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Lasham J, Djurabekova A, Kolypetris G, Zickermann V, Vonck J, Sharma V. Assessment of amino acid charge states based on cryo-electron microscopy and molecular dynamics simulations of respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2025; 1866:149512. [PMID: 39326541 DOI: 10.1016/j.bbabio.2024.149512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/10/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
The charge states of titratable amino acid residues play a key role in the function of membrane-bound bioenergetic proteins. However, determination of these charge states both through experimental and computational approaches is extremely challenging. Cryo-EM density maps can provide insights on the charge states of titratable amino acid residues. By performing classical atomistic molecular dynamics simulations on the high resolution cryo-EM structures of respiratory complex I from Yarrowia lipolytica, we analyze the conformational and charge states of a key acidic residue in its ND1 subunit, aspartic acid D203, which is also a mitochondrial disease mutation locus. We suggest that in the native state of respiratory complex I, D203 is negatively charged and maintains a stable hydrogen bond to a conserved arginine residue. Alternatively, upon conformational change in the turnover state of the enzyme, its sidechain attains a charge-neutral status. We discuss the implications of this analysis on the molecular mechanism of respiratory complex I.
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2
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Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2315568121. [PMID: 38530900 PMCID: PMC10998594 DOI: 10.1073/pnas.2315568121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/24/2024] [Indexed: 03/28/2024] Open
Abstract
Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by N 5-methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na+ transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B12 derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG)3 composed of the central Mtr(ABFG)3 stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na+ were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na+ transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B12, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na+ flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na+ outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B12-carrying domain.
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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 PMCID: PMC11389979 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Laube E, Schiller J, Zickermann V, Vonck J. Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallogr D Struct Biol 2024; 80:159-173. [PMID: 38372588 PMCID: PMC10910544 DOI: 10.1107/s205979832400086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with building blocks of the complex and are involved in the assembly process, but are not part of mature complex I. Although the assembly pathways have been studied extensively, there is limited information on the structure and molecular function of the assembly factors. Here, the insights that have been gained into the assembly process using cryo-EM are reviewed.
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Hau JL, Kaltwasser S, Muras V, Casutt MS, Vohl G, Claußen B, Steffen W, Leitner A, Bill E, Cutsail GE, DeBeer S, Vonck J, Steuber J, Fritz G. Conformational coupling of redox-driven Na +-translocation in Vibrio cholerae NADH:quinone oxidoreductase. Nat Struct Mol Biol 2023; 30:1686-1694. [PMID: 37710014 PMCID: PMC10643135 DOI: 10.1038/s41594-023-01099-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na+-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na+-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na+-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na+ from a binding site localized in subunit NqrB.
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Fuss MF, Wieferig JP, Corey RA, Hellmich Y, Tascón I, Sousa JS, Stansfeld PJ, Vonck J, Hänelt I. Cyclic di-AMP traps proton-coupled K + transporters of the KUP family in an inward-occluded conformation. Nat Commun 2023; 14:3683. [PMID: 37344476 DOI: 10.1038/s41467-023-38944-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Cyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. In Bacillus subtilis, the K+/H+ symporter KimA of the KUP family is inactivated by c-di-AMP. KimA sustains survival at potassium limitation at low external pH by mediating potassium ion uptake. However, at elevated intracellular K+ concentrations, further K+ accumulation would be toxic. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K+ binding site and therefore traps KimA in an inward-occluded conformation.
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Schiller J, Laube E, Wittig I, Kühlbrandt W, Vonck J, Zickermann V. Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling. SCIENCE ADVANCES 2022; 8:eadd3855. [PMID: 36383672 PMCID: PMC9668296 DOI: 10.1126/sciadv.add3855] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/14/2022] [Indexed: 06/02/2023]
Abstract
Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.
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8
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Aziz I, Kaltwasser S, Kayastha K, Khera R, Vonck J, Ermler U. The molybdenum storage protein forms and deposits distinct polynuclear tungsten oxygen aggregates. J Inorg Biochem 2022; 234:111904. [DOI: 10.1016/j.jinorgbio.2022.111904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 11/30/2022]
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9
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Stautz J, Griwatz D, Wunnicke-Kortz D, Schrecker M, Kaltwasser S, Mills DJ, Vonck J, Hánelt I. Allosteric regulation of the potassium channel KtrAB is facilitated by KtrB’s N termini. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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10
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Parey K, Lasham J, Mills DJ, Djurabekova A, Haapanen O, Yoga EG, Xie H, Kühlbrandt W, Sharma V, Vonck J, Zickermann V. High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. SCIENCE ADVANCES 2021; 7:eabj3221. [PMID: 34767441 PMCID: PMC8589321 DOI: 10.1126/sciadv.abj3221] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/24/2021] [Indexed: 05/23/2023]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.
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Ebenhoch R, Prinz S, Kaltwasser S, Mills DJ, Meinecke R, Rübbelke M, Reinert D, Bauer M, Weixler L, Zeeb M, Vonck J, Nar H. A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I. Proc Natl Acad Sci U S A 2020; 117:31838-31849. [PMID: 33229582 PMCID: PMC7750480 DOI: 10.1073/pnas.2013473117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1-GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition.
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12
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Joppe M, D’Imprima E, Salustros N, Paithankar KS, Vonck J, Grininger M, Kühlbrandt W. The resolution revolution in cryoEM requires high-quality sample preparation: a rapid pipeline to a high-resolution map of yeast fatty acid synthase. IUCRJ 2020; 7:220-227. [PMID: 32148850 PMCID: PMC7055384 DOI: 10.1107/s2052252519017366] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Single-particle electron cryo-microscopy (cryoEM) has undergone a 'resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built.
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Parey K, Wirth C, Vonck J, Zickermann V. Respiratory complex I - structure, mechanism and evolution. Curr Opin Struct Biol 2020; 63:1-9. [PMID: 32058886 DOI: 10.1016/j.sbi.2020.01.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Respiratory complex I is an intricate multi-subunit membrane protein with a central function in aerobic energy metabolism. During the last years, structures of mitochondrial complex I and respiratory supercomplexes were determined by cryo-EM at increasing resolution. Structural and computational studies have shed light on the dynamics of proton translocation pathways, the interaction of complex I with lipids and the unusual access pathway of ubiquinone to the active site. Recent advances in understanding complex I function include characterization of specific conformational changes that are critical for proton pumping. Cryo-EM structures of the NADH dehydrogenase-like (NDH) complex of photosynthesis and a bacterial membrane bound hydrogenase (MBH) have provided a broader perspective on the complex I superfamily.
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Tascón I, Sousa JS, Corey RA, Mills DJ, Griwatz D, Aumüller N, Mikusevic V, Stansfeld PJ, Vonck J, Hänelt I. Structural basis of proton-coupled potassium transport in the KUP family. Nat Commun 2020; 11:626. [PMID: 32005818 PMCID: PMC6994465 DOI: 10.1038/s41467-020-14441-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/10/2020] [Indexed: 12/05/2022] Open
Abstract
Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing external conditions. KUP transporters facilitate potassium uptake by the co-transport of protons. Here, we uncover the molecular basis for transport in this widely distributed family. We identify the potassium importer KimA from Bacillus subtilis as a member of the KUP family, demonstrate that it functions as a K+/H+ symporter and report a 3.7 Å cryo-EM structure of the KimA homodimer in an inward-occluded, trans-inhibited conformation. By introducing point mutations, we identify key residues for potassium and proton binding, which are conserved among other KUP proteins. KUP transporters facilitate potassium uptake by the co-transport of protons and are key players in potassium homeostasis. Here authors identify the potassium importer KimA from Bacillus subtilis as a new member of the KUP transporter family and show the cryo-EM structure of KimA in an inward-occluded, trans-inhibited conformation.
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15
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Parey K, Haapanen O, Sharma V, Köfeler H, Züllig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kühlbrandt W, Zickermann V. High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. SCIENCE ADVANCES 2019; 5:eaax9484. [PMID: 31844670 PMCID: PMC6905873 DOI: 10.1126/sciadv.aax9484] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/22/2019] [Indexed: 05/23/2023]
Abstract
Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.
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Pfeil-Gardiner O, Mills DJ, Vonck J, Kuehlbrandt W. A comparative study of single-particle cryo-EM with liquid-nitrogen and liquid-helium cooling. IUCRJ 2019; 6:1099-1105. [PMID: 31709065 PMCID: PMC6830223 DOI: 10.1107/s2052252519011503] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/16/2019] [Indexed: 05/06/2023]
Abstract
Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM.
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Eder M, Dordic A, Sagmeister T, Damisch E, Vejzovic D, Berni F, Codee J, Palva A, Vonck J, Oberer M, Pavkov-Keller T. Surface layer proteins of lactobacilli – determining the cell wall binding and their antibacterial effect. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319093604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Hofer G, Payer SE, Plasch K, Bärland N, Marschall SA, Sheng X, Vonck J, Gruber K, Himo F, Leys D, Faber K, Keller W, Glueck SM, Pavkov-Keller T. Regioselective carboxylation by prenylated flavin and Mn-dependent decarboxylases. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Sagmeister T, Eder M, Damisch E, Vejzovic D, Dordic A, Millán Nebot CL, Usón I, Vonck J, Pavkov-Keller T. The N-terminal domain of Lactobacillus acidophilus SlpA promotes self-assembly of the S-layer array. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Cossio P, Allegretti M, Mayer F, Müller V, Vonck J, Hummer G. Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy (Oxf) 2018; 67:266-273. [PMID: 30032235 DOI: 10.1093/jmicro/dfy033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/20/2018] [Indexed: 12/24/2022] Open
Abstract
The 'Bayesian inference of electron microscopy' (BioEM) framework makes it possible to determine the stoichiometry of protein complexes using 3D coarse-grained models and a relatively small number of cryo-electron microscopy images as input. We applied the method to determine the most probable rotor ring stoichiometry of the archaeal Na+ ATP synthase from Pyrococcus furiosus, a multisubunit complex able to produce ATP under extreme conditions. Archaeal ATP synthases consist of a catalytic A1 part and a membrane-embedded AO portion. The AO portion is composed of a rotor ring and the a-subunit. The rotor ring of P. furiosus ATP synthase is composed of 16-kDa c-subunits, each consisting of four helices forming a bundle, with only one Na+-binding site per bundle. This ring was proposed to be decameric from LILBID-MS analysis of the entire ATP synthase. By contrast, the BioEM posterior favors a c9 ring stoichiometry. With BioEM, we ranked coarse-grained models of the whole complex with different ring geometry, using 6400 unprocessed particle images of the A1AO complex collected in vitreous ice. BioEM makes it possible to probabilistically establish the domain stoichiometry using low-resolution information and comparably few particle images.
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Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kühlbrandt W, Zickermann V. Cryo-EM structure of respiratory complex I at work. eLife 2018; 7:39213. [PMID: 30277212 PMCID: PMC6168287 DOI: 10.7554/elife.39213] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
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Damisch E, Eder M, Dordic A, Mohan K, Das P, Hynönen U, Palva A, Vonck J, Oberer M, Pavkov-Keller T. The attachment of the Lactobacillus surface-layer array to the bacterial cell. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hahn A, Vonck J, Mills DJ, Meier T, Kühlbrandt W. Structure, mechanism, and regulation of the chloroplast ATP synthase. Science 2018; 360:eaat4318. [PMID: 29748256 PMCID: PMC7116070 DOI: 10.1126/science.aat4318] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022]
Abstract
The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded Fo motor drive ATP synthesis in the F1 head by rotary catalysis. We determined the high-resolution structure of the complete cF1Fo complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F1 head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
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Diskowski M, Mikusevic V, Wunnicke D, Mehdipour AR, Mills DJ, Hummer G, Fendler K, Vonck J, Haenelt I. Allosteric Control of the K+ Uptake System KtrAB. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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