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 <afeklis...@rockefeller.edu>:
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
