A new yeast display vector permitting free scFv amino termini can augment ligand binding affinities

Yeast surface display and sorting by flow cytometry are now widely used to direct the evolution of protein binding such as single-chain antibodies or scFvs. The available commercial yeast display vector pYD1 (Invitrogen) displays the protein of interest flanked on the N-terminus by Aga2, the disulfide of which binds the myristylated surface membrane protein Aga1. We have noted that two anti-CD3ε scFvs expressed as fusion proteins suffer a 30- to 100-fold loss of affinity when placed NH2 terminal to either truncated toxins or human serum albumin. In the course of affinity maturing one of these scFv (FN18) using pYD1 we noted that the affinity towards the ectodomain of monkey CD3εγ was too low to measure. Consequently we rebuilt pYD1 tethering the scFv off the NH2 terminus of Aga2. This display vector, pYD5, now gave a positive signal displaying FN18 scFv with its ligand, monkey CD3εγ. The apparent equilibrium association constant of the higher affinity scFv directed at human CD3εγ increased ∼3-fold when displayed on pYD5 compared with pYD1. These data show that for certain yeast-displayed scFvs a carboxy-tethered scFv can result in increased ligand–scFv equilibrium association constants and thereby extend the low range of affinity maturation measurements.