How can Artemis provide structural data of a gene?

It is possible to use Artemis to display certain characteristics of a gene that is of interest.

In the ‘View’ menu, select the ‘Feature Plots’ option. This selection will open an additional window with three plots:

• Top Plot: hydrophobicity
• Middle Plot: hydrophilicity
• Bottom Plot: coiled-coil regions

All of these are applied to the protein product of the selected gene. In each plot the amino acid position is represented in the x-axis.

These plots are made based on the amino acid predictions from the DNA sequence. Although amino acid sequences may be included in the annotation files, Artemis derives its own amino acid prediction based on the DNA sequence of a CDS or gene.

Based on this predicted amino acid sequence, it is possible to calculate the hydrophobicity, hydrophilicity and the probability of coiled-coil regions in the protein product.

Hydrophobicity or hydrophilicity?

Hydrophobicity (‘phobia’ of water) and hydrophilicity (‘love’ or ‘attraction’ to water) are calculated based on how hydrophobic or hydrophilic an amino acid is. Clusters of amino acids with high hydrophobicity will render regions of high hydrophobicity.

Observe the top and middle plots and appreciate that because they represent opposite characteristics, these two plots look almost like mirror images of each other.

Coiled-coil protein domains form conserved structures that have important biological functions. For example, several proteins that are known to interact with DNA do so through their coil-coil domains. If you are interested; you can read more about Coiled-coil domains in this Wikipedia article.

The bottom panel in the Features Plot represent the probability of of each amino acid to be part of a coil-coil domain. Notice that the y-axis ranges between 0 and 1 (approximately). The closer to 1 the more likely that the CDS has a coil-coil domain.