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Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO
Author(s) -
Jiang Tianlong,
Moriwaki Kenta,
Kobayashi Osamu,
Ishimura Kazuya,
Danielache Sebastian O.,
Nanbu Shinkoh
Publication year - 2020
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26156
Subject(s) - rubisco , chemistry , kinetic isotope effect , carboxylation , oniom , isotope fractionation , isotopes of carbon , molecular dynamics , isotope , kinetic energy , computational chemistry , molecule , fractionation , photosynthesis , physics , atomic physics , chromatography , organic chemistry , biochemistry , quantum mechanics , total organic carbon , catalysis , deuterium
Abstract 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 2 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 2 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 2+ , simulations have been performed on several molecular configuration models fixing several distances between CO 2 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 2 containing either 13 C or 12 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.