[gmx-users] Negative arginine?
kay.gottschalk at weizmann.ac.il
Sat Dec 4 08:20:30 CET 2004
I'd mutate. Neg. Arg. will not pass the review process (IMHO). It
sounds too weird and is unphysical.
On Dec 3, 2004, at 9:36 PM, Steven Spronk wrote:
> 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
> 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
>>> response to an electric field. The interaction with the applied
>>> field, of
>>> course, depends only on the charges on the atoms. Hence, I thought
>>> it would be interesting to see how things behaved differently if I
>>> 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
>>> field while not perturbing the rest of the interactions too much. I
>>> 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
>>> and now we want a similar simulation in which we keep the same field
>>> 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
>>> 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!
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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
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
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