B A
Gal4-AD
Gal4-DBD
DBD = transcription factor
AD = activation domain

6. Yeast-two-hybrid screens
RNApol B A
Gal4-AD
Gal4-DBD
Reporter gene
DBD = transcription factor
AD = activation domain

7. Computational methods
Conservation of gene order
In prokaryotes, genes are organized into operons of co-regulated and co-expressed groups of genes
Genes that are consistently part of the same operon across different, distantly related genomes are likely to be part of the same protein complex or functional process across all species
They have been selected to remain as a co-regulated unit throughout the extensive shuffling of gene order that takes place in prokaryote genomes

8. Computational methods

9. Computational methods
Gene fusions
Look for cases across a set of genomes where two or more orthologs are part of the same gene in one genome, presumably as a result of gene fusion
The prediction is that the orthologs that are separate genes in other genomes interact with each other
Fused proteins are not only co-regulated, as in the conservation of gene order, but also permanently co-localized in the cell
This method is limited to certain classes of protein-protein interactions:
members of the same stable complex
proteins in the same metabolic pathway

10. Computational methods
yeast
E. coli

11. Computational methods
Phylogenetic methods
Relies on the detection of homologs in a set of genomes
If the pattern of homolog presence or absence is the same in a group of proteins, then these proteins are clustered together as belonging to the same functional class

12. Computational methods
Predicted to interact
Gene 1
Gene 2
Gene 3
Gene 4
Gene 5
Gene 6
Genome 1
Genome 2
Genome 3
Genome 4

13. Protein chips
Miniature devices on which proteins, or specific capture agents that interact with proteins, are arrayed
Protein chips can act to
separate proteins on the basis of specific affinity
characterize proteins if the capture agent is highly specific (e.g., antibodies)
Advantage: ultra-high throughput analysis

14. Protein chips Antibody chips Antigen chips Universal protein arrays
Arrayed antibodies used to detect and quantify specific proteins
Antigen chips
Arrayed protein antigens used to detect and quantify antibodies
Universal protein arrays
Any kind of proteins arrayed to detect or characterize protein-protein and protein-ligand interactions
Protein capture chips
Arrayed non-protein capture agents
Solution arrays
Coded microspheres or barcoded nanoparticles  next generation

15. Protein chips