AMBER Archive (2003)

Subject: Re: AMBER: aminoacid mutation

From: Osmar Norberto de Souza (osmarns_at_inf.pucrs.br)
Date: Tue Oct 28 2003 - 14:38:00 CST

Dear Iona,
        I think you can do what you want, almost exactly, with DeepViewer
(SwissPDBviewer).
        You can perform anyone of the 20 possible mutations and manually rotate
(phi, psi, and the chi dihedrals if you wish) and inspect the
conformation of the new side chain. When bad contacts occur they're
shown in a pink broken line. If good contacts (hydrogen bonding, for
instance) they're shown in a green broken line. Upon finishing the
manipulation the program asks if you want to keep the mutation. Then,
you can save it in pdb format.
        You can find more information at
http://us.expasy.org/spdbv/text/mutation.htm.
        Hope this helps.
        Best wishes,
        Osmar
        Laboratório de Bioinformática, Modelagem e Simulação de Biossietmas
(LABIO)
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Osmar NORBERTO DE SOUZA, PhD |
LABIO | Tel: +55-51-3320-3611
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Ioana Cozmuta wrote:
>
> Hi Yong and amber users,
>
> I think I am talking about a much simpler case. What you are referring to
> is how difficult/simple the mutation from an AA to another is from
> energetic point of view (alchemy). I may come to that later as well but at
> the moment the AA I want to mutate is a side chain that points towards the
> inside of a beta-barrel that seems large enough. Actually I want to do a
> couple of mutations: MET to ALA, MET to LEU etc and see how this
> influences the properties of ionic solution inside the beta barrel. I
> think for this purpose a simple geometric modification (preserving the
> position of the alpha Carbon only) with local equilibration of the AA
> should work fine. However any comments on possible issues I should be
> aware of are welcome!
>
> THanks,
> Ioana
>
> On Mon, 27 Oct 2003, Yong Duan wrote:
>
> >
> > Dear Ioana:
> >
> > I am interested in that too. So, let me know if you, or anybody else,
> > know a way or a program to do this automatically.
> >
> > LEU -> ALA mutation is simple. But ALA -> LEU can be a bit tricky if it
> > has to potential to bump into other neighboring atoms.
> >
> > yong
> >
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Ioana Cozmuta
> > Sent: Monday, October 27, 2003 7:46 PM
> > To: Amber List
> > Subject: AMBER: aminoacid mutation
> >
> >
> > Hi amber users,
> >
> > Is there a way to "automatically" mutate an aminoacid from a protein
> > structure into another one. Say I want to replace an ALA aminoacid with
> > a
> > LEU aminoacid. Is it possible just to select the ALA aminoacid I want to
> > mutate and turn it into LEU? Is there some software out there that
> > could do this on a more automatic basis?
> > The way I thought doing it was to edit the pdb file myself and try to
> > edit
> > the coordinates of the atoms in the new aminoacid such that the bond
> > lengths are preserved and then equilibrate the new positions. But then
> > my
> > boss told me to try "not to lose time with this" and find a software
> > that
> > does it automatically :)
> >
> > Any suggestions are welcomed!
> > Thanks,
> > Ioana
> >
> >
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