[gmx-users] Negative arginine?

Eric Jakobsson jake at ncsa.uiuc.edu
Tue Dec 7 02:46:53 CET 2004


At 10:24 AM 12/2/2004 -0800, you 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?
>Thank you!
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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