PRINCIPLES AND PITFALLS IN DESIGNING SITE-DIRECTED PEPTIDE LIGANDS

An immunoglobulin light chain dimer with a large generic binding cavit y was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports w ere systematically tested for binding activity by enzyme linked immuno sorbent assays (ELISA). Key members of the binding series were synthes ized in milligram quantities and diffused into crystals of the host mo lecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallogr aphically refined structures of 14 peptide-protein complexes at 2.7 an gstrom resolution. These comparisons led to guidelines for ligand desi gn and also suggested ways to modify previously established binding pa tterns. By manipulating equilibria involving histidine, for example, i t was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a chan ge in conformation of the ligand from a compact to an extended form an d a comprehensive change in the mode of binding to the protein. In dip eptides of histidine and proline, protonation of both imidazolium nitr ogen atoms was used to program an end-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides co crystallized with proteins produced complexes somewhat different in st ructure from those in which ligands were diffused into preexisting cry stals. In such a large and malleable cavity, space utilization was thu s different when a ligand was introduced before the imposition of crys tal packing restraints.