1. ¹Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, La Jolla, CA, USA
2. ²Graduate Program in Molecular Pathology, University of California, San Diego, La Jolla, CA, USA
3. ³Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland

Correspondence: GS Salvesen, Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA. Tel: 858 646 3114; Fax: 858 713 6274; E-mail: gsalvesen@burnham.org

Received 20 August 2007; Revised 10 December 2007; Accepted 4 January 2008; Published online 1 February 2008.

Abstract

We describe the peptide-binding specificity of the baculoviral IAP repeat (BIR) domains of the human inhibitor of apoptosis (IAP) proteins, X-linked IAP, cellular IAP1 and neuronal apoptosis inhibitory protein (NAIP). Synthetic peptide libraries were used to profile each domain, and we distinguish two types of binding specificity, which we refer to as type II and type III BIR domains. Both types have a dominant selectivity for Ala in the first position of the four N-terminal residues of the peptide ligands, which constitute a core recognition motif. Our analysis allows us to define the signature of type III BIRs that demonstrate a preference for Pro in the third residue of the ligand, resembling the classic IAP-binding motif (IBM). The signature of the type II BIRs was similar to type III, but with a striking absence of specificity for Pro in the third position, suggesting that the definition of an IBM must be modified depending on the type of BIR in question. These findings explain how subtle changes in the peptide-binding groove of IAP BIR domains can significantly alter the target protein selectivity. Our analysis allows for prediction of BIR domain protein-binding preferences, provides a context for understanding the mechanism of peptide selection and heightens our knowledge of the specificity of IAP antagonists that are being developed as cancer therapeutics.