Carbon dioxide fixation in RuBisCO is protonation state dependent and irreversible

07 April 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Most CO2 from the atmosphere is assimilated in 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 back reaction (decarboxylation reaction) highly unfavourable. 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.

Keywords

RuBisCO
QM/MM molecular dynamics
projector-embedding approach and post Hartree-Fock electronic structure methods
CO2 fixation

Supplementary materials

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Supporting information
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Figure S1 shows the free energy profiles of the carboxylation reaction with a water molecule occupying the sixth coordination site of the magnesium (II) cation, Figure S2 displays the convergence of the activation energy correction with size of the high-level region in the projector-based embedding electronic structure calculations and Figure S3 provides representative snapshots and average atomic charges of the carbon and oxygen atom of the RuBP substrate dependent on the protonation state of Kcx201.
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