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

Shuaizhen Tian, Changge Ji, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)743-752
Number of pages10
JournalJournal of Biomolecular Structure and Dynamics
Issue number2
StatePublished - 2021


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

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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