Biochimica et Biophysica Acta-Bioenergetics最新文献_第4页

Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I 基于低温电子显微镜和呼吸复合体 I 分子动力学模拟的氨基酸电荷状态评估。

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-09-24 DOI: 10.1016/j.bbabio.2024.149512

Jonathan Lasham , Amina Djurabekova , Georgios Kolypetris , Volker Zickermann , Janet Vonck , Vivek Sharma

{"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}

引用次数: 0

Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP) Heterocapsa pygmaea（HPPCP）的过叶素-叶绿素 a 蛋白（PCP）复合物的结构和光谱特征。

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-09-24 DOI: 10.1016/j.bbabio.2024.149510

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}

引用次数: 0

Stimulation of cytochrome c oxidase activity by detergents 清洁剂对细胞色素 c 氧化酶活性的刺激

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-09-07 DOI: 10.1016/j.bbabio.2024.149509

Irina Smirnova, Fei Wu, Peter Brzezinski

{"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}

引用次数: 0

Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module 洞察 Synechocystis sp. PCC6803 氢酶还原酶模块的电子传递和分叉。

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-09-06 DOI: 10.1016/j.bbabio.2024.149508

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}

引用次数: 0

D1-Tyr246 and D2-Tyr244 in photosystem II: Insights into bicarbonate binding and electron transfer from QA•− to QB 光系统 II 中的 D1-Tyr246 和 D2-Tyr244：对碳酸氢盐结合以及从 QA 到 QB 的电子传递的见解。

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-30 DOI: 10.1016/j.bbabio.2024.149507

Ruri Nihara , Keisuke Saito , Hiroshi Kuroda , Yasuto Komatsu , Yang Chen , Hiroshi Ishikita , Yuichiro Takahashi

{"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}

引用次数: 0

Innovations in Mitochondrial Research: Exploring Exercise-Induced Mitochondrial Adaptations in Skeletal Muscle 线粒体研究的创新：探索运动诱导的骨骼肌线粒体适应性

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-26 DOI: 10.1016/j.bbabio.2024.149156

Kawtar Kathbane , Jorge Alvarez-Luis , Pau Gama-Perez , Livia Neri , Nuria Bosch , Luiza H.D. Cardoso , Timea Komlódi , Erich Gnaiger , Pablo M. Garcia-Roves

引用次数: 0

FOF1-ATP synthase: When it pays to go in reverse FOF1-ATP 合酶：反向操作的好处

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-26 DOI: 10.1016/j.bbabio.2024.149174

Michaela Kunzová , Eva Doleželová , Brian Panicucci , Alena Zíková

引用次数: 0

Regulating the activity of mouse and human UCP1 调节小鼠和人类 UCP1 的活性

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-26 DOI: 10.1016/j.bbabio.2024.149180

Barbara Cannon, Irina G. Shabalina, Beatrice J. Garcia, G. Ruda F. Braz, Jan Nedergaard

引用次数: 0

Monotopic quinone reductases from Staphylococcus aureus: The two alternative NADH: quinone oxidoreductases are players with different molecular and cellular roles 金黄色葡萄球菌的单位醌还原酶：两种可供选择的 NADH：醌氧化还原酶具有不同的分子和细胞作用

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-26 DOI: 10.1016/j.bbabio.2024.149132

Filipa V. Sena , Filipe M. Sousa , Ana R. Pereira , Teresa Catarino , Eurico J. Cabrita , Mariana G. Pinho , Francisco R. Pinto , Manuela M. Pereira

引用次数: 0

Respiratory complexes and supercomplexes of the model yeast S. cerevisiae 模式酵母 S. cerevisiae 的呼吸复合体和超级复合体

IF 3.4 2区生物学

Biochimica et Biophysica Acta-Bioenergetics Pub Date : 2024-08-26 DOI: 10.1016/j.bbabio.2024.149133

Amandine Maréchal , Nikos Pinotsis , Claudia Burn-Leefe , Sarah Jones , Brigitte Meunier

引用次数: 0