From big molecules to smaller ones

Abstract

We have been developing empirical methods to extract information from protein-protein complexes that will facilitate the design of smaller molecular mimics. Protein-protein complexes are considered intractable targets for drug design because they have large Hat interfaces. However, mutationai and structural analysis of the hOH-receplor interface shows that only a portion of the side chains are crucial for binding affinity. Such "hot spots" may provide templates for small molecule mimics. Protein domains are generally considered to be indivisible elements of protein structure and act as portable modules which afford great functional diversity. We were interested in testing whether smaller protein domains could be constructed that maintain function. Atrial Natiuretic Pelide ( ANP) and the B-domain of Protein A arc polypeptides of 2X and 59 residues, respectively, which bind their cognate receptor using discontinuous determinants. Attempts to make simple deletions in these peptides and maintain binding affinity have failed. Phage display can he a powerful tool for peptide and protein design when used in conjunction with high resolution structural information. Using an interalive process of rational protein design and phage methods to rectify defects inherent in the design, we have been able to reduce by half the si/e of ANP and the IgG binding domain of protein A. Such an approach may also facilitate the design of small peptidomclics from larger peptides or proteins.