A template-based approach to the modification of binding properties of globular proteins I: Background and motivations.

Design and production of polypeptide/proteins with desired bind site properties involves utilization of the ligand of interest in selection of those bind sites that yield the desired properties from an assortment bind sites with different structures and properties. Thus, as opposed to an “instructive” role and therefore involvement in determination of these bind site properties, the ligand instead functions in selection of bind sites with preexisting properties. Although there is consensus over this role for ligands, this was not always the case. A debate over the role of cognate ligands dominated discourse during the early- to mid- 20^th century. On one hand were proponents of an instructive role (as a direct template), and on the other hand were those in support of “selective” role. Haurowitz and Pauling proposed a role for ligand in determination of bind site properties, whereas Jerne and Burnet proposed selection. Experimental studies and theoretical considerations in immunology –by Nossal and Tonegawa– and in enzymology –by Anfinsen and Haber– provided results in support of the selection theory. Thus, an acceptance of selection- over instruction theory. However, both the uniqueness of antibody production and polyclonality draw questions to the applicability of such generalization of selection theory to other non-immune proteins. It is based on these notions that we advocate reconsideration of the instruction (direct template) theory as [at least] a partial explanation of origins of ligand binding properties of peptide molecules. Such reconsiderations are especially relevant when considering some of the current challenges regarding optimization of catalytic rates of artificially engineered enzymes. In such cases, the instruction theory may stand as part of a solution. In addition, this may create an avenue for optimization of: antibody-based therapeutics; and quantitative and qualitative immunoassays; for all of which binding interactions is a crucial determinant of affinity, specificity as well as sensitivity of agent.