[gmx-users] mutational analyses: Cystine and indels

[Peter C. Lai]

You might be able to use MODELLER for generating the helix deletions since
it is alignment-based. If you use automodel.make(exit_stage=2) it will
generate coordinates based on the specified sequence-spatial alignment but 
will stop there (otherwise it will try to run simulated annealing in vacuum).
So what it will do is overlay the sideschains in your new sequence over the
backbone of your beginning structure.

You can then parameterize and refine with gromacs. Distance/angle restraints 
will be your friend here (set up distance restraints between N-H to keep the 
helix intact while you run energy minimzation and short relaxation MD).

You are correct in that point indels that do not remove or add a full turn
to the helix will be pretty drastic, so you will obviously have to find some 
ways to do validation, particularly when assessing if vicinal CYS will form 
disulfide bridge or not (which will also obviously do things to helix 
geometry) but I think these are hypotheses still well suited for MD to probe.

On 2012-05-30 03:10:39PM -0300, Frederico Moras Ferreira wrote:
> Hi Gromacs list,
> I would like to study two different mutations in a protein molecule, 
> perhaps using MD.
> One of them is a insert deletion and the other is a mutation to Cys 
> beside an existing Cys.
> The problem is that most of the molecular modeling programs, including 
> Rosetta, do not handle with indels nor with cystine residues.
> Such deletion is located in a helix so as the molecular modeling program 
> should be capable of moving a entire helix and rotate one or both parts 
> it. That's not something trivial!
> The other mutation sounds worse. Rosetta can't even deal with mutation 
> to Cys. Assuming that such mutation is not going to disrupt the protein 
> folding, it probably will form a cystine residue. Not only because of 
> the distance between cysteines, but also because the pH of the 
> crystallization conditions.
> My question is: has anybody managed such kinds of mutations? or perhaps, 
> could someone shade some light on these problems?
> All the best,
> Fred
> 
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