[{"department":[{"_id":"LeSa"}],"ddc":["570"],"date_updated":"2023-08-01T13:45:12Z","status":"public","type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12757","issue":"5","volume":480,"license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1470-8728"],"issn":["0264-6021"]},"publication_status":"published","month":"03","intvolume":" 480","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"article_processing_charge":"No","external_id":{"isi":["000957065700001"],"pmid":["36920092"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285."},"date_published":"2023-03-15T00:00:00Z","doi":"10.1042/BCJ20210285","date_created":"2023-03-26T22:01:06Z","page":"319-333","day":"15","publication":"The Biochemical Journal","has_accepted_license":"1","isi":1,"year":"2023","publisher":"Portland Press","quality_controlled":"1","oa":1},{"date_created":"2023-07-16T22:01:10Z","doi":"10.3390/vaccines11061014","date_published":"2023-06-01T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Vaccines","day":"01","oa":1,"publisher":"MDPI","quality_controlled":"1","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","external_id":{"isi":["001017740000001"]},"article_processing_charge":"No","author":[{"full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin","first_name":"Dmitri"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"first_name":"Maria","full_name":"Stegantseva, Maria","last_name":"Stegantseva"},{"first_name":"Sergey","last_name":"Golenchenko","full_name":"Golenchenko, Sergey"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"first_name":"Simon","last_name":"Dubovik","full_name":"Dubovik, Simon"},{"full_name":"Lutskovich, Dzmitry","last_name":"Lutskovich","first_name":"Dzmitry"},{"id":"62304f89-eb97-11eb-a6c2-8903dd183976","first_name":"Anton","full_name":"Kavaleuski, Anton","orcid":"0000-0003-2091-526X","last_name":"Kavaleuski"},{"first_name":"Alexander","last_name":"Meleshko","full_name":"Meleshko, Alexander"}],"title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","citation":{"ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1014","issue":"6","volume":11,"publication_status":"published","publication_identifier":{"eissn":["2076-393X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","file_id":"13244","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_Vaccines_Dormeshkin.pdf","date_created":"2023-07-18T07:25:43Z","creator":"dernst","file_size":2339746,"date_updated":"2023-07-18T07:25:43Z"}],"scopus_import":"1","intvolume":" 11","month":"06","abstract":[{"lang":"eng","text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study."}],"oa_version":"Published Version","file_date_updated":"2023-07-18T07:25:43Z","department":[{"_id":"LeSa"}],"date_updated":"2023-08-02T06:31:19Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"13232"},{"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_size":6071553,"date_updated":"2023-04-19T14:33:41Z","creator":"vkravchu","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_created":"2023-04-19T14:33:41Z","embargo_to":"local","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-04-20","checksum":"5ebb6345cb4119f93460c81310265a6d","file_id":"12852"},{"creator":"vkravchu","file_size":19468766,"date_updated":"2023-04-20T07:02:59Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","date_created":"2023-04-19T14:33:52Z","relation":"source_file","access_level":"closed","embargo_to":"local","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo":"2024-04-20","checksum":"c12055c48411d030d2afa51de2166221","file_id":"12853"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12138","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"date_updated":"2023-08-04T08:54:51Z","ddc":["570","572"],"file_date_updated":"2023-04-20T07:02:59Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"_id":"12781","type":"dissertation","status":"public","has_accepted_license":"1","year":"2023","day":"23","page":"127","doi":"10.15479/at:ista:12781","date_published":"2023-03-23T00:00:00Z","date_created":"2023-03-31T12:24:42Z","publisher":"Institute of Science and Technology Austria","citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}]},{"article_number":"4681","author":[{"full_name":"Zhao, Ziyu","last_name":"Zhao","first_name":"Ziyu"},{"full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino","first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Knoppová","full_name":"Knoppová, Jana","first_name":"Jana"},{"last_name":"Sobotka","full_name":"Sobotka, Roman","first_name":"Roman"},{"full_name":"Murray, James W.","last_name":"Murray","first_name":"James W."},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"},{"full_name":"Komenda, Josef","last_name":"Komenda","first_name":"Josef"}],"article_processing_charge":"Yes","external_id":{"isi":["001042606700004"]},"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","citation":{"ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","date_published":"2023-08-04T00:00:00Z","doi":"10.1038/s41467-023-40388-6","date_created":"2023-08-13T22:01:13Z","has_accepted_license":"1","isi":1,"year":"2023","day":"04","publication":"Nature Communications","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14040","department":[{"_id":"LeSa"}],"file_date_updated":"2023-08-14T07:01:12Z","date_updated":"2023-12-13T12:06:56Z","ddc":["570"],"scopus_import":"1","month":"08","intvolume":" 14","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster."}],"oa_version":"Published Version","volume":14,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"checksum":"3b9043df3d51c300f9be95eac3ff9d0b","file_id":"14044","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-08-14T07:01:12Z","file_name":"2023_NatureComm_Zhao.pdf","date_updated":"2023-08-14T07:01:12Z","file_size":2315325,"creator":"dernst"}],"language":[{"iso":"eng"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular Cell Biology. Springer Nature, 2022. https://doi.org/10.1038/s41580-021-00415-0.","ista":"Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” Nature Reviews Molecular Cell Biology, vol. 23, Springer Nature, 2022, pp. 141–161, doi:10.1038/s41580-021-00415-0.","ieee":"I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of the mitochondrial respiratory chain,” Nature Reviews Molecular Cell Biology, vol. 23. Springer Nature, pp. 141–161, 2022.","short":"I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161.","ama":"Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 2022;23:141–161. doi:10.1038/s41580-021-00415-0","apa":"Vercellino, I., & Sazanov, L. A. (2022). The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-021-00415-0"},"title":"The assembly, regulation and function of the mitochondrial respiratory chain","author":[{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","full_name":"Vercellino, Irene","orcid":" 0000-0001-5618-3449","last_name":"Vercellino"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["34621061"],"isi":["000705697100001"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"Springer Nature","day":"01","publication":"Nature Reviews Molecular Cell Biology","isi":1,"year":"2022","date_published":"2022-02-01T00:00:00Z","doi":"10.1038/s41580-021-00415-0","date_created":"2021-10-24T22:01:35Z","page":"141–161","_id":"10182","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-02T06:55:42Z","department":[{"_id":"LeSa"}],"pmid":1,"oa_version":"None","abstract":[{"text":"The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases.","lang":"eng"}],"month":"02","intvolume":" 23","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"publication_status":"published","volume":23},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2022-04-15T09:32:35Z","date_published":"2022-06-01T00:00:00Z","doi":"10.1016/j.sbi.2022.102350","year":"2022","isi":1,"has_accepted_license":"1","publication":"Current Opinion in Structural Biology","day":"01","article_number":"102350","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000829029500020"],"pmid":["35316665"]},"author":[{"full_name":"Kampjut, Domen","last_name":"Kampjut","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","citation":{"chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350.","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology, vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” Current Opinion in Structural Biology, vol. 74. Elsevier, 2022.","apa":"Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 74","month":"06","abstract":[{"lang":"eng","text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I."}],"pmid":1,"oa_version":"Published Version","volume":74,"publication_status":"published","publication_identifier":{"issn":["0959-440X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"11725","checksum":"72bdde48853643a32d42b75f54965c44","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-08-05T05:56:03Z","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","creator":"dernst","date_updated":"2022-08-05T05:56:03Z","file_size":815607}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Molecular Biology","Structural Biology"],"status":"public","_id":"11167","department":[{"_id":"LeSa"}],"file_date_updated":"2022-08-05T05:56:03Z","date_updated":"2023-08-03T06:31:06Z","ddc":["570"]},{"date_updated":"2023-08-03T11:51:58Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2022-07-13T07:44:58Z","_id":"11551","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["23993642"]},"publication_status":"published","file":[{"file_id":"11571","checksum":"965f88bbcef3fd0c3e121340555c4467","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-07-13T07:44:58Z","file_name":"2022_communicationsbiology_Molina-Granada.pdf","creator":"kschuh","date_updated":"2022-07-13T07:44:58Z","file_size":2335369}],"language":[{"iso":"eng"}],"volume":5,"issue":"1","abstract":[{"lang":"eng","text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 5","citation":{"chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03568-6.","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” Communications Biology, vol. 5, no. 1, 620, Springer Nature, 2022, doi:10.1038/s42003-022-03568-6.","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ieee":"D. Molina-Granada et al., “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” Communications Biology, vol. 5, no. 1. Springer Nature, 2022.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03568-6","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 2022;5(1). doi:10.1038/s42003-022-03568-6"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Molina-Granada, David","last_name":"Molina-Granada","first_name":"David"},{"first_name":"Emiliano","last_name":"González-Vioque","full_name":"González-Vioque, Emiliano"},{"first_name":"Marris G.","full_name":"Dibley, Marris G.","last_name":"Dibley"},{"full_name":"Cabrera-Pérez, Raquel","last_name":"Cabrera-Pérez","first_name":"Raquel"},{"first_name":"Antoni","full_name":"Vallbona-Garcia, Antoni","last_name":"Vallbona-Garcia"},{"first_name":"Javier","last_name":"Torres-Torronteras","full_name":"Torres-Torronteras, Javier"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"},{"first_name":"Michael T.","full_name":"Ryan, Michael T.","last_name":"Ryan"},{"last_name":"Cámara","full_name":"Cámara, Yolanda","first_name":"Yolanda"},{"last_name":"Martí","full_name":"Martí, Ramon","first_name":"Ramon"}],"external_id":{"isi":["000815098500002"],"pmid":[" 35739187"]},"article_processing_charge":"No","title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","article_number":"620","isi":1,"has_accepted_license":"1","year":"2022","day":"23","publication":"Communications Biology","doi":"10.1038/s42003-022-03568-6","date_published":"2022-06-23T00:00:00Z","date_created":"2022-07-10T22:01:52Z","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","quality_controlled":"1","publisher":"Springer Nature","oa":1},{"issue":"5","volume":71,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"23b51c163636bf9313f7f0818312e67e","file_id":"12498","success":1,"creator":"dernst","date_updated":"2023-02-03T08:34:48Z","file_size":7812696,"date_created":"2023-02-03T08:34:48Z","file_name":"2022_Microscopy_Gerle.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"intvolume":" 71","month":"10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica."}],"department":[{"_id":"LeSa"}],"file_date_updated":"2023-02-03T08:34:48Z","ddc":["570"],"date_updated":"2023-08-03T12:13:37Z","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"11648","date_created":"2022-07-25T10:04:58Z","date_published":"2022-10-01T00:00:00Z","doi":"10.1093/jmicro/dfac037","page":"249-261","publication":"Microscopy","day":"01","year":"2022","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"article_processing_charge":"No","author":[{"full_name":"Gerle, Christoph","last_name":"Gerle","first_name":"Christoph"},{"last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi","first_name":"Jun-ichi"},{"first_name":"Tomoko","full_name":"Yamaguchi, Tomoko","last_name":"Yamaguchi"},{"first_name":"Atsuko","full_name":"Nakanishi, Atsuko","last_name":"Nakanishi"},{"orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"first_name":"Fumiaki","last_name":"Makino","full_name":"Makino, Fumiaki"},{"first_name":"Tomoko","full_name":"Miyata, Tomoko","last_name":"Miyata"},{"last_name":"Kawamoto","full_name":"Kawamoto, Akihiro","first_name":"Akihiro"},{"first_name":"Ken","full_name":"Yokoyama, Ken","last_name":"Yokoyama"},{"last_name":"Namba","full_name":"Namba, Keiichi","first_name":"Keiichi"},{"last_name":"Kurisu","full_name":"Kurisu, Genji","first_name":"Genji"},{"first_name":"Takayuki","full_name":"Kato, Takayuki","last_name":"Kato"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” Microscopy. Oxford University Press, 2022. https://doi.org/10.1093/jmicro/dfac037.","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” Microscopy, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:10.1093/jmicro/dfac037.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. Oxford University Press. https://doi.org/10.1093/jmicro/dfac037","ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 2022;71(5):249-261. doi:10.1093/jmicro/dfac037","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","ieee":"C. Gerle et al., “Structures of multisubunit membrane complexes with the CRYO ARM 200,” Microscopy, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022."}},{"project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020"}],"citation":{"short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” Nature, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. Nature. 2022;609(7928):808-814. doi:10.1038/s41586-022-05199-7","apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., & Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05199-7","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” Nature, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:10.1038/s41586-022-05199-7.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05199-7."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["36104567"],"isi":["000854788200001"]},"author":[{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav"},{"first_name":"Olga","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E","last_name":"Petrova","full_name":"Petrova, Olga"},{"first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","full_name":"Kampjut, Domen"},{"last_name":"Wojciechowska-Bason","full_name":"Wojciechowska-Bason, Anna","first_name":"Anna"},{"first_name":"Zara","full_name":"Breese, Zara","last_name":"Breese"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"title":"A universal coupling mechanism of respiratory complex I","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2022","has_accepted_license":"1","isi":1,"publication":"Nature","day":"22","page":"808-814","date_created":"2023-01-12T12:04:33Z","date_published":"2022-09-22T00:00:00Z","doi":"10.1038/s41586-022-05199-7","_id":"12138","article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","date_updated":"2023-08-04T08:54:52Z","ddc":["572"],"file_date_updated":"2023-05-30T17:07:05Z","department":[{"_id":"LeSa"}],"abstract":[{"text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","intvolume":" 609","month":"09","publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"d42a93e24f59e883ef0b5429832391d0","file_id":"13104","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf","date_created":"2023-05-30T17:05:31Z","creator":"lsazanov","file_size":1425655,"date_updated":"2023-05-30T17:05:31Z"},{"file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","date_created":"2023-05-30T17:07:05Z","file_size":9842513,"date_updated":"2023-05-30T17:07:05Z","creator":"lsazanov","success":1,"checksum":"5422bc0a73b3daadafa262c7ea6deae3","file_id":"13105","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"issue":"7928","volume":609,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12781"}],"link":[{"url":"https://doi.org/10.1038/s41586-022-05457-8","relation":"erratum"},{"url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","relation":"press_release","description":"News on ISTA website"}]}},{"article_number":"965446","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"last_name":"Shapira","full_name":"Shapira, Michail","first_name":"Michail"},{"full_name":"Dubovik, Simon","last_name":"Dubovik","first_name":"Simon"},{"orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","last_name":"Kavaleuski","first_name":"Anton","id":"4968f7ad-eb97-11eb-a6c2-8ed382e8912c"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"first_name":"Alexandr","last_name":"Migas","full_name":"Migas, Alexandr"},{"first_name":"Alexander","full_name":"Meleshko, Alexander","last_name":"Meleshko"},{"last_name":"Semyonov","full_name":"Semyonov, Sergei","first_name":"Sergei"}],"external_id":{"isi":["000862479100001"]},"article_processing_charge":"No","title":"Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library","citation":{"ama":"Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 2022;13. doi:10.3389/fimmu.2022.965446","apa":"Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas, A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. Frontiers Media. https://doi.org/10.3389/fimmu.2022.965446","short":"D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas, A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).","ieee":"D. Dormeshkin et al., “Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library,” Frontiers in Immunology, vol. 13. Frontiers Media, 2022.","mla":"Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology, vol. 13, 965446, Frontiers Media, 2022, doi:10.3389/fimmu.2022.965446.","ista":"Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13, 965446.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” Frontiers in Immunology. Frontiers Media, 2022. https://doi.org/10.3389/fimmu.2022.965446."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Frontiers Media","quality_controlled":"1","oa":1,"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.","doi":"10.3389/fimmu.2022.965446","date_published":"2022-09-16T00:00:00Z","date_created":"2023-01-16T09:56:57Z","isi":1,"has_accepted_license":"1","year":"2022","day":"16","publication":"Frontiers in Immunology","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Immunology","Immunology and Allergy","COVID-19","SARS-CoV-2","synthetic library","RBD","neutralization nanobody","VHH"],"_id":"12252","department":[{"_id":"LeSa"}],"file_date_updated":"2023-01-30T09:22:26Z","date_updated":"2023-08-04T09:49:24Z","ddc":["570"],"scopus_import":"1","month":"09","intvolume":" 13","abstract":[{"lang":"eng","text":"The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 1011 diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\\ml and 9.6 ng\\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants."}],"oa_version":"Published Version","volume":13,"publication_identifier":{"issn":["1664-3224"]},"publication_status":"published","file":[{"creator":"dernst","file_size":5695892,"date_updated":"2023-01-30T09:22:26Z","file_name":"2022_FrontiersImmunology_Dormeshkin.pdf","date_created":"2023-01-30T09:22:26Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"f8f5d8110710033d0532e7e08bf9dad4","file_id":"12443"}],"language":[{"iso":"eng"}]},{"date_updated":"2023-08-04T10:28:04Z","department":[{"_id":"SiHi"},{"_id":"LeSa"}],"_id":"12282","status":"public","type":"journal_article","article_type":"letter_note","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"volume":135,"issue":"8","oa_version":"None","pmid":1,"abstract":[{"text":"From a simple thought to a multicellular movement","lang":"eng"}],"intvolume":" 135","month":"04","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 135(8), 260017.","chicago":"Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science. The Company of Biologists, 2022. https://doi.org/10.1242/jcs.260017.","ieee":"N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole,” Journal of Cell Science, vol. 135, no. 8. The Company of Biologists, 2022.","short":"N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022).","ama":"Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 2022;135(8). doi:10.1242/jcs.260017","apa":"Amberg, N., Stouffer, M. A., & Vercellino, I. (2022). Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260017","mla":"Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” Journal of Cell Science, vol. 135, no. 8, 260017, The Company of Biologists, 2022, doi:10.1242/jcs.260017."},"title":"Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole","article_processing_charge":"No","external_id":{"pmid":["35438168"],"isi":["000798123600015"]},"author":[{"last_name":"Amberg","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"full_name":"Stouffer, Melissa A","last_name":"Stouffer","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","last_name":"Vercellino","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"}],"article_number":"260017","publication":"Journal of Cell Science","day":"19","year":"2022","isi":1,"date_created":"2023-01-16T10:03:14Z","doi":"10.1242/jcs.260017","date_published":"2022-04-19T00:00:00Z","acknowledgement":"The authors want to thank Professors Carrie Bernecky, Tom Henzinger, Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant contribution to the discussion that lead to this article.","publisher":"The Company of Biologists","quality_controlled":"1"},{"citation":{"apa":"Çoruh, M. O., Gündüz, G., Çolak, Ü., & Maviş, B. (2022). pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. MDPI. https://doi.org/10.3390/colorants1020010","ama":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 2022;1(2):149-164. doi:10.3390/colorants1020010","short":"M.O. Çoruh, G. Gündüz, Ü. Çolak, B. Maviş, Colorants 1 (2022) 149–164.","ieee":"M. O. Çoruh, G. Gündüz, Ü. Çolak, and B. Maviş, “pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra,” Colorants, vol. 1, no. 2. MDPI, pp. 149–164, 2022.","mla":"Çoruh, Mehmet Orkun, et al. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants, vol. 1, no. 2, MDPI, 2022, pp. 149–64, doi:10.3390/colorants1020010.","ista":"Çoruh MO, Gündüz G, Çolak Ü, Maviş B. 2022. pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra. Colorants. 1(2), 149–164.","chicago":"Çoruh, Mehmet Orkun, Güngör Gündüz, Üner Çolak, and Bora Maviş. “PH-Dependent Coloring of Combination Effect Pigments with Anthocyanins from Brassica Oleracea Var. Capitata F. Rubra.” Colorants. MDPI, 2022. https://doi.org/10.3390/colorants1020010."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","author":[{"first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh"},{"first_name":"Güngör","last_name":"Gündüz","full_name":"Gündüz, Güngör"},{"full_name":"Çolak, Üner","last_name":"Çolak","first_name":"Üner"},{"full_name":"Maviş, Bora","last_name":"Maviş","first_name":"Bora"}],"title":"pH-dependent coloring of combination effect pigments with anthocyanins from Brassica oleracea var. capitata F. rubra","acknowledgement":"This research was partly funded by Hacettepe University (Bilimsel Ara¸stırma Projeleri\r\nKoordinasyon Birimi), grant number FHD-2015-8094.The authors are indebted to Ahmet Önal for his supports in acquiring the fluorescence spectra and the decision of excitation wavelengths. The authors also acknowledge use of the services and facilities of UNAM-National Nanotechnology Research Center at Bilkent University and mica donation from Sabuncular Mining Co.","oa":1,"quality_controlled":"1","publisher":"MDPI","year":"2022","has_accepted_license":"1","publication":"Colorants","day":"01","page":"149-164","date_created":"2022-04-04T09:03:54Z","doi":"10.3390/colorants1020010","date_published":"2022-04-01T00:00:00Z","_id":"10945","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-09T10:12:22Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2022-04-04T10:39:24Z","abstract":[{"lang":"eng","text":"Mica-titania pearlescent pigments (MTs) were previously coated with organic molecules to obtain combination pigments (CPs) for achieving certain improvements or functionalities. Anthocyanins (ACNs) are molecules that can be extracted from natural resources and exhibit color changes via pH modifications of the enclosing medium. The purpose of the study was to produce a new series of CPs by depositing ACNs on MTs at different pH values, to observe the changes in color, and to associate these changes to thermogravimetrically determined deposition efficiencies in light of spectral differences. The extraction and deposition methods were based on aqueous chemistry and were straightforward. The ACN deposition generally increased with increasing pH and correlated with the consistency between the charges of the MT surfaces and the dominant ACN species at a specific pH value. The fluorescence of the CPs was inversely correlated with the deposition quantities invoking the possibility of a quenching effect."}],"oa_version":"Published Version","intvolume":" 1","month":"04","publication_status":"published","publication_identifier":{"issn":["2079-6447"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10949","checksum":"2c15c8d3041ebc36bc64870247081758","success":1,"creator":"dernst","date_updated":"2022-04-04T10:39:24Z","file_size":2437988,"date_created":"2022-04-04T10:39:24Z","file_name":"2022_Colorants_Coruh.pdf"}],"volume":1,"issue":"2"},{"abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"08","intvolume":" 106","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":106,"_id":"11462","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-10T07:15:02Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","quality_controlled":"1","publisher":"Springer Nature","isi":1,"year":"2022","day":"01","publication":"Applied Microbiology and Biotechnology","page":"5093-5103","doi":"10.1007/s00253-022-12022-w","date_published":"2022-08-01T00:00:00Z","date_created":"2022-06-26T22:01:34Z","citation":{"ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology and Biotechnology. Springer Nature, 2022. https://doi.org/10.1007/s00253-022-12022-w.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 2022;106:5093-5103. doi:10.1007/s00253-022-12022-w","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., & Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. Springer Nature. https://doi.org/10.1007/s00253-022-12022-w","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ieee":"D. Dormeshkin et al., “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” Applied Microbiology and Biotechnology, vol. 106. Springer Nature, pp. 5093–5103, 2022.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” Applied Microbiology and Biotechnology, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:10.1007/s00253-022-12022-w."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"first_name":"Michail","last_name":"Shapira","full_name":"Shapira, Michail"},{"first_name":"Alena","full_name":"Karputs, Alena","last_name":"Karputs"},{"full_name":"Kavaleuski, Anton","orcid":"0000-0003-2091-526X","last_name":"Kavaleuski","first_name":"Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976"},{"full_name":"Kuzminski, Ivan","last_name":"Kuzminski","first_name":"Ivan"},{"last_name":"Stepanova","full_name":"Stepanova, Elena","first_name":"Elena"},{"first_name":"Andrei","last_name":"Gilep","full_name":"Gilep, Andrei"}],"external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"article_processing_charge":"No","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development"},{"article_number":"e2020857118","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","ieee":"L. Abas et al., “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021.","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:10.1073/pnas.2020857118.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"first_name":"Martina","full_name":"Kolb, Martina","last_name":"Kolb"},{"last_name":"Stadlmann","full_name":"Stadlmann, Johannes","first_name":"Johannes"},{"last_name":"Janacek","full_name":"Janacek, Dorina P.","first_name":"Dorina P."},{"first_name":"Kristina","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1581-881X","full_name":"Lukic, Kristina","last_name":"Lukic"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mach","full_name":"Mach, Lukas","first_name":"Lukas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z.","last_name":"Hammes"}],"external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"article_processing_charge":"No","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"05","publication":"PNAS","doi":"10.1073/pnas.2020857118","date_published":"2021-01-05T00:00:00Z","date_created":"2021-01-03T23:01:23Z","_id":"8993","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T13:29:23Z","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"month":"01","intvolume":" 118","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]},"issue":"1","volume":118,"ec_funded":1},{"publication_identifier":{"eissn":["25890042"]},"publication_status":"published","file":[{"date_updated":"2021-03-03T07:38:14Z","file_size":7431411,"creator":"dernst","date_created":"2021-03-03T07:38:14Z","file_name":"2021_iScience_Kampjut.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9219","checksum":"50585447386fe5842f07ab9b3a66e7e9","success":1}],"language":[{"iso":"eng"}],"issue":"3","volume":24,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"abstract":[{"text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 24","date_updated":"2023-08-07T13:54:06Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2021-03-03T07:38:14Z","_id":"9205","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","has_accepted_license":"1","isi":1,"year":"2021","day":"19","publication":"iScience","date_published":"2021-03-19T00:00:00Z","doi":"10.1016/j.isci.2021.102139","date_created":"2021-02-28T23:01:24Z","acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience. Elsevier, 2021. https://doi.org/10.1016/j.isci.2021.102139.","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139.","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” IScience, vol. 24, no. 3, 102139, Elsevier, 2021, doi:10.1016/j.isci.2021.102139.","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” iScience, vol. 24, no. 3. Elsevier, 2021.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).","ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. iScience. 2021;24(3). doi:10.1016/j.isci.2021.102139","apa":"Kampjut, D., Steiner, J., & Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. IScience. Elsevier. https://doi.org/10.1016/j.isci.2021.102139"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Kampjut","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen"},{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Steiner","full_name":"Steiner, Julia"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["33665558"],"isi":["000631646000012"]},"article_processing_charge":"No","title":"Cryo-EM grid optimization for membrane proteins","article_number":"102139","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}]},{"scopus_import":"1","month":"10","intvolume":" 598","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"abstract":[{"text":"The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":598,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/boosting-the-cells-power-house/","relation":"press_release","description":"News on IST Webpage"}]},"issue":"7880","ec_funded":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"10146","department":[{"_id":"LeSa"}],"date_updated":"2023-08-14T08:01:21Z","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411.","page":"364-367","doi":"10.1038/s41586-021-03927-z","date_published":"2021-10-14T00:00:00Z","date_created":"2021-10-17T22:01:17Z","isi":1,"year":"2021","day":"14","publication":"Nature","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"author":[{"first_name":"Irene","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","last_name":"Vercellino"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["34616041"],"isi":["000704581600001"]},"title":"Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV","citation":{"ama":"Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z","apa":"Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z","ieee":"I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021.","short":"I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z.","ista":"Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9.","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","ieee":"M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021.","chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304."},"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun","last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","first_name":"Mehmet Orkun"},{"first_name":"Anna","full_name":"Frank, Anna","last_name":"Frank"},{"last_name":"Tanaka","full_name":"Tanaka, Hideaki","first_name":"Hideaki"},{"first_name":"Akihiro","full_name":"Kawamoto, Akihiro","last_name":"Kawamoto"},{"first_name":"Eithar","last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar"},{"first_name":"Takayuki","full_name":"Kato, Takayuki","last_name":"Kato"},{"first_name":"Keiichi","full_name":"Namba, Keiichi","last_name":"Namba"},{"first_name":"Christoph","last_name":"Gerle","full_name":"Gerle, Christoph"},{"last_name":"Nowaczyk","full_name":"Nowaczyk, Marc M.","first_name":"Marc M."},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"}],"article_number":"304","publication":"Communications Biology","day":"08","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-11-19T11:37:29Z","date_published":"2021-03-08T00:00:00Z","doi":"10.1038/s42003-021-01808-9","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","oa":1,"quality_controlled":"1","publisher":"Springer ","ddc":["570"],"date_updated":"2023-08-14T11:51:19Z","department":[{"_id":"LeSa"}],"file_date_updated":"2021-11-19T15:09:18Z","_id":"10310","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"10318","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"date_updated":"2021-11-19T15:09:18Z","file_size":6030261,"creator":"cchlebak","date_created":"2021-11-19T15:09:18Z","file_name":"2021_CommBio_Çoruh.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"issue":"1","volume":4,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.","lang":"eng"}],"intvolume":" 4","month":"03","scopus_import":"1"},{"volume":1861,"issue":"8","language":[{"iso":"eng"}],"file":[{"file_name":"2020_BBA_Adjobo_Hermans.pdf","date_created":"2020-05-04T12:25:19Z","creator":"dernst","file_size":3826792,"date_updated":"2020-07-14T12:48:03Z","file_id":"7798","checksum":"a9b152381307cf45fe266a8dc5640388","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["18792650"],"issn":["00052728"]},"intvolume":" 1861","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"LeSa"}],"ddc":["570"],"date_updated":"2023-08-21T06:19:18Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"7788","date_created":"2020-05-03T22:00:47Z","doi":"10.1016/j.bbabio.2020.148213","date_published":"2020-08-01T00:00:00Z","publication":"Biochimica et Biophysica Acta - Bioenergetics","day":"01","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","title":"NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2","external_id":{"isi":["000540842000012"],"pmid":["32335026"]},"article_processing_charge":"No","author":[{"first_name":"Merel J.W.","full_name":"Adjobo-Hermans, Merel J.W.","last_name":"Adjobo-Hermans"},{"full_name":"De Haas, Ria","last_name":"De Haas","first_name":"Ria"},{"last_name":"Willems","full_name":"Willems, Peter H.G.M.","first_name":"Peter H.G.M."},{"full_name":"Wojtala, Aleksandra","last_name":"Wojtala","first_name":"Aleksandra"},{"last_name":"Van Emst-De Vries","full_name":"Van Emst-De Vries, Sjenet E.","first_name":"Sjenet E."},{"last_name":"Wagenaars","full_name":"Wagenaars, Jori A.","first_name":"Jori A."},{"full_name":"Van Den Brand, Mariel","last_name":"Van Den Brand","first_name":"Mariel"},{"full_name":"Rodenburg, Richard J.","last_name":"Rodenburg","first_name":"Richard J."},{"first_name":"Jan A.M.","last_name":"Smeitink","full_name":"Smeitink, Jan A.M."},{"first_name":"Leo G.","last_name":"Nijtmans","full_name":"Nijtmans, Leo G."},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wieckowski","full_name":"Wieckowski, Mariusz R.","first_name":"Mariusz R."},{"first_name":"Werner J.H.","full_name":"Koopman, Werner J.H.","last_name":"Koopman"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8). doi:10.1016/j.bbabio.2020.148213","apa":"Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A., Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213","ieee":"M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8. Elsevier, 2020.","short":"M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink, L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica Acta - Bioenergetics 1861 (2020).","mla":"Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213, Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.","ista":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213.","chicago":"Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand, et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213."},"article_number":"148213"},{"_id":"8040","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-22T07:49:38Z","department":[{"_id":"LeSa"}],"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"month":"05","intvolume":" 142","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00027863"],"eissn":["15205126"]},"publication_status":"published","volume":142,"issue":"20","related_material":{"record":[{"relation":"research_data","id":"9326","status":"public"},{"relation":"research_data","status":"public","id":"9713"},{"id":"9878","status":"public","relation":"research_data"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I,” Journal of the American Chemical Society, vol. 142, no. 20. American Chemical Society, pp. 9220–9230, 2020.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142 (2020) 9220–9230.","ama":"Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230. doi:10.1021/jacs.9b13450","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b13450","mla":"Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society, vol. 142, no. 20, American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 142(20), 9220–9230.","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450."},"title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","author":[{"first_name":"Chitrak","last_name":"Gupta","full_name":"Gupta, Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"full_name":"Chan, Chun Kit","last_name":"Chan","first_name":"Chun Kit"},{"full_name":"Dehez, Francois","last_name":"Dehez","first_name":"Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"full_name":"Gunner, M. R.","last_name":"Gunner","first_name":"M. R."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"},{"full_name":"Singharoy, Abhishek","last_name":"Singharoy","first_name":"Abhishek"}],"external_id":{"isi":["000537415600020"],"pmid":["32347721"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"American Chemical Society","day":"20","publication":"Journal of the American Chemical Society","isi":1,"year":"2020","doi":"10.1021/jacs.9b13450","date_published":"2020-05-20T00:00:00Z","date_created":"2020-06-29T07:59:35Z","page":"9220-9230"},{"year":"2020","day":"20","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2021-04-14T12:05:20Z","date_published":"2020-05-20T00:00:00Z","doi":"10.1021/jacs.9b13450.s002","related_material":{"record":[{"status":"public","id":"8040","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1"}],"oa":1,"publisher":"American Chemical Society","month":"05","date_updated":"2023-08-22T07:49:37Z","citation":{"mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. 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