Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO
Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO
复制标题
RubisCO 羧化动力学同位素效应的理论分析
DOI：
10.1002/jcc.26156
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发表时间：
2020
影响因子：
3
通讯作者：
Nanbu Shinkoh
中科院分区：
文献类型：
--
作者：
Jiang Tianlong;Moriwaki Kenta;Kobayashi Osamu;Ishimura Kazuya;Danielache Sebastian O.;Nanbu Shinkoh
核酮糖-1，5-二磷酸羧化酶/加氧酶（RubisCO）将大气中的二氧化碳固定为生物可利用的糖分子。还众所周知，动力学同位素效应（KIE; CO2碳原子）伴随羧化过程。为了描述该反应和KIE α，使用Own N-layered Integrated Molecular Orbitals and Molecular Mechanics（ONIOM）-hybrid模型进行了两种不同类型的分子动力学（MD）模拟（从头算MD和经典MD）。在RubisCO中的MD模拟过程中观察到了CO2传输的通道结构，并假设从入口到产物的反应路径通过与Mg 2+的配位络合物，对几种分子构型模型进行了模拟，固定了CO2和核酮糖-1，5-二磷酸沿着通道的几个距离。自由能分析和扩散系数分析已被评估的过程的不同阶段。证实了含13 C或12 C的CO2的同位素分馏效应是通过RubisCO通道结构中的渡越路径实现的。估算的同位素分馏常数与实验值非常接近。
Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RubisCO) fixes atmospheric carbon dioxide into bioavailable sugar molecules. It is also well known that a kinetic isotope effect (KIE; CO2carbon atoms) accompanies the carboxylation process. To describe the reaction and the KIE α, two different types of molecular dynamics (MD) simulations (ab initio MD and classical MD) have been performed with an Own N‐layered Integrated molecular Orbitals and molecular Mechanics (ONIOM)‐hybrid model. A channel structure for CO2transport has been observed during the MD simulation in RubisCO, and assuming the reaction path from the inlet to the product through the coordinate complex with Mg2+, simulations have been performed on several molecular configuration models fixing several distances between CO2and ribulose‐1,5‐bisphosphate along the channel. Free energy analysis and diffusion coefficient analysis have been evaluated for different phases of the process. It is confirmed that the isotopic fractionation effect for CO2containing either13C or12C would appear through the transiting path in the channel structure identified in RubisCO. The estimated isotope fractionation constant was quite close to the experimental value.