Transcript Protein-protein interactions - Brigham Young University

Protein-protein interactions
Three types of interactions
• Interactions between domains in
multidomain proteins
• Interactions between the domains in stable
complexes
• Interactions between proteins in transient
interactions
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
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
Yeast-two-hybrid screens
Gal4-AD
A
B
RNApol
Gal4-DBD
DBD = transcription factor
AD = activation domain
Yeast-two-hybrid screens
Gal4-AD
A
B
Reporter gene
RNApol
Gal4-DBD
DBD = transcription factor
AD = activation domain
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
Computational methods
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 colocalized in the cell
– This method is limited to certain classes of proteinprotein interactions:
• members of the same stable complex
• proteins in the same metabolic pathway
Computational methods
yeast
E. coli
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
Computational methods
Predicted to interact
Gene 1
Genome 1
Genome 2
Genome 3
Genome 4
Gene 2
Gene 3
Gene 4
Gene 5
Gene 6
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
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 proteinprotein and protein-ligand interactions
• Protein capture chips
– Arrayed non-protein capture agents
• Solution arrays
– Coded microspheres or barcoded nanoparticles  next
generation
Protein chips