Comparing Protein Structure And Sequence

Protein Structure

In order to better understand the structure conservation between aligned molecules, certain tools involving the coloring of molecules are used within Multiple Alignment. In particular, Q per residue measures structure conservation. Structure conservation occurs when the structures between aligned proteins are similar.

Q per residue, is accessed by:

1

Click on the View menu on the Multiple Alignment window.

2

Select Molecule Coloring.

Figure 7: Molecule Coloring

When you select Molecule Coloring another side menu should appear with the following options: Q per residue and Sequence Identity per residue.

Select Q per residue to visualize structural conservation. Look at the OpenGL Display window to see the impact this selection has made on the molecules.
 

Figure 8: Structure Conservation

 
You will probably notice that several portions within the interior of the aligned molecules have turned blue. Rotate the molecule to see how much of it has turned blue. The blue areas indicate that the molecules are structurally conserved at those points. The red regions are not structurally conserved, and these correspond to insertions, which are typically found on the periphery of the molecule as shown in Figure 7 of O'Donoghue et al.
 

Protein Sequence

Now that we have examined the structural conservation between the molecules, it is important to examine the sequence conservation. Sequence conservation occurs when amino acid identity of the aligned residues match.
In order to access Sequence Identity per residue:

1

Click on the View menu.

2

Select Molecule Coloring $\rightarrow$ Sequence Identity per residue.

Figure 9: Sequence Identity per residue

 
Now take a look at the OpenGL Display window. As you can see, the majority of the aligned molecules have turned red. Notice that only 10 residues are strictly conserved (blue), and these areas are important for catalysis and dimerization.

Figure 10: Sequence Conservation

 
The coloring of the molecules using Sequence Identity per residue indicates that the sequence conservation is much less in comparison to the structural conservation. This may be difficult to see right now. However, in Residue Selection sequence conservation is easier to observe, using the Sequence Display.

 
To examine the relationship between sequence and structure in more detail, we will use the Residue Selection feature.