In naturally occurring proteins most peptide bonds are in the trans configuration (see Fig. 6). However, sometimes cis peptide bonds do occur. The vast majority of cis peptides is observed at a proline, Xaa-Pro, Xaa being any amino acid. But non-proline Xaa-non Pro cis bonds are also found in proteins, although they occur much less frequently than Xaa-Pro (see A. Jabs et al., JMB, 286, 291-304 (1999)).
![\begin{figure}\begin{center}
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The configuration of the peptide bond is central to the sort of secondary structure the
protein backbone can adopt. It is easy to understand by imagining a normal 
helix
and converting a trans peptide bond into its cis form. The result is that the hydrogen
bond network stabilising the helix is broken (see Fig. 6) and the helix will be unstable in long
simulations.
To demonstrate the usage of the plugin we will start by checking a structure consisting of the protein EF-Tu in complex with a tRNA-Phe, although it is clear that in this example only the protein part will contain peptide bonds. The used structure is based on the the PDB structure 1OB2 in which errors have been introduced manually.
Currently, the cispeptide plugin can be used from the text console and through a GUI. The available commands provided by the pugin can be obtained by typing Type cispeptide. The following information should be printed in the console:
Usage: cispeptide <command> [args...] Commands: check -- identify cis peptide bonds list -- list identified cis peptide bonds minimize -- fix cis peptide bonds using energy minimization move -- move specified atom to convert to trans reset -- reinitialize plugin state restrain -- generate NAMD extrabonds file to restrain peptide bonds set -- define how to modify a given cis peptide bond show -- visualize identified cis peptide bondsIn the same way the usage information for any of the provided commands can be obtained. For example, typing cispeptide restrain will show the syntax of the command that generates restraints for the dihedral angle at the peptide bond which can be used in NAMD.
In the following, we will describe how to use the cispeptide plugin through its GUI, but all of the tasks can also be accomplished from the console.
Modeling Fix Cis Peptide Bonds in the
VMD Main menu. In the upper part of the GUI (see Fig. 7) the user can
specify the molecule and the atom selection to be tested.
WARNING: The cispeptide plugin identifies all cis peptide bonds. As noted in the introduction, there are cases in which cis peptides do occur in proteins. Thus, it should be checked if a given cis peptide is real or is a mistake. This can be done by literature research, by comparing high resolution crystallographic models, or by comparing crystallographic models of similar proteins.
WARNING: The choice which atom to move is crucial and has to be made based on the
local structure around the peptide under consideration. The decision is particularly
critical helices and 
-sheets: the relaxed backbone should integrate in the
existing hydrogen bond network characteristic for the specific secondary structure motif
(see Fig. 6).
If the identified cis peptide bond is supposed to be there, nothing needs to be done. It is also possible to untag a tagged atom by selecting the corresponding cis peptide and hitting none.
Minimization Mode in the
AutoIMD Controls window and hit then the Submit
button. Once the AutoIMD session started, hit the Connect button and a minimization will start. Finish the
simulation when the structure relaxed. Usually, it takes up to a few
thousand steps until atoms do not move anymore. Is the structure minimized, hit
the Finish in the AutoIMD Controls window.
For more details about using the AutoIMD plugin, the user is
referred to the AutoIMD user's guide
Equilibration Mode and submitting a new AutoIMD run.
Minimization Mode in the
AutoIMD Controls window, which is still open from the last AutoIMD session,
and hit then the Submit button. As mentioned in the introduction, additional
restraints during the correction of cis peptides. The restraints will be used always
when AutoIMD is started from the cispeptide window. The equilibrium values
for these restraints are very approximate and bring the configuration in the correct
region. Thus, in order to obtain a optimized structure, it is necessary NOT to use the
restraints defined by cispeptide. This is achieved by reusing the AutoIMD
window from the previous minimization/equilibration; the restraints will not be taken into
account.
Save Coordinates in the VMD main window.
Select all in the Selected atoms and hit Save. Finally, specify the file
name in the Chose filename to save trajectory and hit OK.
As mentioned in the introduction, structure optimizations and MD protocols applying external forces can flip the configuration of a peptide bond in the the simulated structure. To preserve peptide configuration, the cispeptide plugin offers the possibility to generate restraints in form of extrabonds which can be used in a NAMD simulations. This feature currently is available only from the console.
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