Department of Materials and Life Sciences, Sophia University, Tokyo, Japan.
Department of Nanosystem Science, Yokohama City University, Yokohama, Japan.
J Comput Chem. 2020 Apr 30;41(11):1116-1123. doi: 10.1002/jcc.26156. Epub 2020 Jan 26.
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; CO 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 CO 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 Mg , simulations have been performed on several molecular configuration models fixing several distances between CO 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 CO containing either C or C 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.
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；CO 碳原子）。为了描述反应和 KIEα，使用 Own N-layered Integrated molecular Orbitals and molecular Mechanics (ONIOM)-hybrid 模型对两种不同类型的分子动力学（MD）模拟（从头算 MD 和经典 MD）进行了研究。在 RubisCO 的 MD 模拟中观察到了 CO 传输的通道结构，并且假设反应路径从入口到通过带有 Mg 的坐标络合物的产物，在沿着通道固定 CO 和核酮糖-1,5-二磷酸之间的几个距离的几个分子构象模型上进行了模拟。对不同阶段的过程进行了自由能分析和扩散系数分析。证实了对于含有 C 或 C 的 CO，同位素分馏效应将通过在 RubisCO 中确定的通道结构中的过渡路径出现。估计的同位素分馏常数与实验值非常接近。
