Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO,Journal of Computational Chemistry

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Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2020-01-26 , DOI: 10.1002/jcc.26156
Tianlong Jiang ₁ , Kenta Moriwaki ₁ , Osamu Kobayashi _{1,

2} , Kazuya Ishimura ₃ , Sebastian O Danielache ₁ , Shinkoh Nanbu ₁

Affiliation

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; CO2 carbon 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 CO2 transport 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 CO2 and 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 CO2 containing either 13C or 12C 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.

中文翻译：

动力学同位素对 RubisCO 中羧化作用的理论分析

核酮糖-1,5-二磷酸羧化酶/加氧酶（RubisCO）将大气二氧化碳固定为生物可利用的糖分子。众所周知，羧化过程伴随着动力学同位素效应（KIE；CO2 碳原子）。为了描述反应和 KIE α，已经使用自己的 N 层集成分子轨道和分子力学 (ONIOM) 混合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 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 Mg2+ 的配合物，对固定 CO2 和核酮糖之间若干距离的几个分子构型模型进行了模拟‐1,5-二磷酸沿通道。已针对该过程的不同阶段评估了自由能分析和扩散系数分析。已证实，含 13C 或 12C 的 CO2 的同位素分馏效应将通过 RubisCO 中确定的通道结构中的传输路径出现。估计的同位素分馏常数非常接近实验值。

更新日期：2020-01-26

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