Phylogenetic Tree

The Phylogenetic Tree feature, in the Multiseq program, elucidates the structure-based relationships between the four aquaporins considered.
 
Structure based phylogenetic trees can be constructed according to the RMSD or Q values between the molecules after alignment. Here we use the Q values to obtain the phylogenetic tree of four aquaporins.

To utilize this feature:

1

Align the structures again, by going to the Multiseq program window and selecting Tools $\rightarrow$ Stamp Structural Alignment.

2

In the Stamp Structural Alignment window, select All Structures, and keep the default values for the rest of the parameters. Press the OK button to align the structures.

3

In the Multiseq program window choose Tools $\rightarrow$ Phylogenetic Tree. The Create Phylogenetic Tree dialog will appear (Fig. 31).

Figure: Create Phylogenetic Tree window.

Here you can choose to construct a structure based phylogenetic tree according to the $Q_H$ values or RMSD. $Q_H$ is a variation of Q (see below) that accounts for both gapped and aligned regions.

Figure: Structure-based phylogenetic tree, for the aquaporins in Table 1.2.

4

Select Structural tree using $Q_H$, and press the OK button. A phylogenetic tree based on the $Q_H$ values will be calculated and drawn as shown in Figure 32. Here you can see the relationship between the four aquaporin, e.g., how the E.Coli AqpZ (1r2c) is related to human AQP1 (1fqy). Identify bovine and human aquaporins in the Tree.

5

You can choose to construct the phylogenetic tree of the four aquaporins based on their sequence information, and will be discussed further is section 8.

6

You can close the Phylogenetic tree window.

7

Quit VMD.