Comparing Protein Sequence and Structure

In this unit you will study the structure and sequence conservation of the different aquaporins you have aligned in the Multiseq window. Conservation is a term we will use frequently in exercises from this point forward. Within the context of protein analysis, conservation refers to high levels of similarity contingent on the employed metric. Structure conservation occurs when the structural aspects (e.g. $\alpha$ helix, $\beta$ sheets), of the aligned proteins are highly similar. Likewise, sequence conservation happens when at certain points of the aligned protein molecules the amino acid of each molecule is the same.

Protein Structure

In order to better understand the structural conservation within the aligned molecules, Multiseq provides tools that allow you to color the molecules according to their Q value (Qres), a measure of structural conservation.

You will now color the molecules according to the value of Q per residue obtained in the alignment.

1

In the Multiseq program window, choose the View $\rightarrow$ Coloring $\rightarrow$ Qres (Fig. 13).

Figure: Molecule Coloring

2

Look at the OpenGL window to see the impact this selection has made on the coloring of the aligned molecules (Figure 14).

Figure: Molecules colored by Qres value

Rotate the molecule to see how much of it has turned blue. Notice that the transmembrane helices of the aligned molecules have turned blue. The blue areas indicate that the molecules are structurally conserved at those points. If there is no correspondence in structural proximities at these points, the points appear red. Observe how the structurally least similar segments tend to be on the periphery of the aligned molecule. Note that the loops tend to be red, while the helices are blue.

Protein Sequence

You have examined the structural similarity between the molecules. Now you will look at the sequence conservation. Multiseq has a feature to color the molecules according to how much the sequence is conserved within the aligned molecules. This tool, Sequence identity, colors each amino acid according to the degree of conservation within the alignment: blue means highly conserved, whereas red means very low or no conservation.

1

Choose View $\rightarrow$ Coloring $\rightarrow$ Sequence Identity.

Before you look at the viewer window, can you anticipate what will happen to the coloring of the molecules? Will the molecules still be blue in the transmembrane region, as they were when Qres was used to determine structure conservation?

2

Now take a look at the viewer window. As you can see (Fig. 15), a fair portion of the molecules has turned red, indicating less sequence conservation than structural similarity.

Figure: Molecules colored by sequence identity

3

Note that the residues at the site where the two short helices interact are blue. Look at the molecules from the top (c.f. Fig. 16). Do you notice the blue residues tend to be on the inside of the pore?

Figure: Conserved residues (shown in blue) are located inside the pore.

Note that the coloring of the molecules using Sequence Identity indicates that the sequence conservation is much less in comparison to the structural conservation. Sometimes structures from the same family have less than 10% sequence identity, yet are structurally similar. A well known example is the protein myoglobin that we recommend for self-study.

To examine the relationship between sequence and structure in more detail, in the next section you will use the Select Residues feature.