The mechanism of peptide-binding specificity of IAP BIR domains

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. Cell Death and Differentiation (2008) 15, 920-928; doi:10.1038/cdd.2008 ; published online 1 February 2008Apoptosis is a highly regulated cellular signaling pathway that results in the elimination of unwanted cells from multicellular animals. The apoptotic signaling cascades can be initiated by various extracellular (extrinsic pathway) or intracellular (intrinsic pathway) stimuli and ultimately converge on the activation of a family of proteases known as the caspasesreviewed in Fuentes-Prior and Salvesen. 1 Once active, caspases cleave a limited number of substrates that results in the destruction of the cell and its eventual disposal by phagocytic cells.Members of the inhibitor of apoptosis (IAP) protein family have the unique ability to attenuate apoptosis induced through both intrinsic and extrinsic stimuli. It is well established that the X-linked IAP (XIAP) is capable of blocking apoptosis by direct inhibition of caspase-3, -7, and -9 -reviewed in Salvesen and Duckett 2 and Eckelman et al. 3 The means by which the other members of the IAP family inhibit apoptosis is less understood. Many IAPs have the capacity to bind caspases, yet lack the ability to directly inhibit the proteolytic activity of these enzymes -reviewed in Eckelman et al. 3 The defining feature of the IAP family is the presence of 1-3 baculoviral IAP repeat (BIR) domains. BIRs are small, B70-residue zinc-coordinated domains that have been identified as the regions essential to the IAP-caspase interaction. The BIR domain(s) are necessary for the antiapoptotic activity of most IAPs. Often a surface groove on the BIR domain endows it with an affinity toward extreme N-terminal epitopes...

Role of Apollon in Human Melanoma Resistance to Antitumor Agents That Activate the Intrinsic or the Extrinsic Apoptosis Pathways

“…Several of these are SMAC mimetics developed to target the BIR3 and/or the BIR2 domains of XIAP, c-IAP1, and c-IAP2, and have shown promising preclinical results even in melanoma (39, 40). Although Apollon binds SMAC (14) and its only BIR domain belongs to the type II class, as the BIR2 domain of XIAP, c-IAP1, and c-IAP2 (41), it is not clear whether available SMAC mimetics also inhibit Apollon. However, other recently developed IAP antagonists are antisense oligonucleotides targeting XIAP or survivin (see ref.…”

IAP proteins as targets for drug development in oncology

“…Indeed, cIAPs, XIAP and ML-IAP can bind caspase-3, -7, and -9 via the BIRs10,11,45,46 and can induce their ubiquitination or neddylation via the RING domain 19,22–24. The influence of the ubiquitination is still not very well established, triggering degradative or nondegradative consequences,22–24 while the neddylation of caspase-7, by XIAP, inhibits its activity 19.…”

Physiological apoptosis of polar cells during Drosophila oogenesis is mediated by Hid-dependent regulation of Diap1

“…5,6 In the presence of apoptotic stimuli, IAP antagonists are activated and competitively bind to IAPs through an IAP-binding motif (IBM) leading to IAP ubiquitination and consequent degradation of both IAPs and IBM-domain proteins. 7,8 In mammals, both IAPs and IBM-domain proteins of the Smac/Diablo and Omi/HtrA2 families are also present, but they are ubiquitously expressed. In contrast, the IBM-domain proteins Reaper, Hid and Grim (RHG) in Drosophila are transcriptionally activated in response to many different hormonal, stress and developmental signals.…”