Yes, the two arginines are from two different models. One has the antibody and the other one the ligand. But if you imagine that both are bound to the receptor, asp still can't be entrapped between the arginines.
And if the asp was entrapped between the two arginine it would also mean that the antibody stabilizes the ligand receptor interaction. What we see is the opposite.
Do you have any references about asp-arg as "hot spots"?
Thanks,
Sent from my iPod
On Oct 8, 2013, at 12:58 PM, "Nadir T. Mrabet" <[log in to unmask]> wrote:
> Jan,
>
> Ionic interaction does reduce the charges born by the partners in isolation.
> This is why charged residues found in the protein core are always paired.
> Furthermore, concerning arg, beyond the fact that they are found to autointeract as Andrey pointed out, the charge they bear is spread over all the guanidinium group so that it is not punctual as is the case for lys NZ.
> H-bonds also solvate charges.
>
> Are you stating that asp can in no way be entrapped between the arginines?
> Recall arg-asp interactions in proteins are "hot spots".
>
> Cheers,
>
> Nadir
>
> Pr. Nadir T. Mrabet
> Structural & Molecular Biochemistry
> N-gere - INSERM U-954
> University of Lorraine, Nancy
> School of Sciences and Technologies
> & School of Medicine
> 9, Avenue de la Foret de Haye, BP 184
> 54505 Vandoeuvre-les-Nancy Cedex
> France
> Phone: +33 (0)3.83.68.32.73
> Fax: +33 (0)3.83.68.32.79
> E-mail: Nadir.Mrabet <at> univ-lorraine.fr
>
> On 08/10/2013 18:33, Jan van Agthoven wrote:
>> Thanks for your responses,
>>
>> Andrey, I had no idea about these arginine associations. In this case
>> the arginines are facing each other guanidinium to guanidinium. I
>> guess they wouldn't attract. Nadir, the asp is not entrapped between
>> the two arginines. But Hermann is probably right by saying that the
>> asp is too close to the antibody arginine.
>>
>> Our binding essays were done by fluorescent labeling of the ligand.
>> Clustering shouldn't play a role. It's hard to explain, there is no
>> steric hindrance. I guess I'll have to drop this idea of repulsion.
>>
>> 2013/10/8, Andrey Feklistov <[log in to unmask]>:
>>> Hi Jan,
>>>
>>> please note, Arg-Arg proximity is not always repulsive: guanidinium groups
>>> can associate bridged by H-bonds and interactions with water molecules or
>>> neighboring amino acids. There are many examples of these unusual Arg
>>> formations, see for reference:
>>>
>>> Neves, Yeager and Abagyan (2012) "Unusual Arginine Formations in Protein
>>> Function and Assembly: Rings, Strings and Stacks", J. Phys. Chem. B 116,
>>> 7006-7013
>>>
>>> Hope this is helpful,
>>>
>>> Andrey
>
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