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 > >
