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

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

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

机译：SMAC-XIAP结合的分子基础及静电极化的影响

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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.

机译：X染色体连锁凋亡抑制剂（XIAP）抑制细胞凋亡。XIAP的过度表达广泛存在于人类癌症中。第二种线粒体源性半胱天冬酶激活剂（SMAC）蛋白通过与XIAP的杆状病毒凋亡抑制蛋白重复序列（BIR）3或BIR2结构域结合来抑制XIAP。本研究采用分子动力学（MD）模拟和MM-GBSA_IE方法的丙氨酸扫描计算，研究了XIAP和SMAC肽的BIR3和BIR2结构域之间的蛋白质-肽相互作用。计算了每个结合残基的能量贡献，并利用计算丙氨酸扫描和相互作用熵方法确定了XIAP和SMAC上的热点。我们发现，在MD模拟中，静电极化对于稳定蛋白质-蛋白质复合物结构非常重要。与用非极性场计算的蛋白质结合能相比，用非极性场计算的蛋白质结合能更符合实验结果。特别是，对于BIR3/SMAC结合，丙氨酸扫描计算的结合自由能与突变实验数据之间获得了极好的相关性。由拉玛斯瓦米·H·萨尔玛传达。

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来源
《Journal of Biomolecular Structure and Dynamics》 |2021年第2期|共10页
作者
Tian Shuaizhen; Ji Changge; Zhang John Z. H.;
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作者单位

East China Normal Univ State Key Lab Precis Spect Shanghai Peoples R China;

East China Normal Univ State Key Lab Precis Spect Shanghai Peoples R China;

East China Normal Univ State Key Lab Precis Spect Shanghai Peoples R China;

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正文语种 eng
中图分类分子生物学;
关键词
Computational alanine scanning; interaction entropy; hot spots; XIAP; BIR3 domain; BIR2 domain; SMAC; selectivity; GBSA; polarization; PPC;

机译：计算丙氨酸扫描;相互作用熵;热点;xiap;bir3结构域;bir2结构域;smac;选择性;gbsa;极化;ppc;

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

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