Changing the Apoptosis Pathway through Evolutionary Protein Design.
Changing the Apoptosis Pathway through Evolutionary Protein Design.
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DOI：
10.1016/j.jmb.2018.12.016
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发表时间：
2019-02
影响因子：
5.6
通讯作者：
D. Shultis;Pralay Mitra;Xiaoqiang Huang;Jarrett S Johnson;Naureen Aslam Khattak;F. Gray;Clint Piper;Jeff Czajka;Logan Hansen;B. Wan;Krishnapriya Chinnaswamy;Liu Liu-Liu;Mi Wang;Jingxi Pan;J. Stuckey;T. Cierpicki;C. Borchers;Shaomeng Wang;M. Lei;Yang Zhang
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文献类型：
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作者：
D. Shultis;Pralay Mitra;Xiaoqiang Huang;Jarrett S Johnson;Naureen Aslam Khattak;F. Gray;Clint Piper;Jeff Czajka;Logan Hansen;B. Wan;Krishnapriya Chinnaswamy;Liu Liu-Liu;Mi Wang;Jingxi Pan;J. Stuckey;T. Cierpicki;C. Borchers;Shaomeng Wang;M. Lei;Yang Zhang
新蛋白设计的一个障碍是需要搜索巨大的序列空间来获得功能蛋白。我们开发了一种新的方法，使用从进化相关蛋白质创建的结构概况来约束模拟搜索过程，其功能由原子水平的配体-蛋白质结合相互作用指定。该方法用于重新设计X-linked inhibitor of apoptosis protein （XIAP）的BIR3结构域，XIAP的主要功能是通过抑制caspase-9活性来抑制细胞死亡；然而，野生型XIAP的功能可以通过与Smac肽的结合而被消除。等温热分析和荧光分析表明，与野生型XIAP蛋白相比，所设计的XIAP结构域可以与Smac肽强结合，但在体外对caspase-9蛋白水解活性没有明显抑制。详细的突变分析实验表明，设计中的结合特异性本质上是由结构轮廓和物理相互作用的相互作用决定的，这表明通过计算设计可以改变细胞凋亡途径。
One obstacle inde novoprotein 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 activityin vitrocompared 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.