Global shape and ligand binding efficiency of the HIV-1 neutralizing antibodies differs from the ones which cannot neutralize [Molecular Biophysics]

October 20th, 2014 by Solanki, A. K., Rathore, Y. S., Badmalia, M. D., Dhoke, R. R., Nath, S. K., Nihalani, D., Ashish

Asymmetric disposition of Fab arms in the structures solved for broadly neutralizing-monoclonal antibody (nmAb) IgG1 b12, brought forth queries if the unusual shape observed for b12 is common for all IgG1 mAbs, or there lies a difference in the overall shape of nmAbs vs. non-nmAbs? We compared small angle X-ray scattering (SAXS) data based models and limited proteolysis profiles of some IgG1 mAbs known to be having and lacking HIV-1 neutralizing potency. In non-nmAbs, the Fab arms were found to be symmetrically disposed in space relative to central Fc, but in most nmAbs, the Fab arms were asymmetrically disposed as seen for IgG1 b12. Only exceptions were 2G12 and 4E10, where both Fab arms were closed above Fc suggesting some Fab/Fc and/or Fab/Fab interaction in the nmAbs which constrained extension of the Fab-Fc linker. Interestingly, these observations were correlated with differential proteolysis profiles of the mAbs by papain. Under conditions when papain could ″cut″ both Fab arms of non-nmAbs, only one Fab arm could be removed from neutralizing ones (except 2G12 and 4E10). Chromatography and SAXS results of papain digested products revealed that 1) the Fab/Fc or Fab/Fab interactions in unliganded mAbs are retained in digested products, and 2) while anti-gp120 non-nmAbs could bind two gp120 molecules, nmAbs could bind only one gp120. Additional experiments showed that except for 2G12 and 4E10, unopen shapes of nmAbs remain uninfluenced by ionic strength, but can be reversibly opened by low pH of buffer accompanied by loss of ligand binding ability.
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