Dear Jan, since electrostatics go with one over distance-square, there may still be some electrostatic repulsion if the aspartic acid is further away as the arginine. Another question is, what happens with the arginine of the ligand in absence of the antibody? Does it then make a salt bridge with the aspartic acid of the receptor? I expect that losing an a salt-bridge interaction between ligand and receptor will cause a significant drop in affinity which may explain the effect of the antibody.
Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Jan van Agthoven Gesendet: Montag, 7. Oktober 2013 22:47 An: [email protected] Betreff: [ccp4bb] repulsive effects of arginine Hi everyone, I'm working on structure of an antibody that inhibits a receptor. The antibody doesn't induce any conformational change in the receptor and doesn't bind the ligand binding site. If we superimpose the receptor with antibody and ligand the only hindrance we find is a electrostatic repulsion between two arginines (3.3A): one is part of the antibody and one is part of the ligand and involved in ligand binding. However the arginine coming from the antibody makes a salt bridge with an aspartic acid from the receptor. Does this neutralize it's charge? Can we still say that it has a repulsive effect? Thanks
