[gmx-users] Negative arginine?

David spoel at xray.bmc.uu.se
Thu Dec 2 21:02:38 CET 2004

On Thu, 2004-12-02 at 10:24 -0800, Steven Spronk wrote:
> On Tue, 30 Nov 2004, Anton Feenstra wrote:
> > IMHO, it is not reasonable at all. You'd want a 'physical system' that
> > could at least in principle correspond to a real state, which in your
> > proposed case you clearly have not. What kind of 'control' simulations for
> > your WT (as per your previous mail) did you have in mind?
> >
> > --
> > Groetjes,
> >
> > Anton
> 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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