I have a few questions on a paper from Kuhlman's group "Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface"
In the method section, there is an MSD protocol for CL-CH1 interface. And following is the fitness file:
#-12 is the energy cap, determined empirically as the rough value of redocked binding energy for the worst mutations
1) SCALAR_EXPRESSION clipped_dGbindLHp = ite( lt( dGbind_LHp, -12.0 ), dGbind_LHp, ( -12.0 + 0 * dGbind_LHp) )
---> is the 0 in the 0*dGbind_LHp just a place holder for a weight number (ex. 1 – 12 or 0 – 1) ?
2) FITNESS 1.0 * bestLpHp - 0 * dGbind_LpHp + 0.5 * ( clipped_dGbindLpH + clipped_dGbindLHp ) + 1.0 * cstE
---> is the 0 in the 0 * dGbind_LpHp also just a place holder for a weight number (ex. 1 – 12 or 0 – 1) ?
---> There is a ‘-‘ before 0 * dGbind_LpHp. I recall it was a ‘+’ in the previous MSD paper. So is there a special reason for it?
3) Is there a protocol example for VH-VL interface? I am working on bispecific antibody design. I want to enhance the VL's affinity to one VH, while reduce the affinity to another VH. Is there there a good MSD design example for it?
Thank you so much!