Introduction

PACKAGE:charite.christo.strap.extensions. This tutorial shows how protein structures can be superimposed three-dimensionally and how a multiple sequence alignment can be computed from WIKI:Structural_alignment. The three proteins of this tutorial PDB:1eje, PDB:1axj and PDB:1nrg can be loaded with the dialog BUTTON:DialogFetchPdb! (Or you can simply click).

Backbone representation

Select the three proteins and open the 3D-backbone with the tool-button JCOMPONENT:StrapView#button(BUT_3D)!. The three proteins are at different coordinates in 3D-space.

3D-Superposition

When the 3D-view is clicked, then the 3D-menu-bar appears. Click the menu-item "Superimpose" to superimpose the proteins. Also try the dialog BUTTON:DialogSuperimpose3D! which provides more options.

Aligning the proteins

Press the button BUTTON:StrapView#button(BUT_ALIGN)!. Since the sequences differ, the alignment can be best evaluated with "Secondary structure" in the choice menu JCOMPONENT:ShadingAA#choice()! for residue coloring.

Visualization of 3D-distance in the alignment

3D-distances between C-alpha atoms can be visualized in the alignment pane. This option can be used for proteins that had been superimposed. Select COMBO:Distance3DToCursor in the dialog BUTTON:DialogSelectionOfResiduesMain! and select all proteins. Click into the alignment pane. Residues in spatial neighborhood to the cursor position are highlighted. This highlighting is updated when the cursor is moved.