Altering 3D protein models.

Daniel MacArthur dmac125 at hotmail.com
Thu Apr 12 05:43:50 EST 2001


Hi everyone,

I was wondering (probably in vain) whether there was any relatively
user-friendly software out there that I could use to model the effects of an
amino acid substitution on a protein's 3D structure.

I work in a diagnostic lab and don't have a great deal of experience with
structure modelling software (I've used RasWin and Cn3D a fair bit recently,
but on a fairly superficial level). We recently identified a mutation in a
patient which results in a Gly-->Arg substitution in a muscle protein. The
mutation falls within a well-characterised domain that is present in a large
number of other proteins, and the glycine is conserved at the position in
almost all proteins with this particular domain type. Crystal structures for
quite a few of these proteins have been determined and are available as PDB
files.

What I'd really like to do is take the 3D structure of the protein that is
most similar to our protein of interest, and somehow produce the Gly-->Arg
substitution in the model. I know that modelling the resultant (undoubtedly
quite major) conformational changes would be very difficult, so
realistically I'd be happy just to be able to have an Arg residue at the
site instead of a Gly residue. Anything more sophisticated would be a
welcome bonus.

I thought of trying to fiddle with the actual PDB file but that is way
beyond my meagre programming skills, so I was hoping someone out there knew
of a program (preferably available as freeware) that could make the process
easier for me, or any other helpful advice. Any help at all would be greatly
appreciated.

Thanks in advance,


Daniel MacArthur

Institute for Neuromuscular Research
Children's Hospital at Westmead
Sydney, Australia
dmac125 at hotmail.com


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