Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible

Abstract

Most CO2 from the atmosphere is assimilated into photosynthetic organisms by the ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) enzyme as part of the Calvin cycle. Despite its relevance and many efforts in the last few decades, the mechanistic picture of the catalytic CO2 fixation reaction is still under debate. Here, we combine QM/MM molecular dynamics simulations with high-level electronic structure methods and the projector-embedding approach to provide reference values for the activation and reaction free energies of the catalytic CO2 fixation reaction. Our results show that carboxylation is protonation-state-dependent and irreversible, making the reverse reaction (decarboxylation reaction) highly unfavorable. The carbamylated lysine residue, Kcx201, coordinated to the magnesium­(II) cation in the active site plays a central role shuffling protons from and to the substrate, creating the proper reactive enolate species that adds CO2. The emerging microscopic picture that involves several protonation equilibria and the free-energy profile of the CO2 fixation reaction provides insights that may be used in the future to improve enzymatic efficiency in RuBisCO.

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…187,188 Douglas-Gallardo et al used ChemShell QM/MM calculations and high-level projectorembedding calculations with Molpro to provide corrections to free energy barriers for carbon dioxide formation by the RuBisCO enzyme, calculated using semi-empirical QM/MM molecular dynamics, to increase the accuracy of the reaction profiles obtained for different protonation states of key amino acid residues. 189 Free energies may also be estimated at the DFT/MM level using QM/MM free energy perturbation, as in the study of Zheng et al on HCV protease. 190…”

“…profiles obtained for different protonation states of key amino acid residues. 189 Free energies may also be estimated at the DFT/MM level using QM/MM free energy perturbation, as in the study of Zheng et al on HCV protease. 190 Biomolecular workflows in Py-ChemShell…”

The power of magnesium: unlocking the potential for increased yield, quality, and stress tolerance of horticultural crops

“…This electron flow is vital for synthesizing ATP and fueling a myriad of cellular processes, including the conversion of carbon dioxide into organic compounds ( Figure 2 ) ( Jiao et al., 2023 ). Furthermore, Mg 2+ ’s significance in photosynthesis permeates dark reactions, most notably in its role with the enzyme RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), which catalyzes the fixation of carbon dioxide (CO 2 ) and the subsequent formation of carbohydrates ( Douglas-Gallardo et al., 2022 ). As an essential cofactor, Mg 2+ empowers RuBisCO activation and optimization, facilitating the transformation of CO 2 into organic molecules ( Douglas-Gallardo et al., 2022 ).…”

“…Furthermore, Mg 2+ ’s significance in photosynthesis permeates dark reactions, most notably in its role with the enzyme RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), which catalyzes the fixation of carbon dioxide (CO 2 ) and the subsequent formation of carbohydrates ( Douglas-Gallardo et al., 2022 ). As an essential cofactor, Mg 2+ empowers RuBisCO activation and optimization, facilitating the transformation of CO 2 into organic molecules ( Douglas-Gallardo et al., 2022 ). Conclusively, Mg 2+ central position within the chlorophyll molecule is indispensable for light energy absorption and the onset of photosynthesis ( Tang et al., 2023 ).…”

“…Mg 2+ serves as a multifunctional catalyst in plant physiology, playing a critical role in various aspects of enzyme activation and metabolism ( Figure 1 ). Its function as a cofactor in numerous enzymatic reactions emphasizes its significance in the synthesis and metabolism of carbohydrates, proteins, and nucleic acids ( Farhat et al., 2016 ; Douglas-Gallardo et al., 2022 ; Tang et al., 2022a ). The influence of Mg 2+ extends to essential processes such as protein synthesis, cell division, and DNA replication, reflecting its pervasive impact on plant metabolism ( Gerendás and Führs, 2013 ; Wang et al., 2020 ; Zhang B, et al., 2020 ).…”