[gmx-users] Negative arginine?
spronk at its.caltech.edu
Fri Dec 3 20:36:12 CET 2004
Sorry, I guess I didn't make myself very clear...
I have already performed a simulation with the (positive) arginine with a
given electric field. Now I want to run a simulation with the same
electric field, but I'd like to see how a "negatively-charged" arginine
would affect things differently. This way the arginine would move the
opposite direction in the same field.
Does anyone think that this technique would have any advantages over the
mutation of the arginine to an acidic residue like glutamate?
Thanks for your responses!
On Thu, 2 Dec 2004, David wrote:
> On Thu, 2004-12-02 at 10:24 -0800, Steven Spronk wrote:
> > Thank you David, Anton, and Erik for your comments so far. It sounds like
> > it's difficult to justify arbitrarily messing with charges. I'm glad that
> > I'm getting this feedback before I'm very far into the simulations.
> > Let me explain a little more why we're thinking about these charge
> > manipulations. The particular arginine I'm talking about is on a
> > transmembrane helix of a voltage sensitive protein, and is exposed to
> > lipid, not solvent. Obviously this is an unusual arginine. We're
> > exploring the idea that the arginine contributes to the voltage
> > sensitivity of the protein by moving vertically through the bilayer in
> > response to an electric field. The interaction with the applied field, of
> > course, depends only on the charges on the atoms. Hence, I thought that
> > it would be interesting to see how things behaved differently if I changed
> > the charges on the atoms while not changing all the interactions with the
> > lipids. We're trying to manipulate the arginine's ability to sense the
> > field while not perturbing the rest of the interactions too much. I do
> > realize, however, that the charges of the side chain interact with all the
> > charges around (although the lipid atoms are all uncharged, there are
> > other side chains and backbone atoms around).
> > But basically, we have a simulation of the protein in an electric field,
> > and now we want a similar simulation in which we keep the same field on
> > the system but force the arginine to move against the field, not with it.
> > Do any of you think that such a manipulation has any real advantage over,
> > say, mutating the arginine to a glutamate?
> But why should it be negative? A positve arginine will also respond to
> the field (but the other way). Is there any charge transfer going on?
> > Thank you!
> > Steve
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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