Protein Structure

In order to better understand the structural conservation between aligned molecules, certain tools involving the coloring of molecules are used within MultiSeq. 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 MultiSeq 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.