A model for the interaction between NF‐kappa‐B and ASPP2 suggests an I‐kappa‐B‐like binding mechanism

We used computational methods to study the interaction between two key proteins in apoptosis regulation: the transcription factor NF-κ-B (NFκB) and the proapoptotic protein ASPP2. The C-terminus of ASPP2 contains ankyrin repeats and SH3 domains (ASPP2ANK-SH3) that mediate interactions with numerous apoptosis-related proteins, including the p65 subunit of NFκB (NFκBp65). Using peptide-based methods, we have recently identified the interaction sites between NFκBp65 and ASPP2ANK-SH3 (Rotem et al., J Biol Chem 283, 18990–18999). Here we conducted a computational study of protein docking and molecular dynamics to obtain a structural model of the complex between the full length proteins and propose a mechanism for the interaction. We found that ASPP2ANK-SH3 binds two sites in NFκBp65, at residues 236–253 and 293–313 that contain the nuclear localization signal (NLS). These sites also mediate the binding of NFκB to its natural inhibitor IκB, which also contains ankyrin repeats. Alignment of the ankyrin repeats of ASPP2ANK-SH3 and IκB revealed that both proteins share highly similar interfaces at their binding sites to NFκB. Protein docking of ASPP2ANK-SH3 and NFκBp65, as well as molecular dynamics simulations of the proteins, provided structural models of the complex that are energetically similar to the NFκB-IκB determined structure. Our results show that ASPP2ANK-SH3 binds NFκBp65 in a similar manner to its natural inhibitor IκB, suggesting a possible novel role for ASPP2 as an NFκB inhibitor. Proteins 2009. © 2009 Wiley-Liss, Inc.