Influence of canonical structure determining residues on antibody affinity and stability

Thermodynamic analyses of amino acid residues at the interface of an antibody B2212A and its antigen roundabout homolog 1

Artificial affinity maturation of antibodies is promising but often shows difficulties because the roles of each amino acid residue are not well known. To elucidate their roles in affinity against the antigen and thermal stability, interface residues in single-chain Fv of an antibody B2212A with its antigen roundabout homolog 1 were mutated and analyzed. Some amino acids played important roles in the affinity while others contributed to thermal stability.

Computationally Designed Bispecific Antibodies using Negative State Repertoires

A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally and rationally designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG-bispecific antibodies.