Identification of Interactive Sites of Proteins and Protein Receptors by Computer-Assisted Searches for Complementary Peptide Sequences

Abstract

Protein sites important for receptor binding have been identified in several systems by searching for protein/receptor stretches characterized by hydropathic anti-complementarity. A computer-assisted method [SITESEARCH] has been developed to identify protein sites responsible for receptor recognition, once the amino acid sequences of the protein ligand and its receptor are available. The software first determines the hydropathic profiles of the two polypeptide chains under investigation, and then compares profiles of preselected length, determining at the same time the degree of their hydropathic complementarity. The procedure is repeated until all the different segments in the two chains are compared. Fragments characterized by the maximal level of hydropathic complementarity are selected as putative binding sites. This approach has been initially applied to the interleukin-1β (IL-1β)/receptor type I case. SITESEARCH identified residues 88-99 in IL-1β and 151-162 in the receptor as the sequence pair characterized by the maximal level of hydropathic complementarity. These fragments, once produced by chemical synthesis, have displayed specific recognition properties for each other, as detected by solid-phase binding assays. The IL-1β sequence identified corresponds to a highly exposed part of the protein molecule, and substitution of this sequence with another of the same length but with different hydropathic characteristics generated mutants with drastically reduced binding activity to the receptor. Mutations in this sequence did not alter the protein biological activity, thus suggesting the structural integrity of the mutants. Cumulatively, these results validate the SITESEARCH prediction, suggesting that IL-1β sequence 88-99 is involved in at least a portion of the protein/receptor binding site.