Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization

Abstract

X-chromosome-linked inhibitor of apoptosis (XIAP) inhibits cell apoptosis. Overexpression of XIAP is widely found in human cancers. Second mitochondria-derived activator of caspase (SMAC) protein inhibits XIAP through binding with Baculovirus Inhibitor of apoptosis protein Repeat (BIR) 3 or BIR2 domain of XIAP. In this study, molecular dynamics (MD) simulations and the alanine scanning calculations by MM-GBSA_IE method were used to investigate the protein–peptide interaction between BIR3 and BIR2 domains of XIAP and SMAC peptide. Energetic contribution of each binding residue is calculated and hotspots on both XIAP and SMAC were identified using computational alanine scanning with interaction entropy method. We found that electrostatic polarization is important in stabilizing the protein–protein complex structure in MD simulation. By using polarized protein-specific charges, much better agreement with experimental result is obtained for calculated binding free energies compared to those using standard (nonpolarizable) AMBER force field. In particular, excellent correlation between calculated binding free energies in alanine scanning with mutational experimental data was obtained for BIR3/SMAC binding.

Communicated by Ramaswamy H. Sarma.

Keywords:

• Computational alanine scanning
• interaction entropy
• hot spots
• XIAP
• BIR3 domain
• BIR2 domain
• SMAC
• selectivity
• GBSA
• polarization
• PPC

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by National Key R&D Program of China (Grant no. 2016YFA0501700), National Natural Science Foundation of China (Grant nos. 21433004 and 91753103) and NYU Global Seed Grant.