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Akutsu H. Strategies for elucidation of the structure and function of the large membrane protein complex, F oF 1-ATP synthase, by nuclear magnetic resonance. Biophys Chem 2023; 296:106988. [PMID: 36898347 DOI: 10.1016/j.bpc.2023.106988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
Nuclear magnetic resonance (NMR) investigation of large membrane proteins requires well-focused questions and critical techniques. Here, research strategies for FoF1-ATP synthase, a membrane-embedded molecular motor, are reviewed, focusing on the β-subunit of F1-ATPase and c-subunit ring of the enzyme. Segmental isotope-labeling provided 89% assignment of the main chain NMR signals of thermophilic Bacillus (T)F1β-monomer. Upon nucleotide binding to Lys164, Asp252 was shown to switch its hydrogen-bonding partner from Lys164 to Thr165, inducing an open-to-closed bend motion of TF1β-subunit. This drives the rotational catalysis. The c-ring structure determined by solid-state NMR showed that cGlu56 and cAsn23 of the active site took a hydrogen-bonded closed conformation in membranes. In 505 kDa TFoF1, the specifically isotope-labeled cGlu56 and cAsn23 provided well-resolved NMR signals, which revealed that 87% of the residue pairs took a deprotonated open conformation at the Foa-c subunit interface, whereas they were in the closed conformation in the lipid-enclosed region.
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Affiliation(s)
- Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan.
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Todokoro Y, Kang SJ, Suzuki T, Ikegami T, Kainosho M, Yoshida M, Fujiwara T, Akutsu H. Chemical Conformation of the Essential Glutamate Site of the c-Ring within Thermophilic Bacillus F oF 1-ATP Synthase Determined by Solid-State NMR Based on its Isolated c-Ring Structure. J Am Chem Soc 2022; 144:14132-14139. [PMID: 35905443 DOI: 10.1021/jacs.2c03580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton translocation through the membrane-embedded Fo component of F-type ATP synthase (FoF1) is facilitated by the rotation of the Fo c-subunit ring (c-ring), carrying protons at essential acidic amino acid residues. Cryo-electron microscopy (Cryo-EM) structures of FoF1 suggest a unique proton translocation mechanism. To elucidate it based on the chemical conformation of the essential acidic residues of the c-ring in FoF1, we determined the structure of the isolated thermophilic Bacillus Fo (tFo) c-ring, consisting of 10 subunits, in membranes by solid-state NMR. This structure contains a distinct proton-locking conformation, wherein Asn23 (cN23) CγO and Glu56 (cE56) CδOH form a hydrogen bond in a closed form. We introduced stereo-array-isotope-labeled (SAIL) Glu and Asn into the tFoc-ring to clarify the chemical conformation of these residues in tFoF1-ATP synthase (tFoF1). Two well-separated 13C signals could be detected for cN23 and cE56 in a 505 kDa membrane protein complex, respectively, thereby suggesting the presence of two distinct chemical conformations. Based on the signal intensity and structure of the tFoc-ring and tFoF1, six pairs of cN23 and cE56 surrounded by membrane lipids take the closed form, whereas the other four in the a-c interface employ the deprotonated open form at a proportion of 87%. This indicates that the a-c interface is highly hydrophilic. The pKa values of the four cE56 residues in the a-c interface were estimated from the cN23 signal intensity in the open and closed forms and distribution of polar residues around each cE56. The results favor a rotation of the c-ring for ATP synthesis.
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Affiliation(s)
- Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Technical Support Division, School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043, Japan
| | - Su-Jin Kang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,College of Pharmacy, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Toshiharu Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama 226-0026, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masatsune Kainosho
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masasuke Yoshida
- Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto 603-8555, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan.,Department of Biophysics and Chemical Biology, Seoul National University, Gwanak-Gu, Seoul 151-742, Republic of Korea.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
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Kovalčíková J, Vrbacký M, Pecina P, Tauchmannová K, Nůsková H, Kaplanová V, Brázdová A, Alán L, Eliáš J, Čunátová K, Kořínek V, Sedlacek R, Mráček T, Houštěk J. TMEM70 facilitates biogenesis of mammalian ATP synthase by promoting subunit c incorporation into the rotor structure of the enzyme. FASEB J 2019; 33:14103-14117. [DOI: 10.1096/fj.201900685rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jana Kovalčíková
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Marek Vrbacký
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Pecina
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Kateřina Tauchmannová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Nůsková
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Vilma Kaplanová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Andrea Brázdová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Alán
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Eliáš
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Kristýna Čunátová
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimír Kořínek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Institute of Molecular Genetics, The Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Mráček
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
| | - Josef Houštěk
- Department of Bioenergetics, Institute of Physiology, The Czech Academy of Sciences, Prague, Czech Republic
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Kang SJ, Todokoro Y, Bak S, Suzuki T, Yoshida M, Fujiwara T, Akutsu H. Direct assignment of 13C solid-state NMR signals of TF oF 1 ATP synthase subunit c-ring in lipid membranes and its implication for the ring structure. JOURNAL OF BIOMOLECULAR NMR 2018; 70:53-65. [PMID: 29197977 DOI: 10.1007/s10858-017-0158-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
FoF1-ATP synthase catalyzes ATP hydrolysis/synthesis coupled with a transmembrane H+ translocation in membranes. The Fo c-subunit ring plays a major role in this reaction. We have developed an assignment strategy for solid-state 13C NMR (ssNMR) signals of the Fo c-subunit ring of thermophilic Bacillus PS3 (TFo c-ring, 72 residues), carrying one of the basic folds of membrane proteins. In a ssNMR spectrum of uniformly 13C-labeled sample, the signal overlap has been a major bottleneck because most amino acid residues are hydrophobic. To overcome signal overlapping, we developed a method designated as COmplementary Sequential assignment with MInimum Labeling Ensemble (COSMILE). According to this method, we generated three kinds of reverse-labeled samples to suppress signal overlapping. To assign the carbon signals sequentially, two-dimensional Cα(i+1)-C'Cα(i) correlation and dipolar assisted rotational resonance (DARR) experiments were performed under magic-angle sample spinning. On the basis of inter- and intra-residue 13C-13C chemical shift correlations, 97% of Cα, 97% of Cβ and 92% of C' signals were assigned directly from the spectra. Secondary structure analysis predicted a hairpin fold of two helices with a central loop. The effects of saturated and unsaturated phosphatidylcholines on TFo c-ring structure were examined. The DARR spectra at 15 ms mixing time are essentially similar to each other in saturated and unsaturated lipid membranes, suggesting that TFo c-rings have similar structures under the different environments. The spectrum of the sample in saturated lipid membranes showed better resolution and structural stability in the gel state. The C-terminal helix was suggested to locate in the outer layer of the c-ring.
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Affiliation(s)
- Su-Jin Kang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Yasuto Todokoro
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Suyeon Bak
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea
| | - Toshiharu Suzuki
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masasuke Yoshida
- Department of Molecular Bioscience, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, 603-8555, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan.
- Department of Biophysics and Chemical Biology, Seoul National University, Kwanak-Gu, Seoul, 151-742, Republic of Korea.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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Expression and Characterization of a Recombinant Laccase with Alkalistable and Thermostable Properties from Streptomyces griseorubens JSD-1. Appl Biochem Biotechnol 2015; 176:547-62. [PMID: 25820450 DOI: 10.1007/s12010-015-1594-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
Streptomyces griseorubens JSD-1 is a novel actinomycete that could grow efficiently upon lignin, and the ligninolytic genes active in this biotransformation were expected to be crucial. To investigate the molecular mechanism of utilizing lignin, genome sequencing was carried out to obtain its draft genome, which was deposited at GenBank under the accession No. JJMG00000000. Multiple copper oxidase (MCO) was obtained, which proved to be an extracellular enzyme and have relative high expression with the stimulation of ligninolytic materials. Judging from its putative 3D structure, the N-terminal of MCO was bared, which was fit for the linkage of poly-HIS10 tag. As a result, heterogeneous expression conditions of recombinant laccase was achieved with TransB(DE3) grown in a modified terrific broth (TB) medium with an extra addition of 0.5% glucose at 30 °C until optical density at 600 nm (OD600) reached 0.8 when expression was induced by 25 μM isopropyl β-D-1-thiogalactopyranoside (IPTG) and also 100 μM copper sulphate as supplement. Finally, it exhibited special characters of thermal robustness, alkaline activity profiles, high resistance to metallic ions and chemical inhibitors as well as dye decolourization. In summary, our findings illustrated the genetic basic of utilizing lignin in this isolate. Additionally, a novel laccase expected to be potential in agricultural and industrial application was expressed and characterized as well.
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Su CH, McStay GP, Tzagoloff A. Assembly of the rotor component of yeast mitochondrial ATP synthase is enhanced when Atp9p is supplied by Atp9p-Cox6p complexes. J Biol Chem 2014; 289:31605-16. [PMID: 25253699 DOI: 10.1074/jbc.m114.602706] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Atp9p ring is one of several assembly modules of yeast mitochondrial ATP synthase. The ring, composed of 10 copies of Atp9p, is part of the rotor that couples proton translocation to synthesis or hydrolysis of ATP. We present evidence that before its assembly with other ATP synthase modules, most of Atp9p is present in at least three complexes with masses of 200-400 kDa that co-immunopurify with Cox6p. Pulse-labeling analysis disclosed a time-dependent reduction of radiolabeled Atp9p in the complexes and an increase of Atp9p in the ring form of wild type yeast and of mss51, pet111, and pet494 mutants lacking Cox1p, Cox2p, and Cox3p, respectively. Ring formation was not significantly different from wild type in an mss51 or atp10 mutant. The atp10 mutation blocks the interaction of the Atp9p ring with other modules of the ATP synthase. In contrast, ring formation was reduced in a cox6 mutant, consistent with a role of Cox6p in oligomerization of Atp9p. Cox6p involvement in ATP synthase assembly is also supported by studies showing that ring formation in cells adapting from fermentative to aerobic growth was less efficient in mitochondria of the cox6 mutant than the parental respiratory-competent strain or a cox4 mutant. We speculate that the constitutive and Cox6p-independent rate of Atp9p oligomerization may be sufficient to produce the level of ATP synthase needed for maintaining a membrane potential but limiting for optimal oxidative phosphorylation.
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Affiliation(s)
- Chen-Hsien Su
- From the Department of Biological Sciences, Columbia University, New York, New York 10128 and
| | - Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, Old Westbury, New York 11568
| | - Alexander Tzagoloff
- From the Department of Biological Sciences, Columbia University, New York, New York 10128 and
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Active-site structure of the thermophilic Foc-subunit ring in membranes elucidated by solid-state NMR. Biophys J 2014; 106:390-8. [PMID: 24461014 DOI: 10.1016/j.bpj.2013.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/07/2013] [Accepted: 12/03/2013] [Indexed: 11/20/2022] Open
Abstract
FoF1-ATP synthase uses the electrochemical potential across membranes or ATP hydrolysis to rotate the Foc-subunit ring. To elucidate the underlying mechanism, we carried out a structural analysis focused on the active site of the thermophilic c-subunit (TFoc) ring in membranes with a solid-state NMR method developed for this purpose. We used stereo-array isotope labeling (SAIL) with a cell-free system to highlight the target. TFoc oligomers were purified using a virtual ring His tag. The membrane-reconstituted TFoc oligomer was confirmed to be a ring indistinguishable from that expressed in E. coli on the basis of the H(+)-translocation activity and high-speed atomic force microscopic images. For the analysis of the active site, 2D (13)C-(13)C correlation spectra of TFoc rings labeled with SAIL-Glu and -Asn were recorded. Complete signal assignment could be performed with the aid of the C(α)i+1-C(α)i correlation spectrum of specifically (13)C,(15)N-labeled TFoc rings. The C(δ) chemical shift of Glu-56, which is essential for H(+) translocation, and related crosspeaks revealed that its carboxyl group is protonated in the membrane, forming the H(+)-locked conformation with Asn-23. The chemical shift of Asp-61 C(γ) of the E. coli c ring indicated an involvement of a water molecule in the H(+) locking, in contrast to the involvement of Asn-23 in the TFoc ring, suggesting two different means of proton storage in the c rings.
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Bak S, Kang SJ, Suzuki T, Yoshida M, Fujiwara T, Akutsu H. Improved Purification of Thermophilic FoF1-ATP Synthase c-Subunit Rings and Solid-State NMR Characterization of Them in Different Lipid Membranes. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2013. [DOI: 10.6564/jkmrs.2013.17.2.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Carraher C, Nazmi AR, Newcomb RD, Kralicek A. Recombinant expression, detergent solubilisation and purification of insect odorant receptor subunits. Protein Expr Purif 2013; 90:160-9. [PMID: 23770557 DOI: 10.1016/j.pep.2013.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 12/16/2022]
Abstract
Insect odorant receptors (ORs) are seven transmembrane domain proteins that comprise a novel family of ligand-gated non-selective cation channels. The functional channel is made up of an odour activated ligand-binding OR and the OR co-receptor, Orco. However, the structure, stoichiometry and mechanism of activation of the receptor complex are not well understood. Here we demonstrate that baculovirus-mediated Sf9 cell expression and wheat germ cell-free expression, but not Escherichia coli cell-based or cell-free expression, can be used successfully to over-express a selection of insect ORs. From a panel of 19 detergents, 1%w/v Zwittergent 3-16 was able to solubilise five Drosophila melanogaster ORs produced from both eukaryotic expression systems. A large-scale purification protocol was then developed for DmOrco and the ligand-binding receptor, DmOr22a. The proteins were nickel-affinity purified using a deca-histidine tag in a buffer containing 0.2 mM Zwittergent 3-16, followed by size exclusion chromatography. These purified ORs appear to form similarly sized protein-detergent complexes when isolated from both expression systems. Circular dichroism analysis of both purified proteins suggests they are folded correctly. We also provide evidence that when DmOrco is expressed in Sf9 cells it undergoes post translational modification, probably glycosylation. Finally we show that the recombinant ORs can be incorporated into pre-formed liposomes. The ability to recombinantly express and purify insect ORs to homogeneity on a preparative scale, as well as insert them into liposomes, is a major step forward in enabling future structural and functional studies, as well as their use in OR based biosensors.
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Affiliation(s)
- Colm Carraher
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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