Introduction

A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of development (morphogenesis) in animals, fungi and plants. Homeodomain proteins are transcription factors that bind bind DNA. In this example we assume, that the protein structure PDB:2E1O should be analyzed in the complex with DNA. Unfortunately, there is no DNA structure recorded in PDB:2E1O. Here we show, how the DNA structure from a related structure can be copied.

Visualization of the example structures

First download PDB:2E1O and PDB:1IG7. This can be done by clicking these two links in this document. For loading, it should be clicked right from the colon, otherwise the proteins are opened in the browser instead. Please note the mouse pointer either saying "Load" or showing a Web-browser symbol. To look at these two structures individually, select the structures and click JCOMPONENT:StrapView#button(BUT_WIRE)! in the tool-bar.

3D-Superposition

By pressing the toolbar-button BUTTON:StrapView#button(BUT_ALIGN)!, the two sequences can be aligned. They amino acid sequences do not look very similar. But the helices (red in the alignment) are well aligned, indicating, that the alignment is correct.

Using WIKI:Drag_and_drop, the two proteins can be dragged into the same 3D view. Initially, they are not aligned three-dimensionally. Use the menu "Superimpose" of the 3D-view both peptide chains can be superimposed three-dimensionally. It is undetermined whether 2E1O is moved upon 1IG7 or the other way round. In the first case, a structure composed of the transfered peptide chain 2E1O and the DNA of 1IG7 in original coordinates will be created. In the second case the peptide of 2E1O will stay but the DNA will move.

If you wish control, then you should use the dialog BUTTON:DialogSuperimpose3D!. For this dialog it is important to know, that the superposition results are shown as a preview. For the result to take effect, the button BUTTON:DialogSuperimpose3D#BUT_LAB_Apply needs to be pressed.

Transferring the DNA

After superposition, the two peptide chains coincide in 3D. This is the precondition that the DNA can be copied from 1IG7 to 2E1O. For this purpose, open the context menu of 1IG7 by right click. Find the item "Child objects/List nucleotide chain structures ...". This opens a list representation of all DNA/RNA objects. In this case you find two DNA chains since the DNA in 1IG7 is double stranded. Drag the two DNA-molecules with the to 2E1O. Check the result by opening a 3D view of only 2E1O. You should see DNA and protein.

File Export

Open the dialog BUTTON:DialogExportProteins! and select 2E1O. Chose PDB-format and press the Go-button. The resulting protein file can now be inspected (right click for file context menu) or used for other programs.

For example energy minimization by molecular dynamics could be used to improve the interface between DNA and protein.