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.