We used computational methods to study the interaction between two key proteins in apoptosis regulation: the transcription factor NFκ-B (NFκB) and the proapoptotic protein ASPP2. The C-terminus of ASPP2 contains ankyrin repeats and SH3 domains (ASPP2 ANKSH3) that mediate interactions with numerous apoptosis-related proteins, including the p65 subunit of NFjB (NFκB p65). Using peptidebased methods, we have recently identified the interaction sites between NFκB 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 NFκB p65, 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 ASPP2 ANK-SH3 and IκB revealed that both proteins share highly similar interfaces at their binding sites to NFκB. Protein docking of ASPP2 ANK-SH3 and NFκB p65, 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 ASPP2 ANK-SH3 binds NFκB p65 in a similar manner to its natural inhibitor IκB, suggesting a possible novel role for ASPP2 as an NFκB inhibitor.
- Molecular dynamics