Incorporating an allosteric regulatory site in an antibody through backbone design

Abstract Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling‐molecule concentrations, but the ability to computationally design allosteric regulation into non‐allosteric proteins has been elusive. Allosteric‐site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy‐chain complementarity‐determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn 2+ ‐coordination site in a fluorescein‐binding antibody. We predicted that due to HCDR3's flexibility, the fluorescein‐binding pocket would configure properly only upon Zn 2+ application. We found that regulation by Zn 2+ was reversible and sensitive to the divalent ion's identity, and came at the cost of reduced antibody stability and fluorescein‐binding affinity. Fluorescein bound at an order of magnitude higher affinity in the presence of Zn 2+ than in its absence, and the increase in fluorescein affinity was due almost entirely to faster fluorescein on‐rate, suggesting that Zn 2+ preorganized the antibody for fluorescein binding. Mutation analysis demonstrated the extreme sensitivity of Zn 2+ regulation on the atomic details in and around the metal‐coordination site. The designed antibody could serve to study how allosteric regulation evolved from non‐allosteric binding proteins, and suggests a way to designing molecular sensors for environmental and biomedical targets.