[gmx-users] mutational analyses: Cystine and indels

Frederico Moraes Ferreira ferreirafm at usp.br
Thu May 31 19:51:01 CEST 2012

Hi List,
Has anybody have something else to add to the Peter's comments?
Basically, I'm still unsure about modeling deletions.
Any help is appreciated.

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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