Phylogenetic Tree

Determining Structure-based Relationships

The Phylogenetic Tree feature in Multiple Alignment helps in determining the structure-based relationships between the four AARSs. To do this, it uses a modification of Q that accounts for both gapped and aligned regions. This new metric, $Q_H$, creates a structure-based phylogeny that is congruent to the sequence-based phylogenies of AARSs previously reported by Woese et al.⁵ (also see Ref. 1).

 
To utilize this feature:

1

Go to Tools $\rightarrow$ Phylogenetic Tree. A new window entitled Phylogenetic Tree will open.

2

To display the structure-based Phylogenetic Tree with appropriate labelling, refer to figure 20.

3

To compute and display the tree, select by which measure - RMSD or QH - you would like to view the tree.

For our first example, let's select all four options at the bottom of the window and use $Q_H$ as our measure to generate the structure-based relationships.

Can you guess as to how the protein molecules will fall relatively to one another on the tree, considering where they fall on the Phylogenetic tree?

Figure 20: Example of structure-based phylogenetic tree.

1.5in

If you guessed that the SerRS would be the furthest out and that the P.kodakaraensis AspRS and S.cerevisiae AspRS would be the closest, you are correct. Note that P.kodakaraensis is from the Archaea branch of the phylogenetic tree and S.Cerevisiae is from the Eucarya. The SerRS is used as an outlier case for this alignment, as demonstrated in Residue Selection.
 
To continue to the next section of the tutorial, close the Phylogenetic Tree window.