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

Oscar A. Douglas-Gallardo; Juliana A. Murillo-López; Javier Oller; Adrian J. Mulholland; Esteban Vöhringer-Martinez

doi:10.1021/acscatal.2c01677

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

Oscar A. Douglas-Gallardo, Juliana A. Murillo-López, Javier Oller, Adrian J. Mulholland, Esteban Vöhringer-Martinez^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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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.

Original language	English
Pages (from-to)	9418-9429
Number of pages	12
Journal	ACS Catalysis
Volume	12
Issue number	15
Early online date	19 Jul 2022
DOIs	https://doi.org/10.1021/acscatal.2c01677
Publication status	Published - 5 Aug 2022

Bibliographical note

Funding Information:
The authors want to thank Simon Bennie for his contributions in the calculations with the projector-embedding method. O.A.D-G., J.O and E.V.M acknowledge financial support by Comisión Nacional de Investigaciones Científicas y Tecnológicas (CONICYT-Chile). O.A.D.-G. thanks Fondo Nacional de Desarrollo Cientifico y Tecnologico (Fondecyt) for his postdoctoral fellowship No. 3170029 and European Molecular Biology Organization (EMBO) for his EMBO short-term fellowship STF 8022 to visit Prof A. J. Mulholland’s Lab. J.O thanks Fondecyt for his postdoctoral fellowship No. 3210287. E. V.-M. and J.M thanks for his Fondecyt grant No. 1200369, and the financial support provided by CONICYT PCI instituto Max Planck for terrestial microbiology Marburg MPG190003 collaboration project and Max-Planck Society through a Partner Group. A.J.M. thanks the Engineering and Physical Sciences Research Council (EPSRC) UK for support (grant number EP/M022609/1).

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© 2022 American Chemical Society.

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@article{b834d777bceb4728ab5f6652d485b9be,

title = "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.",

author = "Douglas-Gallardo, {Oscar A.} and Murillo-L{\'o}pez, {Juliana A.} and Javier Oller and Mulholland, {Adrian J.} and Esteban V{\"o}hringer-Martinez",

note = "Funding Information: The authors want to thank Simon Bennie for his contributions in the calculations with the projector-embedding method. O.A.D-G., J.O and E.V.M acknowledge financial support by Comisi{\'o}n Nacional de Investigaciones Cient{\'i}ficas y Tecnol{\'o}gicas (CONICYT-Chile). O.A.D.-G. thanks Fondo Nacional de Desarrollo Cientifico y Tecnologico (Fondecyt) for his postdoctoral fellowship No. 3170029 and European Molecular Biology Organization (EMBO) for his EMBO short-term fellowship STF 8022 to visit Prof A. J. Mulholland{\textquoteright}s Lab. J.O thanks Fondecyt for his postdoctoral fellowship No. 3210287. E. V.-M. and J.M thanks for his Fondecyt grant No. 1200369, and the financial support provided by CONICYT PCI instituto Max Planck for terrestial microbiology Marburg MPG190003 collaboration project and Max-Planck Society through a Partner Group. A.J.M. thanks the Engineering and Physical Sciences Research Council (EPSRC) UK for support (grant number EP/M022609/1). Publisher Copyright: {\textcopyright} 2022 American Chemical Society.",

year = "2022",

month = aug,

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doi = "10.1021/acscatal.2c01677",

language = "English",

volume = "12",

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journal = "ACS Catalysis",

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T1 - Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible

AU - Douglas-Gallardo, Oscar A.

AU - Murillo-López, Juliana A.

AU - Oller, Javier

AU - Mulholland, Adrian J.

AU - Vöhringer-Martinez, Esteban

N1 - Funding Information: The authors want to thank Simon Bennie for his contributions in the calculations with the projector-embedding method. O.A.D-G., J.O and E.V.M acknowledge financial support by Comisión Nacional de Investigaciones Científicas y Tecnológicas (CONICYT-Chile). O.A.D.-G. thanks Fondo Nacional de Desarrollo Cientifico y Tecnologico (Fondecyt) for his postdoctoral fellowship No. 3170029 and European Molecular Biology Organization (EMBO) for his EMBO short-term fellowship STF 8022 to visit Prof A. J. Mulholland’s Lab. J.O thanks Fondecyt for his postdoctoral fellowship No. 3210287. E. V.-M. and J.M thanks for his Fondecyt grant No. 1200369, and the financial support provided by CONICYT PCI instituto Max Planck for terrestial microbiology Marburg MPG190003 collaboration project and Max-Planck Society through a Partner Group. A.J.M. thanks the Engineering and Physical Sciences Research Council (EPSRC) UK for support (grant number EP/M022609/1). Publisher Copyright: © 2022 American Chemical Society.

PY - 2022/8/5

Y1 - 2022/8/5

N2 - 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.

AB - 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.

UR - https://doi.org/10.1021/acscatal.2c01677

U2 - 10.1021/acscatal.2c01677

DO - 10.1021/acscatal.2c01677

M3 - Article (Academic Journal)

SN - 2155-5435

VL - 12

SP - 9418

EP - 9429

JO - ACS Catalysis

JF - ACS Catalysis

IS - 15

ER -

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

Abstract

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

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