[gmx-users] mutational analyses: Cystine and indels

Frederico Moras Ferreira ferreirafm at usp.br
Wed May 30 20:10:39 CEST 2012

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,

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