{"title":"ROS production by cytochrome bc1: Its mechanism as inferred from the effects of heme b cofactor mutants","authors":"Jakub Pagacz , Arkadiusz Borek , Artur Osyczka","doi":"10.1016/j.bbabio.2024.149513","DOIUrl":"10.1016/j.bbabio.2024.149513","url":null,"abstract":"<div><div>Cytochrome <em>bc</em><sub>1</sub> is one of the enzymes of electron transport chain responsible for generation of reactive oxygen species (ROS). While ROS are considered to be products of side reactions of quinol oxidation site (Q<sub>o</sub>), molecular aspects of their generation remain unclear. One of them concerns significance of hemes <em>b</em> (<em>b</em><sub>L</sub> and <em>b</em><sub>H</sub>) redox potentials (<em>E</em><sub>m</sub>) and properties on ROS generation by Q<sub>o</sub>. Here we addressed this question by examining ROS production in mutants of bacterial cytochrome <em>bc</em><sub>1</sub> that replaced one of the His ligand of either heme <em>b</em><sub>L</sub> or <em>b</em><sub>H</sub> with Lys or Asn. We observed that severe slowing down of electron flow by the Asn mutants induces similar effects on ROS production as inhibition by antimycin in the native cytochrome <em>bc</em><sub>1</sub> (WT). An increase in the <em>E</em><sub>m</sub> of hemes <em>b</em> (either <em>b</em><sub>L</sub> or <em>b</em><sub>H</sub>) in Lys mutants does not exert major effect on the ROS production level, compared to WT. The experimental data were analyzed in the frame of a dynamic model to conclude that the observed ROS rates and levels reflect a combinatory effect of two factors: probability of heme <em>b</em><sub>L</sub> being in the reduced state and probability of electron transfer from heme <em>b</em><sub>L</sub> towards Q<sub>o</sub>. A significant contribution from short-circuits maintains the ROS levels at ~15 % in all tested forms. Overall, ROS production by cytochrome <em>bc</em><sub>1</sub> shows remarkably low susceptibility to changes in the <em>E</em><sub>m</sub> of heme <em>b</em> cofactors, leaving significance of tuning the <em>E</em><sub>m</sub> of hemes <em>b</em> as factor limiting superoxide production an open question.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149513"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"GTP before ATP: The energy currency at the origin of genes","authors":"Natalia Mrnjavac, William F. Martin","doi":"10.1016/j.bbabio.2024.149514","DOIUrl":"10.1016/j.bbabio.2024.149514","url":null,"abstract":"<div><div>Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthase, which harnesses chemiosmotic ion gradients. Because the ATP synthase is a protein, it arose after the ribosome did. What was the energy currency of metabolism before the origin of the ATP synthase and how (and why) did ATP come to be the universal energy currency? About 27 % of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA. And what came before GTP? Recent findings indicate that the energy supporting the origin of LUCA's metabolism stemmed from H<sub>2</sub>-dependent CO<sub>2</sub> reduction along routes that strongly resemble the reactions and transition metal catalysts of the acetyl-CoA pathway.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149514"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Anaesthetics disrupt complex I-linked respiration and reverse the ATP synthase","authors":"Enrique Rodriguez , Bella Peng , Nick Lane","doi":"10.1016/j.bbabio.2024.149511","DOIUrl":"10.1016/j.bbabio.2024.149511","url":null,"abstract":"<div><div>The mechanism of volatile general anaesthetics has long been a mystery. Anaesthetics have no structural motifs in common, beyond lipid solubility, yet all exert a similar effect. The fact that the inert gas xenon is an anaesthetic suggests their common mechanism might relate to physical rather than chemical properties. Electron transfer through chiral proteins can induce spin polarization. Recent work suggests that anaesthetics dissipate spin polarization during electron transfer to oxygen, slowing respiration. Here we show that the volatile anaesthetics isoflurane and sevoflurane specifically disrupt complex I-linked respiration in the thoraces of <em>Drosophila melanogaster</em>, with less effect on maximal respiration. Suppression of complex I-linked respiration was greatest with isoflurane. Using high-resolution tissue fluorespirometry, we show that these anaesthetics simultaneously increase mitochondrial membrane potential, implying reversal of the ATP synthase. Inhibition of ATP synthase with oligomycin prevented respiration and increased membrane potential back to the maximal (LEAK state) potential. Magnesium-green fluorescence predicted a collapse in ATP availability following a single anaesthetic dose, consistent with ATP hydrolysis through reversal of the ATP synthase. Raised membrane potential corresponded to a rise in ROS flux, especially with isoflurane. Anaesthetic doses causing respiratory suppression were in the same range as those that induce anaesthesia, although we could not establish tissue concentrations. Our findings show that anaesthetics suppress complex I-linked respiration with concerted downstream effects. But we cannot explain why only mutations in complex I, and not elsewhere in the electron-transfer system, confer hypersensitivity to anaesthetics.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149511"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I","authors":"Jonathan Lasham , Amina Djurabekova , Georgios Kolypetris , Volker Zickermann , Janet Vonck , Vivek Sharma","doi":"10.1016/j.bbabio.2024.149512","DOIUrl":"10.1016/j.bbabio.2024.149512","url":null,"abstract":"<div><div>The charge states of titratable amino acid residues play a key role in the function of membrane-bound bioenergetic proteins. However, determination of these charge states both through experimental and computational approaches is extremely challenging. Cryo-EM density maps can provide insights on the charge states of titratable amino acid residues. By performing classical atomistic molecular dynamics simulations on the high resolution cryo-EM structures of respiratory complex I from <em>Yarrowia lipolytica</em>, we analyze the conformational and charge states of a key acidic residue in its ND1 subunit, aspartic acid D203, which is also a mitochondrial disease mutation locus. We suggest that in the native state of respiratory complex I, D203 is negatively charged and maintains a stable hydrogen bond to a conserved arginine residue. Alternatively, upon conformational change in the turnover state of the enzyme, its sidechain attains a charge-neutral status. We discuss the implications of this analysis on the molecular mechanism of respiratory complex I.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149512"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tim Schulte , Nikki Cecil M. Magdaong , Marilena Di Valentin , Alessandro Agostini , Claudia E. Tait , Dariusz M. Niedzwiedzki , Donatella Carbonera , Eckhard Hofmann
{"title":"Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP)","authors":"Tim Schulte , Nikki Cecil M. Magdaong , Marilena Di Valentin , Alessandro Agostini , Claudia E. Tait , Dariusz M. Niedzwiedzki , Donatella Carbonera , Eckhard Hofmann","doi":"10.1016/j.bbabio.2024.149510","DOIUrl":"10.1016/j.bbabio.2024.149510","url":null,"abstract":"<div><div>Light harvesting proteins are optimized to efficiently collect and transfer light energy for photosynthesis. In eukaryotic dinoflagellates these complexes utilize chlorophylls and a special carotenoid, peridinin, and arrange them for efficient excitation energy transfer. At the same time, the carotenoids protect the system by quenching harmful chlorophyll triplet states. Here we use advanced spectroscopic techniques and X-ray structure analysis to investigate excitation energy transfer processes in the major soluble antenna, the peridinin chlorophyll <em>a</em> protein (PCP) from the free living dinoflagellate <em>Heterocapsa pygmaea</em>. We determined the 3D-structure of this complex at high resolution (1.2 Å). For better comparison, we improved the reference structure of this protein from <em>Amphidinium carterae</em> to a resolution of 1.15 Å. We then used fs and ns time-resolved absorption spectroscopy to study the mechanisms of light harvesting, but also of the photoprotective quenching of the chlorophyll triplet state. The photoprotection site was further characterized by Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy to yield information on water molecules involved in triplet-triplet energy transfer.</div><div>Similar to other PCP complexes, excitation energy transfer from peridinin to chlorophyll is found to be very efficient, with transfer times in the range of 1.6–2.1 ps. One of the four carotenoids, the peridinin 614, is well positioned to quench the chlorophyll triplet state with high efficiency and transfer times in the range of tens of picoseconds. Our structural and dynamic data further support, that the intrinsic water molecule coordinating the chlorophyll Mg ion plays an essential role in photoprotection.</div></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149510"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142331806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Stimulation of cytochrome c oxidase activity by detergents","authors":"Irina Smirnova, Fei Wu, Peter Brzezinski","doi":"10.1016/j.bbabio.2024.149509","DOIUrl":"10.1016/j.bbabio.2024.149509","url":null,"abstract":"<div><p>Cytochrome <em>c</em> oxidase (Cyt<em>c</em>O) is an integral membrane protein, which catalyzes four-electron reduction of oxygen linked to proton uptake and pumping. Amphipathic molecules bind in sites near the so-called K proton pathway of Cyt<em>c</em>O to reversibly modulate its activity. However, purification of Cyt<em>c</em>O for mechanistic studies typically involves the use of detergents, which may interfere with binding of these regulatory molecules. Here, we investigated the Cyt<em>c</em>O enzymatic activity as well as intramolecular electron transfer linked to proton transfer upon addition of different detergents to bovine heart mitoplasts. The Cyt<em>c</em>O activity increased upon addition of alkyl glucosides (DDM and DM) and the steroid analog GDN. The maximum stimulating effect was observed for DDM and DM, and the half-stimulating effect correlated with their CMC values. With GDN the stimulation effect was smaller and occurred at a concentration higher than CMC. A kinetic analysis suggests that the stimulation of activity is due to removal of a ligand bound near the K proton pathway, which indicates that in the native membrane this site is occupied to yield a lower than maximal possible Cyt<em>c</em>O activity. Possible functional consequences are discussed.</p></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149509"},"PeriodicalIF":3.4,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0005272824004791/pdfft?md5=b1e7ca0b37361a04561096943b6c6ddd&pid=1-s2.0-S0005272824004791-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elisabeth Lettau , Christian Lorent , Jens Appel , Marko Boehm , Paul R.F. Cordero , Lars Lauterbach
{"title":"Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module","authors":"Elisabeth Lettau , Christian Lorent , Jens Appel , Marko Boehm , Paul R.F. Cordero , Lars Lauterbach","doi":"10.1016/j.bbabio.2024.149508","DOIUrl":"10.1016/j.bbabio.2024.149508","url":null,"abstract":"<div><p>The NAD<sup>+</sup>-reducing soluble [NiFe] hydrogenase (SH) is the key enzyme for production and consumption of molecular hydrogen (H<sub>2</sub>) in <em>Synechocystis</em> sp. PCC6803. In this study, we focused on the reductase module of the <em>Syn</em>SH and investigated the structural and functional aspects of its subunits, particularly the so far elusive role of HoxE. We demonstrated the importance of HoxE for enzyme functionality, suggesting a regulatory role in maintaining enzyme activity and electron supply. Spectroscopic analysis confirmed that HoxE and HoxF each contain one [2Fe2S] cluster with an almost identical electronic structure. Structure predictions, alongside experimental evidence for ferredoxin interactions, revealed a remarkable similarity between <em>Syn</em>SH and bifurcating hydrogenases, suggesting a related functional mechanism. Our study unveiled the subunit arrangement and cofactor composition essential for biological electron transfer. These findings enhance our understanding of NAD<sup>+</sup>-reducing [NiFe] hydrogenases in terms of their physiological function and structural requirements for biotechnologically relevant modifications.</p></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149508"},"PeriodicalIF":3.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S000527282400478X/pdfft?md5=48c6997ccfd028521473cfcb1e16d60b&pid=1-s2.0-S000527282400478X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142156563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"D1-Tyr246 and D2-Tyr244 in photosystem II: Insights into bicarbonate binding and electron transfer from QA•− to QB","authors":"Ruri Nihara , Keisuke Saito , Hiroshi Kuroda , Yasuto Komatsu , Yang Chen , Hiroshi Ishikita , Yuichiro Takahashi","doi":"10.1016/j.bbabio.2024.149507","DOIUrl":"10.1016/j.bbabio.2024.149507","url":null,"abstract":"<div><p>In photosystem II (PSII), D1-Tyr246 and D2-Tyr244 are symmetrically located at the binding site of the bicarbonate ligand of the non-heme Fe complex. Here, we investigated the role of the symmetrically arranged tyrosine pair, D1-Tyr246 and D2-Tyr244, in the function of PSII, by generating four chloroplast mutants of PSII from <em>Chlamydomonas reinhardtii</em>: D1-Y246F, D1-Y246T, D2-Y244F, and D2-Y244T. The mutants exhibited altered photoautotrophic growth, reduced PSII protein accumulation, and impaired O<sub>2</sub>-evolving activity. Flash-induced fluorescence yield decay kinetics indicated a significant slowdown in electron transfer from Q<sub>A</sub><sup>•−</sup> to Q<sub>B</sub> in all mutants. Bicarbonate reconstitution resulted in enhanced O<sub>2</sub>-evolving activity, suggesting destabilization of bicarbonate binding in the mutants. Structural analyses based on a quantum mechanical/molecular mechanical approach identified the existence of a water channel that leads to incorporation of bulk water molecules and destabilization of the bicarbonate binding site. The water intake channels, crucial for bicarbonate stability, exhibited distinct paths in the mutants. These findings shed light on the essential role of the tyrosine pair in maintaining bicarbonate stability and facilitating efficient electron transfer in native PSII.</p></div>","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1866 1","pages":"Article 149507"},"PeriodicalIF":3.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michaela Kunzová , Eva Doleželová , Brian Panicucci , Alena Zíková
{"title":"FOF1-ATP synthase: When it pays to go in reverse","authors":"Michaela Kunzová , Eva Doleželová , Brian Panicucci , Alena Zíková","doi":"10.1016/j.bbabio.2024.149174","DOIUrl":"10.1016/j.bbabio.2024.149174","url":null,"abstract":"","PeriodicalId":50731,"journal":{"name":"Biochimica et Biophysica Acta-Bioenergetics","volume":"1865 ","pages":"Article 149174"},"PeriodicalIF":3.4,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142076168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}