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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK₂ Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

ABSTRACT: Ubiquinone (UQ) is a polyisoprenoid lipid found in the membranes of bacteria and eukaryotes. UQ has important roles, notably in respiratory metabolisms which sustain cellular bioenergetics. Most steps of UQ biosynthesis take place in the cytosol of E. coli within a multiprotein complex called the Ubi metabolon, that contains five enzymes and two accessory proteins, UbiJ and UbiK. The SCP2 domain of UbiJ was proposed to bind the hydrophobic polyisoprenoid tail of UQ biosynthetic intermediates in the Ubi metabolon. How the newly synthesised UQ might be released in the membrane is currently unknown. In this paper, we focused on better understanding the role of the UbiJ-UbiK₂ heterotrimer forming part of the metabolon. Given the difficulties to gain functional insights using biophysical techniques, we applied a multiscale molecular modelling approach to study the UbiJ-UbiK₂ heterotrimer. Our data show that UbiJ-UbiK₂ interacts closely with the membrane and suggests possible pathways to enable the release of UQ into the membrane. This study highlights the UbiJ-UbiK₂ complex as the likely interface between the membrane and the enzymes of the Ubi metabolon and supports that the heterotrimer is key to the biosynthesis of UQ₈ and its release into the membrane of E. coli.

SUBMITTER: Launay R

PROVIDER: S-EPMC9499169 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK<sub>2</sub> Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

Launay Romain R Teppa Elin E Martins Carla C Abby Sophie S SS Pierrel Fabien F André Isabelle I Esque Jérémy J

International journal of molecular sciences 20220907 18

Ubiquinone (UQ) is a polyisoprenoid lipid found in the membranes of bacteria and eukaryotes. UQ has important roles, notably in respiratory metabolisms which sustain cellular bioenergetics. Most steps of UQ biosynthesis take place in the cytosol of <i>E. coli</i> within a multiprotein complex called the Ubi metabolon, that contains five enzymes and two accessory proteins, UbiJ and UbiK. The SCP2 domain of UbiJ was proposed to bind the hydrophobic polyisoprenoid tail of UQ biosynthetic intermedia ...[more]

PMID: 36142227

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Project description:Propane (C3H8) and butane (C4H10) are short straight-chain alkane molecules that are difficult to convert catalytically. Analogous to propane, butane can be dehydrogenated to butenes (also known as butylenes) or butadiene, which are used industrially as raw materials when synthesizing various chemicals (plastics, rubbers, etc.). In this study, we present results of detailed first-principles-based multiscale modelling of butane dehydrogenation, consisting of three size- and time-scales. The reaction is modelled over Cr2O3(0001) chromium oxide, which is commonly used in the industrial setting. A complete 108-step reaction pathway of butane (C4H10) dehydrogenation was studied, yielding 1-butene (CH2CHCH2CH3) and 2-butene (CH3CHCHCH3), 1-butyne (CHCCH2CH3) and 2-butyne (CH3CCCH3), butadiene (CH2CHCHCH2), butenyne (CH2CHCCH), and ultimately butadiyne (CHCCCH). We include cracking and coking reactions (yielding C1, C2, and C3 hydrocarbons) in the model to provide a thorough description of catalyst deactivation as a function of the temperature and time. Density functional theory calculations with the Hubbard U model were used to study the reaction on the atomistic scale, resulting in the complete energetics and first-principles kinetic parameters for the dehydrogenation reaction. They were cast in a kinetic model using mean-field microkinetics and kinetic Monte Carlo simulations. The former was used to obtain gas equilibrium conditions in the steady-state regime, which were fed in the latter to provide accurate surface kinetics. A full reactor simulation was used to account for the macroscopic properties of the catalytic particles: their loading, specific surface area, and density and reactor parameters: size, design, and feed gas flow. With this approach, we obtained first-principles estimates of the catalytic conversion, selectivity to products, and time dependence of the catalyst activity, which can be paralleled to experimental data. We show that 2-butene is the most abundant product of dehydrogenation, with selectivity above 90% and turn-over frequency above 10-3 s-1 at T = 900 K. Butane conversion is below 5% at such low temperature, but rises above 40% at T > 1100 K. Activity starts to drop after ∼6 h because of surface poisoning with carbon. We conclude that the dehydrogenation of butane is a viable alternative to conventional olefin production processes.

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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK₂ Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

Publications

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK<sub>2</sub> Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

Publications

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK<sub>2</sub> Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK₂ Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies.