通过计算质子化微状态的集合来找到E频道质子加载点
Md Raihan Uddin1, Umesh Khaniya2, Chitrak Gupta3
1Department of Physics, The City College of New York, NY 10031, USA; Graduate Program In Biochemistry, The Graduate Center of CUNY, 365 5th Avenue, NY 10031, USA.
Biochimica et biophysica acta. Bioenergetics
|October 23, 2024
概括
综合体I使用质子合电子转移来出质子,从而产生梯度. 本研究使用先进的计算方法分析了复杂I的E通道内的质子结合点.
科学领域:
- 生物化学 生物化学
- 分子生物学分子生物学
- 计算生物学 计算生物学
背景情况:
- 有氧电子转移链通过质子合电子转移构建质子梯度.
- 复合物I,最初的酶,将电子从NADH转移到子,将质子穿过膜.
- 质子穿过反载体路径和E通道,涉及可质子化的残留物和水分子.
研究的目的:
- 为了分析Thermus thermophilus复合体I的E通道内的质子结合.
- 研究质子载荷场所 (PLS) 在质子运输中的作用.
- 了解E频道子单元的复杂质子微态.
主要方法:
- 使用了MCCE程序与蒙特卡洛采样.
- 分析的分子动力学快照的复合物I在apo,和结合状态.
- 研究了pH 7的质子结合平衡和微态.
主要成果:
- 在五个E频道子单元中识别了超过25,000个质子化微态.
- 分析了沿着质子转移路径的相互连接的残留集群.
- 在N侧和蛋白质中心的合残留集群中发现了质子结合和释放.
- 观察到负载微态将质子与P侧更接近.
结论:
- MCCE微态分析有效地管理了E频道质子结合的复杂性.
- 强度合的质子结合发生在已识别的PLS集群中的个体残留物中.
- 这项研究阐明了复杂I复合体中质子转位的复杂机制.
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