从酸酶的E状态形成H2-E4
1Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden. Ulf.Ryde@compchem.lu.se.
Physical chemistry chemical physics : PCCP
|December 18, 2023
概括
基酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶酶
科学领域:
- 生物化学 生物化学
- 计算化学的计算化学
- 酶学 是一种酶学.
背景情况:
- 酶是唯一能够固定N2的酶,将大气中的转化为生物可用的形式.
- 酶的活性部位,MoFe7S9C集群 (FeMo集群),在催化过程中循环通过八个中间状态 (E0-E7).
- (N2) 结合发生在E4状态, (H2) 作为已知的副产品,尽管其形成可能是一个非生产性的副作用反应.
研究的目的:
- 在E2-E4催化状态期间,研究H2的形成作为酶中的副作用反应.
- 使用计算方法评估E2-E4状态的不同结构解释.
- 确定FeMo星团内H2形成和质子转移的动力可行性.
主要方法:
- 采用了量子力学和分子力学 (QM/MM) 的结合计算.
- 使用了四种不同的密度函数理论 (DFT) 方法:B3LYP,TPSS,r2SCAN和TPSSh.
- 分析了酶催化循环的E2-E4中间状态的各种结构模型.
主要成果:
- DFT方法在预测H2形成路径方面显示出显著的差异.
- B3LYP计算表明,由于中央碳化物的有利质子化,H2不能形成.
- TPSS,r2SCAN和TPSSh预测了外热H2形成,特别是在E3和E4状态,两种桥接化物活性障碍较低 (29-57kJ mol-1).
- 在FeMo集群的不同状态之间进行质子转移很容易,激活障碍很低 (12-69kJ mol-1).
结论:
- 在E3和E4状态下,H2的形成在动力学上是可行的,并且在E3和E4状态下可能是快速的,超过了酶的周转率.
- 在E3/E4状态下的特定桥接化物配置促进了快速的H2形成.
- 在FeMo集群内,高效的质子流动性允许质子状态的快速相互转换,从而影响反应路径.
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