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-kappa-B (NF kappa B) and the proapoptotic protein ASPP2. The C-terminus of ASPP2 contains ankyrin repeats and SH3 domains (ASPP2(ANK-SH3)) that mediate interactions with numerous apoptosis-related proteins, including the p65 subunit of NF kappa B (NF kappa B-p65). Using peptide-based methods, we have recently identified the interaction sites between NF kappa B-p65 and ASPP2(ANK-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 ASPP2(ANK-SH3) binds two sites in NF kappa B-p65, at residues 236-253 and 293-313 that contain the nuclear localization signal (NLS). These sites also mediate the binding of NF kappa B to its natural inhibitor I kappa B, which also contains ankyrin repeats. Alignment of the ankyrin repeats of ASPP2(ANK-SH3) and I kappa B revealed that both proteins share highly similar interfaces at their binding sites to NF kappa B. Protein docking of ASPP2(ANK-SH3) and NF kappa B-p65, as well as molecular dynamics simulations of the proteins, provided structural models of the complex that are energetically similar to the NF kappa B-I kappa B determined structure. Our results show that ASPP2(ANK-SH3) binds NF kappa B-p65 in a similar manner to its natural inhibitor I kappa B, suggesting a possible novel role for ASPP2 as an NF kappa B inhibitor. Proteins 2009; 77:602-611. (C) 2009 Wiley-Liss, Inc.