Changing the Apoptosis Pathway through Evolutionary Protein Design

David Shultis, Pralay Mitra, Xiaoqiang Huang, Jarrett Johnson, Naureen Aslam Khattak, Felicia Gray, Clint Piper, Jeff Czajka, Logan Hansen, Bingbing Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, Jeanne Stuckey, Tomasz Cierpicki, Christoph H. Borchers, Shaomeng Wang, Ming Lei, Yang Zhang

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)


One obstacle in de novo protein design is the vast sequence space that needs to be searched through to obtain functional proteins. We developed a new method using structural profiles created from evolutionarily related proteins to constrain the simulation search process, with functions specified by atomic-level ligand–protein binding interactions. The approach was applied to redesigning the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP), whose primary function is to suppress the cell death by inhibiting caspase-9 activity; however, the function of the wild-type XIAP can be eliminated by the binding of Smac peptides. Isothermal calorimetry and luminescence assay reveal that the designed XIAP domains can bind strongly with the Smac peptides but do not significantly inhibit the caspase-9 proteolytic activity in vitro compared with the wild-type XIAP protein. Detailed mutation assay experiments suggest that the binding specificity in the designs is essentially determined by the interplay of structural profile and physical interactions, which demonstrates the potential to modify apoptosis pathways through computational design.

Original languageEnglish
Pages (from-to)825-841
Number of pages17
JournalJournal of Molecular Biology
Issue number4
Publication statusPublished - 15 Feb 2019
Externally publishedYes


  • apoptosis pathway
  • evolutionary profile
  • isothermal calorimetry
  • protein design
  • XIAP


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