Protein-protein interactions

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

6. Gal4-AD A B RNApol Gal4-DBD Yeast-two-hybrid screens 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. yeast E. coli Computational methods

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

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 • 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