Changing the Apoptosis Pathway through Evolutionary Protein Design. Issue 4 (15th February 2019)

• Record Type: Journal Article
• Authors: Shultis, David; Mitra, Pralay; Huang, Xiaoqiang; Johnson, Jarrett; Khattak, Naureen Aslam; Gray, Felicia; Piper, Clint; Czajka, Jeff; Hansen, Logan; Wan, Bingbing; Chinnaswamy, Krishnapriya; Liu, Liu; Wang, Mi; Pan, Jingxi; Stuckey, Jeanne; Cierpicki, Tomasz; Borchers, Christoph H.; Wang, Shaomeng; Lei, Ming; Zhang, Yang
• Is Part Of: Journal of molecular biology. Volume 431:Issue 4(2019)
• Page Start: 825
• Page End: 841
• Publication Date: 2019-02-15
• Subjects: protein design -- evolutionary profile -- apoptosis pathway -- XIAP -- isothermal calorimetry; XIAP X-linked inhibitor of apoptosis protein -- HDX hydrogen–deuterium exchange -- MS mass spectroscopy -- DI-XIAP Dynamic-Interface XIAP -- FI-XIAP Fixed-Interface XIAP -- REMC replica-exchange Monte Carlo -- ECD electron capture dissociation -- PCCs Pearson correlation coefficients -- ITC isothermal calorimetry -- MSA multiple structure alignment; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2018.12.016
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: 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. Graphical abstract: Unlabelled Image Highlights: Potential to modify apoptosis pathways through computational protein design New protein design algorithm built on evolutionary profiles Design functional XIAP BIR3 domain using evolutionary profiles Design binding specificity by combining profile and physical interactions Testify protein design by hybrid structure prediction and biochemistry experiments