[gmx-users] mutational analyses: Cystine and indels

Frederico Moraes Ferreira ferreirafm at usp.br
Thu May 31 00:05:06 CEST 2012

Hi Peter,
Thanks for helping. I might not have been clear. The cys mutation is in 
a different location of the indel.
I'm particularly worried about how the molecular modelling programs will 
treat indels. Several things can
happen upon deletion of an helix residue. In this context, just take the 
structural information of the
experimental model may not be something reliable.

Em 30-05-2012 17:37, Peter C. Lai escreveu:
> 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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