Creating a peptide bond between two protein structures in Chimera

This tutorial shows the step-by-step procedure to join two protein structures via a new peptide bond

in the Chimera software. A few checks are necessary beforehand.

Both proteins must contain the N/C-terminal nitrogen and carbon atoms to be joined. Some

structures available at the PDB may be lacking these atoms. If that is the case, use a command such

as swapaa (to replace the first or last residue) or addaa (to add N/C-terminal residues, useful if you

intend to have a linker region) to correct the structure file. All of this is done in Chimera.

Be acquainted with Chimera syntax to select the correct atoms. For example, entering the following

in Select > Atom Specifier:

#0:129.B@C

Means “select atom C in residue 129 of chain B in structure model 0”.

# (model number)

: (residue number)

. (chain name)

@ (atom name)

Bear in mind “C” is the name of the atom, not the element. Other carbons in the same residue will

have names such as “CA”, “CB”, etc. By convention, the carbon contained in the peptide bond is

named just “C” and the nitrogen is named “N”. But if something goes wary, check if the

nomenclature in your .pdb file is different.

Here is the step-by-by step procedure to fuse the gPFD structure to the YFP (Venus) structure in

Chimera. The fusion will be done at the C-terminus of gPFD.

1. Open both .pdb files in the same Chimera session. The first model to be opened will be

numbered 0, and the next will be numbered 1.

2. Using Select > Atom Specifier, select the C-terminal carbon of gPFD and the N-terminal

nitrogen of Venus. Since gPFD was opened first (model 0) and Venus was opened next

(model 1), the command will look like this: #0:147.A@C #1:0.A@N – a little unusual, but the

first residue in the Venus structure is numbered “0”.

Note that the N/C-terminal residues of Venus/gPFD are now highlighted. If the representation was

set to showing all atoms instead of ribbons, the exact selected atoms would be highlighted.

3. Open Tools > Structure Editing > Build Structure

4. In the top drop-down menu of the new window, choose Join Models.

5. Tick C-N peptide bond

The Apply option will only be available if two “compatible” nitrogen and carbon atoms have been

selected (sometimes I need to untick and re-tick the C-N peptide bond option). This prevents

mistakes but the action is irreversible.

6. Modify the bond properties if desired. Bond angles can be changed later in Tools > Structure

Editing > Build Structure and then Adjust Torsions or Adjust Bond Angles in the drop-down

menu.

7. Choose whether you want to move Venus to the end of gPFD (i.e. gPFD stays in place) or

conversely. To move Venus, leave the drop-down menu at “selected N atom” (since the

selected nitrogen atom is in the Venus structure).

8. Hit Apply and hope for the best.

As you can see, this results in some clashes where the structures were joined. This can be either

fixed by adjusting bond angles or prevented by including a linker sequence (e.g. using the addaa

command). It’s also much easier to adjust angles in linker sequences since they are meant to be (and

look) unstructured.