Peroxynitrite与铁的相互作用机制M. 尼特罗宾丁:一个计算研究
Andresa Messias1,2, Luciana Capece1,2, Giovanna De Simone3
1Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina.
尼特罗宾丁 (Nbs) 将过氧酸 (ONOO-) 排毒为酸盐. 计算机模拟显示,ONOOH比ONOO更容易在活性部位促进水位移,有助于酸盐的形成.
科学领域:
- 生物化学 生化学
- 结构生物学 结构生物学
- 计算化学的计算化学
背景情况:
- 尼特罗宾丁 (Nbs) 是所有β-桶的血红蛋白.
- 铁二丁 (Nb(III)) 将有毒的过氧酸 (ONOO-) 转化为无害的酸盐.
- Nb(III) 与ONOO-的反应性取决于pH值,这表明与过氧酸 (ONOOH) 的反应优先.
研究的目的:
- 阐明与ONOO-和ONOOH的铁 *Mycobacterium tuberculosis* nitrobindin (Mt-Nb(III)) 反应性背后的分子机制.
- 为了研究连接体迁移,水分子释放和连接体结合过程.
- 通过计算模拟来理解pH依赖的反应性.
主要方法:
- 经典分子动力学 (MD) 模拟使用引导的MD和Jarzynski等式.
- 计算ONOO-和ONOOH的连接体迁移自由能量概况.
- 混合量子力学/分子力学 (QM/MM) 使用 DFT 和推推弹性带 (NEB) 进行水位移能量配置文件.
主要成果:
- 无论是ONOO-还是ONOOH的体迁移到Mt-Nb(III) 活性部位基本上不受阻碍,这与其暴露的体一致.
- ONOO-的水位移障碍明显高于ONOOH的水位移障碍.
- 水位移是通过输入的ONOOH对离开的水分子的质子化来促进的.
结论:
- 暴露的Mt-Nb(III) 的活性部位允许快速的连接体接入.
- ONOOH的更高的反应性归因于它能够质子化协调水,降低位移屏障.
- 这种由质子辅助的机制解释了在过氧酸排毒过程中观察到的依赖pH值的尼特罗宾丁的反应性.
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