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!.

Backbone representation

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

3D-Superposition

When the 3D-view is clicked, then the 3D-menu-bar is shown. The alignment-menu-bar is re-installed when the alignment-pane is clicked. There is a menu-item "Superimpose". Activate this menu-item to move the protein chains in 3D-space together. Advanced users can also use BUTTON:DialogSuperimpose3D! which provides more options.

Aligning the proteins

Press the button BUTTON:StrapView#button(BUT_ALIGN)!.

Visualization of 3D-distance in the alignment

3D-distances between C-alpha atoms can be visualized in the alignment pane. This is 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. You should see a highlighting around the cursor position. This highlighting moves together with the cursor. Since all proteins are in the same coordinates the structurally equivalent positions in all proteins are highlighted together.

Multiple alignment

With the dialog BUTTON:DialogAlign! you can compare the different alignment algorithms regarding their capability to align these three proteins. To evaluate the alignment results you can use the WIKI:Protein_structure#Secondary_structure. Select "secondary structures" in JCOMPONENT:StrapView#choiceShading()!.