[gmx-users] Negative arginine?

[Kay Gottschalk]

I'd mutate. Neg. Arg. will not pass the review process (IMHO). It  
sounds too weird and is unphysical.
Cheers,
K.

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  
> the
> mutation of the arginine to an acidic residue like glutamate?
>
> Thanks for your responses!
> Steve
>
> 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.
>> ______________________________________________________________________ 
>> __
>> 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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>
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
+972-8-934 3639