Rotary Ion-Translocating ATPases/ATP Synthases: Diversity, Similarities, and Differences

Zubareva, V M; Lapashina, Anna S.; Shugaeva, Tatiana E.; Litvin, A V; Feniouk, Boris A.

doi:10.1134/s0006297920120135

Cited by 15 publications

(4 citation statements)

References 153 publications

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“…Adenosine triphosphate (ATP) synthases are crucial enzymes present in every living cell as they convert energy of the transmembrane potential into that of ATP’s chemical bonds (Junge and Nelson 2015; Kühlbrandt 2019; Nirody, Budin and Rangamani 2020; Zubareva et al . 2020).…”

Section: Introductionmentioning

confidence: 99%

High-throughput algorithm predicts F-Type ATP synthase rotor ring stoichiometries of 8 to 27 protomers

Osipov,

Zinovev,

Anuchina

et al. 2024

Preprint

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ATP synthases are large enzymes present in every living cell. They consist of a transmembrane and a soluble domain, each comprising multiple subunits. The transmembrane part contains an oligomeric rotor ring (c-ring), whose stoichiometry defines the ratio between the number of synthesized ATP molecules and the number of ions transported through the membrane. Currently, c-rings of F-Type ATP synthases consisting of 8 to 17 (except 16) subunits have been experimentally demonstrated. Here, we present an easy-to-use high-throughput computational approach based on AlphaFold that allows us to estimate the stoichiometry of all homooligomeric c-rings, whose sequences are present in genomic databases. We validate the approach on the available experimental data, obtaining the correlation as high as 0.94 for the reference data set, and use it to predict the existence of c-rings with stoichiometry varying from 8 to 27. We then conduct molecular dynamics simulations of two c-rings with stoichiometry above 17 to corroborate the machine learning-based predictions. Our work strongly suggests existence of rotor rings with previously undescribed high stoichiometry in natural organisms and highlights the utility of AlphaFold-based approaches for studying homooligomeric proteins.

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Section: Introductionmentioning

confidence: 99%

High-throughput algorithm predicts F-Type ATP synthase rotor ring stoichiometries of 8 to 27 protomers

Osipov,

Zinovev,

Anuchina

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Section: Introductionmentioning

confidence: 99%

“…The rotary mechanism of F-type ATP synthases is shared by the related type-A ATP synthases (Archaebacteria) and type-V ATPases (vacuolar and other cellular membranes), the latter functioning in vivo for ATP hydrolysis ( Zubareva et al, 2020 ). The three enzyme types also share some regulatory features, in particular the non-competitive inhibition by low ADP concentrations, which locks the enzyme in an inhibited conformation ( Vasilyeva and Forgac, 1998 ; Feniouk and Yoshida, 2008 ; Sielaff et al, 2018 ; Zubareva et al, 2020 ). In the F-type enzymes, the tightly bound ADP is released, thus recovering the catalytic activity, at high ATP concentrations or high H + -gradients ( Lapashina and Feniouk, 2018 ), by switching to a different conformation, which is metastable in the absence of a H + -gradient ( Fischer et al, 2000 , and references therein).…”

Section: Introductionmentioning

confidence: 99%

Modulation of the H+/ATP coupling ratio by ADP and ATP as a possible regulatory feature in the F-type ATP synthases

Turina

2022

Front. Mol. Biosci.

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F-type ATP synthases are transmembrane enzymes, which play a central role in the metabolism of all aerobic and photosynthetic cells and organisms, being the major source of their ATP synthesis. Catalysis occurs via a rotary mechanism, in which the free energy of a transmembrane electrochemical ion gradient is converted into the free energy of ATP phosphorylation from ADP and Pi, and vice versa. An ADP, tightly bound to one of the three catalytic sites on the stator head, is associated with catalysis inhibition, which is relieved by the transmembrane proton gradient and by ATP. By preventing wasteful ATP hydrolysis in times of low osmotic energy and low ATP/ADP ratio, such inhibition constitutes a classical regulatory feedback effect, likely to be an integral component of in vivo regulation. The present miniview focuses on an additional putative regulatory phenomenon, which has drawn so far little attention, consisting in a substrate-induced tuning of the H+/ATP coupling ratio during catalysis, which might represent an additional key to energy homeostasis in the cell. Experimental pieces of evidence in support of such a phenomenon are reviewed.

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“…During OxPhos, respiratory chain enzymes generate the transmembrane difference of electrochemical proton potential (Δ μ˜ H + ) that powers H + -transport through F O F 1 ATP-synthase coupled to synthesis of ATP from ADP and inorganic phosphate. When Δ μ˜ H + decreases below the thermodynamic threshold for ATP synthesis, F O F 1 activity reverses and the enzyme works as an ATP-driven proton pump and generates Δ μ˜ H + ( Zubareva et al, 2020 ). Surprisingly, complete dissipation of Δ μ˜ H + often leads to inhibition of F O F 1 ATPase activity.…”

Section: Introductionmentioning

confidence: 99%

Heterogeneity of Starved Yeast Cells in IF1 Levels Suggests the Role of This Protein in vivo

et al. 2022

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In mitochondria, a small protein IF1 suppresses the hydrolytic activity of ATP synthase and presumably prevents excessive ATP hydrolysis under conditions of energy deprivation. In yeast Saccharomyces cerevisiae, IF1 homologs are encoded by two paralogous genes: INH1 and STF1. INH1 expression is known to aggravate the deleterious effects of mitochondrial DNA (mtDNA) depletion. Surprisingly, no beneficial effects of INH1 and STF1 were documented for yeast so far, and the functions of INH1 and STF1 in wild type cells are unclear. Here, we put forward a hypothesis that INH1 and STF1 bring advantage during the fast start of proliferation after reentry into exponential growth from post-diauxic or stationary phases. We found that yeast cells increase the concentration of both proteins in the post-diauxic phase. Post-diauxic phase yeast cells formed two subpopulations distinct in Inh1p and Stf1p concentrations. Upon exit from the post-diauxic phase cells with high level of Inh1-GFP started growing earlier than cells devoid of Inh1-GFP. However, double deletion of INH1 and STF1 did not increase the lag period necessary for stationary phase yeast cells to start growing after reinoculation into the fresh medium. These results point to a redundancy of the mechanisms preventing uncontrolled ATP hydrolysis during energy deprivation.

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Rotary Ion-Translocating ATPases/ATP Synthases: Diversity, Similarities, and Differences

Cited by 15 publications

References 153 publications

High-throughput algorithm predicts F-Type ATP synthase rotor ring stoichiometries of 8 to 27 protomers

High-throughput algorithm predicts F-Type ATP synthase rotor ring stoichiometries of 8 to 27 protomers

Modulation of the H+/ATP coupling ratio by ADP and ATP as a possible regulatory feature in the F-type ATP synthases

Heterogeneity of Starved Yeast Cells in IF1 Levels Suggests the Role of This Protein in vivo

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