Bacteriophage T4

Protein interaction mapping

8/1/03. By Richard Twyman

The function of a newly discovered protein can often be established by identifying its interaction partners, if their functions are already known.

One of the best ways to determine the function of a newly discovered protein is to identify its friends. For example, if uncharacterised protein X interacts with proteins Y and Z, both of which are required for cell division to occur normally, it is likely that protein X is also involved in this process.

Proteins linked in functional networks may represent useful drug targets. If protein X is the product of a human disease gene and turns out to be an ineffective drug target, proteins Y and Z may be useful alternative targets because they are involved in the same process.

How are protein interactions studied? There are many methods that can be used to study individual interactions but only a few are suitable for analysis at the level of the proteome. Two widely used technologies are described below. In addition, mass spectrometry can be used to identify all of the components in an isolated complex of proteins.

Yeast two-hybrid system

The yeast two-hybrid system exploits protein interactions to assemble a functional transcription factor. The transcription factor then activates a test gene, allowing yeast cells containing interacting proteins to be identified. The principle of the method can be summarised as follows:

  • Transcription factors are proteins required for gene expression. They have at least two functional domains: a DNA-binding domain and a transcriptional activation domain.
  • The function of protein X is unknown. The sequence of protein X is joined to the sequence of a transcription factor's DNA-binding domain and expressed in one strain of yeast cells to produce a hybrid protein known as the bait.
  • All the other genes in the genome are expressed as hybrid proteins with the transcription factor's transcriptional activation domain. This forms a library of potential prey.
  • In a large-scale cross, the bait yeast strain is mated to each member of the prey library, so all possible interactions are tested in the resulting cells.
  • In those cells where the bait interacts with the prey, a functional transcription factor is assembled and the test gene is activated.

The two-hybrid system can be scaled up so that multiple baits can be tested. For example, every yeast protein has been used as a bait and tested systematically against every other yeast protein. There are at least 6000 proteins in yeast and this represents 36 million possible interactions.

Phage display

Like the two-hybrid system, phage display is used for the high-throughput screening of protein interactions. The principle of this method is summarised as follows:

1 The function of protein X is unknown. The protein is used to coat the surface of a small plastic dish.

2 All the other genes in the genome are expressed as fusions with the coat protein of a bacteriophage (a virus that infects bacteria), so that they are displayed on the surface of the viral particle.

3 This phage-display library is added to the dish. After a while, the dish is washed.

4 Phage-displaying proteins that interact with protein X remain attached to the dish, while all others are washed away. DNA extracted from interacting phage contains the sequences of interacting proteins.

Image credit: David Grgory and Debbie Marshall

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