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Krawinski P, Smithers L, van Dalsen L, Boland C, Ostrovitsa N, Pérez J, Caffrey M. 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins. CRYSTAL GROWTH & DESIGN 2024; 24:2985-3001. [PMID: 38585376 PMCID: PMC10995948 DOI: 10.1021/acs.cgd.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
A novel monoacylglycerol, 7.10 MAG, has been produced for use in the in meso (lipid cubic phase) crystallization of membrane proteins and complexes. 7.10 MAG differs from monoolein, the most extensively used lipid for in meso crystallization, in that it is shorter in chain length by one methylene and its cis olefinic bond is two carbons closer to the glycerol headgroup. These changes in structure alter the phase behavior of the hydrated lipid and the microstructure of the corresponding mesophases formed. Temperature-composition phase diagrams for 7.10 MAG have been constructed using small- and wide-angle X-ray scattering over a range of temperatures and hydration levels that span those used for crystallization. The phase diagrams include lamellar crystalline, fluid isotropic, lamellar liquid-crystalline, cubic-Ia3d, and cubic-Pn3m phases, as observed with monoolein. Conspicuous by its absence is the inverted hexagonal phase which is rationalized on the basis of 7.10 MAG's chemical constitution. The cubic phase prepared with the new lipid facilitates the growth of crystals that were used to generate high-resolution structures of intramembrane β-barrel and α-helical proteins. Compatibility of fully hydrated 7.10 MAG with cholesterol and phosphatidylcholine means that these two lipids can be used as additives to optimize crystallogenesis in screening trials with 7.10 MAG as the host lipid.
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Affiliation(s)
- Pawel Krawinski
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Luke Smithers
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Leendert van Dalsen
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Coilin Boland
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
| | - Nikita Ostrovitsa
- School
of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Javier Pérez
- SWING
Beamline, Synchrotron Soleil, Saint-Aubin 91190, France
| | - Martin Caffrey
- Membrane
Structural and Functional Biology Group, School of Medicine and School
of Biochemistry and Immunology, Trinity
College Dublin, Dublin D02 R590, Ireland
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2
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Safari C, Ghosh S, Andersson R, Johannesson J, Båth P, Uwangue O, Dahl P, Zoric D, Sandelin E, Vallejos A, Nango E, Tanaka R, Bosman R, Börjesson P, Dunevall E, Hammarin G, Ortolani G, Panman M, Tanaka T, Yamashita A, Arima T, Sugahara M, Suzuki M, Masuda T, Takeda H, Yamagiwa R, Oda K, Fukuda M, Tosha T, Naitow H, Owada S, Tono K, Nureki O, Iwata S, Neutze R, Brändén G. Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. SCIENCE ADVANCES 2023; 9:eadh4179. [PMID: 38064560 PMCID: PMC10708180 DOI: 10.1126/sciadv.adh4179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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Affiliation(s)
- Cecilia Safari
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Rebecka Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Jonatan Johannesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Owens Uwangue
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Doris Zoric
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Sandelin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Per Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Elin Dunevall
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Matthijs Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Toshi Arima
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mamoru Suzuki
- Laboratory of Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Tetsuya Masuda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Hanae Takeda
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Raika Yamagiwa
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hisashi Naitow
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kuoto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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3
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Hon-Nami K, Hijikata A, Yura K, Bessho Y. Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus. J GEN APPL MICROBIOL 2023; 69:68-78. [PMID: 37394433 DOI: 10.2323/jgam.2023.06.005] [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] [Indexed: 07/04/2023]
Abstract
In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the results of surveying genes with the heme c motif, CxxCH, in a genome database comprising four strains of Thermus thermophilus, including strain HB8, and the confirmation of 19 c-type cytochromes among 27 selected genes. We analyzed the 19 genes, including the expression of four, by a bioinformatics approach to elucidate their individual attributes. One of the approaches included an analysis based on the secondary structure alignment pattern between the heme c motif and the 6th ligand. The predicted structures revealed many cyt c domains with fewer β-strands, such as mitochondrial cyt c, in addition to the β-strand unique to Thermus inserted in cyt c domains, as in T. thermophilus cyt c552 and caa3 cyt c oxidase subunit IIc. The surveyed thermophiles harbor potential proteins with a variety of cyt c folds. The gene analyses led to the development of an index for the classification of cyt c domains. Based on these results, we propose names for T. thermophilus genes harboring the cyt c fold.
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Affiliation(s)
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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4
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Bian C, Zheng Z, Su J, Chang S, Yu H, Bao J, Xin Y, Jiang X. Copper homeostasis and cuproptosis in tumor pathogenesis and therapeutic strategies. Front Pharmacol 2023; 14:1271613. [PMID: 37767404 PMCID: PMC10520736 DOI: 10.3389/fphar.2023.1271613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Copper is an indispensable micronutrient for the development and replication of all eukaryotes, and its redox properties are both harmful and beneficial to cells. An imbalance in copper homeostasis is thought to be involved in carcinogenesis. Importantly, cancer cell proliferation, angiogenesis, and metastasis cannot be separated from the effects of copper. Cuproposis is a copper-dependent form of cell death that differs from other existing modalities of regulatory cell death. The role of cuproptosis in the pathogenesis of the nervous and cardiovascular systems has been widely studied; however, its impact on malignant tumors is yet to be fully understood from a clinical perspective. Exploring signaling pathways related to cuproptosis will undoubtedly provide a new perspective for the development of anti-tumor drugs in the future. Here, we systematically review the systemic and cellular metabolic processes of copper and the regulatory mechanisms of cuproptosis in cancer. In addition, we discuss the possibility of targeting copper ion drugs to prolong the survival of cancer patients, with an emphasis on the most representative copper ionophores and chelators. We suggest that attention should be paid to the potential value of copper in the treatment of specific cancers.
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Affiliation(s)
- Chenbin Bian
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Zhuangzhuang Zheng
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Jing Su
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Sitong Chang
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Huiyuan Yu
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Jindian Bao
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Xin Jiang
- Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
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5
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Wang X, Zhou M, Liu Y, Si Z. Cope with copper: From copper linked mechanisms to copper-based clinical cancer therapies. Cancer Lett 2023; 561:216157. [PMID: 37011869 DOI: 10.1016/j.canlet.2023.216157] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/04/2023]
Abstract
Recent studies have established a strong link between copper and cancer biology, as copper is necessary for cancer growth and metastasis. Beyond the conventional concept of copper serving as a catalytic cofactor of metalloenzymes, emerging evidence demonstrates copper as a regulator for signaling transduction and gene expression, which are vital for tumorigenesis and cancer progression. Interestingly, strong redox-active properties make copper both beneficial and detrimental to cancer cells. Cuproplasia is copper-dependent cell growth and proliferation, whereas cuproptosis is copper-dependent cell death. Both mechanisms act in cancer cells, suggesting that copper depletion and copper supplementation may be viable approaches for developing novel anticancer therapies. In this review, we summarized the current understanding of copper's biological role and related molecular mechanisms in cancer proliferation, angiogenesis, metastasis, autophagy, immunosuppressive microenvironment development, and copper-mediated cancer cell death. We also highlighted copper-based strategies for cancer treatment. The current challenges of copper in cancer biology and therapy and their potential solutions were also discussed. Further investigation in this field will yield a more comprehensive molecular explanation for the causal relationship between copper and cancers. It will reveal a series of key regulators governing copper-dependent signaling pathways, thereby providing potential targets for developing copper-related anticancer drugs.
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Affiliation(s)
- Xidi Wang
- Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, PR China; Department of Pathology, Health Science Center, Ningbo University, Ningbo, Ningbo, PR China.
| | - Miao Zhou
- Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, PR China
| | - Yu Liu
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo, PR China
| | - Zizhen Si
- Department of Physiology and Pharmacology, Health Science Center, Ningbo University, Ningbo, PR China.
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6
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Muramoto K, Shinzawa-Itoh K. Calcium-bound structure of bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148956. [PMID: 36708913 DOI: 10.1016/j.bbabio.2023.148956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
The crystal structure of bovine cytochrome c oxidase (CcO) shows a sodium ion (Na+) bound to the surface of subunit I. Changes in the absorption spectrum of heme a caused by calcium ions (Ca2+) are detected as small red shifts, and inhibition of enzymatic activity under low turnover conditions is observed by addition of Ca2+ in a competitive manner with Na+. In this study, we determined the crystal structure of Ca2+-bound bovine CcO in the oxidized and reduced states at 1.7 Å resolution. Although Ca2+ and Na+ bound to the same site of oxidized and reduced CcO, they led to different coordination geometries. Replacement of Na+ with Ca2+ caused a small structural change in the loop segments near the heme a propionate and formyl groups, resulting in spectral changes in heme a. Redox-coupled structural changes observed in the Ca2+-bound form were the same as those previously observed in the Na+-bound form, suggesting that binding of Ca2+ does not severely affect enzymatic function, which depends on these structural changes. The relation between the Ca2+ binding and the inhibitory effect during slow turnover, as well as the possible role of bound Ca2+ are discussed.
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Affiliation(s)
- Kazumasa Muramoto
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
| | - Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
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7
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Shojapour M, Farahmand S. Point mutation consideration in CcO protein of the electron transfer chain by MD simulation. J Mol Graph Model 2022; 117:108309. [PMID: 36037732 DOI: 10.1016/j.jmgm.2022.108309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 01/14/2023]
Abstract
In Acidithiobacillus ferrooxidans, proteins such as CcO are present in the electron transport pathway. They cause ferrous iron oxidation to ferric leading to the electron release. CcO has two copper atoms (CuA, CuB). CuA plays an important role in electron transfer. According to previous studies, the conversion of histidine to methionine in a similar protein increased the redox potential and was directly related to the number of electrons received. Also, the binding of methionine 233 to CuA and CuB in the wild protein structure is the reason for the selection of the H230 M mutation in the CuA site. Then, wild-type and H230 M mutant were simulated in the presence of a bilayer membrane POPC using the gromacs version 5.1.4. The changes performed in the H230 M mutant were evaluated by MD simulations analyzes. CcO and CoxA proteins are the last two proteins in the chain and were docked by the PatchDock server. By H230 M mutation, the connection between CuA and M230 weakens. The M230 moves further away from CuA, resulting become more flexible. Therefore, the Methionine gets closer to E149 of the CoxA leading to the higher stability of the CcO/CoxA complex. The results of RMSF analysis at the mutation point showed a significant increase. This indicates more flexibility in the active site. And leads to an increase in E0 in the mutation point, an increase in the rate of electron reception, and an improved bioleaching process.
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Affiliation(s)
- Mahnaz Shojapour
- Department of Biology, Payame Noor University (PNU), P.O.Box, 19395-4697, Tehran, Iran.
| | - Somayeh Farahmand
- Department of Biology, Payame Noor University (PNU), P.O.Box, 19395-4697, Tehran, Iran.
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8
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Li J, Zheng W, Gu M, Han L, Luo Y, Yu K, Sun M, Zong Y, Ma X, Liu B, Lowder EP, Mendez DL, Kranz RG, Zhang K, Zhu J. Structures of the CcmABCD heme release complex at multiple states. Nat Commun 2022; 13:6422. [PMID: 36307425 PMCID: PMC9616876 DOI: 10.1038/s41467-022-34136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Cytochromes c use heme as a cofactor to carry electrons in respiration and photosynthesis. The cytochrome c maturation system I, consisting of eight membrane proteins (CcmABCDEFGH), results in the attachment of heme to cysteine residues of cytochrome c proteins. Since all c-type cytochromes are periplasmic, heme is first transported to a periplasmic heme chaperone, CcmE. A large membrane complex, CcmABCD has been proposed to carry out this transport and linkage to CcmE, yet the structural basis and mechanisms underlying the process are unknown. We describe high resolution cryo-EM structures of CcmABCD in an unbound form, in complex with inhibitor AMP-PNP, and in complex with ATP and heme. We locate the ATP-binding site in CcmA and the heme-binding site in CcmC. Based on our structures combined with functional studies, we propose a hypothetic model of heme trafficking, heme transfer to CcmE, and ATP-dependent release of holoCcmE from CcmABCD. CcmABCD represents an ABC transporter complex using the energy of ATP hydrolysis for the transfer of heme from one binding partner (CcmC) to another (CcmE).
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Affiliation(s)
- Jiao Li
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Wan Zheng
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Ming Gu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Long Han
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Yanmei Luo
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Koukou Yu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Mengxin Sun
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Yuliang Zong
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Xiuxiu Ma
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Bing Liu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Ethan P. Lowder
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Deanna L. Mendez
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Robert G. Kranz
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Kai Zhang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Jiapeng Zhu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
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9
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Shortall K, Magner E, Soulimane T. Expression, Purification, and in vitro Enzyme Activity Assay of a Recombinant Aldehyde Dehydrogenase from Thermus thermophilus, Using an Escherichia coli Host. Bio Protoc 2022; 12:e4401. [PMID: 35800460 PMCID: PMC9090581 DOI: 10.21769/bioprotoc.4401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/10/2022] [Indexed: 12/29/2022] Open
Abstract
Based on previous in-depth characterisation, aldehyde dehydrogenases (ALDH) are a diverse superfamily of enzymes, in terms of both structure and function, present in all kingdoms of life. They catalyse the oxidation of an aldehyde to carboxylic acid using the cofactor nicotinamide adenine dinucleotide (phosphate) (NAD(P)+), and are often not substrate-specific, but rather have a broad range of associated biological functions, including detoxification and biosynthesis. We studied the structure of ALDHTt from Thermus thermophilus, as well as performed its biochemical characterisation. This allowed for insight into its potential substrates and biological roles. In this protocol, we describe ALDHTt heterologous expression in E. coli, purification, and activity assay (based on Shortall et al., 2021 ). ALDHTt was first copurified as a contaminant during caa3-type cytochrome oxidase isolation from T. thermophilus. This recombinant production system was employed for structural and biochemical analysis of wild-type and mutants, and proved efficient, yielding approximately 15-20 mg/L ALDHTt. For purification of the thermophilic his-tagged ALDHTt, heat treatment, immobilized metal affinity chromatography (IMAC), and gel filtration chromatography were used. The enzyme activity assay was performed via UV-Vis spectrophotometry, monitoring the production of reduced nicotinamide adenine dinucleotide (NADH). Graphical abstract: Flow chart outlining the steps in ALDHTt expression and purification, highlighting the approximate time required for each step.
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Affiliation(s)
- Kim Shortall
- Department of Chemical Sciences, Bernal Institute, University of Limerick, V94 T9PX, Limerick, Ireland
| | - Edmond Magner
- Department of Chemical Sciences, Bernal Institute, University of Limerick, V94 T9PX, Limerick, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, Bernal Institute, University of Limerick, V94 T9PX, Limerick, Ireland,
*For correspondence:
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10
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Evaluation of Cyc 1 protein stability in Acidithiobacillus ferrooxidans bacterium after E121D mutation by molecular dynamics simulation to improve electron transfer. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:526-532. [PMID: 35286603 DOI: 10.1007/s12275-022-1645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 10/18/2022]
Abstract
Cyc1 (Cytochrome c552) is a protein in the electron transport chain of the Acidithiobacillus ferrooxidans (Af) bacteria which obtain their energy from oxidation Fe2+ to Fe3+. The electrons are directed through Cyc2, RCY (rusticyanin), Cyc1 and Cox aa3 proteins to O2. Cyc1 protein consists of two chains, A and B. In the present study, a novel mutation (E121D) in the A chain of Cyc1 protein was selected due to electron receiving from Histidine 143 of RCY. Then, the changes performed in the E121D mutant were evaluated by MD simulations analyzes. Cyc1 and RCY proteins were docked by a Patchdock server. By E121D mutation, the connection between Zn 1388 of chain B and aspartate 121 of chain A weaken. Asp 121 gets farther from Zn 1388. Therefore, the aspartate gets closer to Cu 1156 of the RCY leading to the higher stability of the RCY/Cyc1 complex. Further, an acidic residue (Glu121) becomes a more acidic residue (Asp121) and improves the electron transfer to Cyc1 protein. The results of RMSF analysis showed further ligand flexibility in mutation. This leads to fluctuation of the active site and increases redox potential at the mutation point and the speed of electron transfer. This study also predicts that in all respiratory chain proteins, electrons probably enter the first active site via glutamate and exit histidine in the second active site of each respiratory chain protein.
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11
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Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy. Biochem Soc Trans 2022; 50:877-893. [PMID: 35356963 PMCID: PMC9162462 DOI: 10.1042/bst20190963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.
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12
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Ishigami I, Russi S, Cohen A, Yeh SR, Rousseau DL. Temperature-dependent structural transition following X-ray-induced metal center reduction in oxidized cytochrome c oxidase. J Biol Chem 2022; 298:101799. [PMID: 35257742 PMCID: PMC8971940 DOI: 10.1016/j.jbc.2022.101799] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in the inner membrane of mitochondria. It contains four metal redox centers, two of which, CuB and heme a3, form the binuclear center (BNC), where dioxygen is reduced to water. Crystal structures of CcO in various forms have been reported, from which ligand-binding states of the BNC and conformations of the protein matrix surrounding it have been deduced to elucidate the mechanism by which the oxygen reduction chemistry is coupled to proton translocation. However, metal centers in proteins can be susceptible to X-ray-induced radiation damage, raising questions about the reliability of conclusions drawn from these studies. Here, we used microspectroscopy-coupled X-ray crystallography to interrogate how the structural integrity of bovine CcO in the fully oxidized state (O) is modulated by synchrotron radiation. Spectroscopic data showed that, upon X-ray exposure, O was converted to a hybrid O∗ state where all the four metal centers were reduced, but the protein matrix was trapped in the genuine O conformation and the ligands in the BNC remained intact. Annealing the O∗ crystal above the glass transition temperature induced relaxation of the O∗ structure to a new R∗ structure, wherein the protein matrix converted to the fully reduced R conformation with the exception of helix X, which partly remained in the O conformation because of incomplete dissociation of the ligands from the BNC. We conclude from these data that reevaluation of reported CcO structures obtained with synchrotron light sources is merited.
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Affiliation(s)
- Izumi Ishigami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Silvia Russi
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Aina Cohen
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Syun-Ru Yeh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Denis L Rousseau
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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13
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Chen J, Xie P, Huang Y, Gao H. Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide. Int J Mol Sci 2022; 23:979. [PMID: 35055165 PMCID: PMC8780969 DOI: 10.3390/ijms23020979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Affiliation(s)
| | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (J.C.); (P.X.); (Y.H.)
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14
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Study of ALDH from Thermus thermophilus-Expression, Purification and Characterisation of the Non-Substrate Specific, Thermophilic Enzyme Displaying Both Dehydrogenase and Esterase Activity. Cells 2021; 10:cells10123535. [PMID: 34944041 PMCID: PMC8699947 DOI: 10.3390/cells10123535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 01/16/2023] Open
Abstract
Aldehyde dehydrogenases (ALDH), found in all kingdoms of life, form a superfamily of enzymes that primarily catalyse the oxidation of aldehydes to form carboxylic acid products, while utilising the cofactor NAD(P)+. Some superfamily members can also act as esterases using p-nitrophenyl esters as substrates. The ALDHTt from Thermus thermophilus was recombinantly expressed in E. coli and purified to obtain high yields (approximately 15–20 mg/L) and purity utilising an efficient heat treatment step coupled with IMAC and gel filtration chromatography. The use of the heat treatment step proved critical, in its absence decreased yield of 40% was observed. Characterisation of the thermophilic ALDHTt led to optimum enzymatic working conditions of 50 °C, and a pH of 8. ALDHTt possesses dual enzymatic activity, with the ability to act as a dehydrogenase and an esterase. ALDHTt possesses broad substrate specificity, displaying activity for a range of aldehydes, most notably hexanal and the synthetic dialdehyde, terephthalaldehyde. Interestingly, para-substituted benzaldehydes could be processed efficiently, but ortho-substitution resulted in no catalytic activity. Similarly, ALDHTt displayed activity for two different esterase substrates, p-nitrophenyl acetate and p-nitrophenyl butyrate, but with activities of 22.9% and 8.9%, respectively, compared to the activity towards hexanal.
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15
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Siletsky SA, Borisov VB. Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives. Int J Mol Sci 2021; 22:10852. [PMID: 34639193 PMCID: PMC8509429 DOI: 10.3390/ijms221910852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.
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Affiliation(s)
- Sergey A. Siletsky
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia;
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16
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Rivett ED, Heo L, Feig M, Hegg EL. Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Crit Rev Biochem Mol Biol 2021; 56:640-668. [PMID: 34428995 DOI: 10.1080/10409238.2021.1957668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many heme-copper oxidases, including mitochondrial cytochrome c oxidases, possess a second heme a cofactor. Despite the critical role of heme a in the electron transport chain, the details of the mechanism by which heme b, the prototypical cellular heme, is converted to heme o and then to heme a remain poorly understood. Recent structural investigations, however, have helped clarify some elements of heme a biosynthesis. In this review, we discuss the insight gained from these advances. In particular, we present a new structural model of heme o synthase (HOS) based on distance restraints from inferred coevolutionary relationships and refined by molecular dynamics simulations that are in good agreement with the experimentally determined structures of HOS homologs. We also analyze the two structures of heme a synthase (HAS) that have recently been solved by other groups. For both HOS and HAS, we discuss the proposed catalytic mechanisms and highlight how new insights into the heme-binding site locations shed light on previously obtained biochemical data. Finally, we explore the implications of the new structural data in the broader context of heme trafficking in the heme a biosynthetic pathway and heme-copper oxidase assembly.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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17
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Linhua Tai
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Danyang Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoyun Pang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Sin Man Lam
- LipidALL Technologies Company Limited Changzhou 213022 Jiangsu Province China
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101 China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guohong Peng
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Center for Biological Imaging Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
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18
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021; 60:13323-13330. [PMID: 33665933 PMCID: PMC8251803 DOI: 10.1002/anie.202016785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 02/03/2023]
Abstract
The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.
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Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Hui Zeng
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Shuangbo Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jana Juli
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Linhua Tai
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Danyang Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiaoyun Pang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Yan Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Sin Man Lam
- LipidALL Technologies Company LimitedChangzhou213022Jiangsu ProvinceChina
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesNo.1 West Beichen Road, Chaoyang DistrictBeijing100101China
| | - Yun Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Guohong Peng
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Hartmut Michel
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Fei Sun
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- Center for Biological ImagingInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
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19
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Abstract
Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na+ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.
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20
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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21
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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22
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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23
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Integral caa 3-Cytochrome c Oxidase from Thermus thermophilus: Purification and Crystallization. Methods Mol Biol 2020. [PMID: 31342419 DOI: 10.1007/978-1-4939-9678-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cytochrome c oxidase is a respiratory enzyme catalyzing the energy-conserving reduction of molecular oxygen to water-a fundamental biological process of cell respiration. The first crystal structures of the type A cytochrome c oxidases, bovine heart and Paracoccus denitrificans cytochrome c oxidases, were published in 1995 and contributed immensely to the understanding of the enzyme's mechanism of action. The senior author's research focus was directed toward understanding the structure and function of the type B cytochrome c oxidases, ba3-oxidase and type A2 caa3-oxidase, both from the extreme thermophilic bacterium Thermus thermophilus. While the ba3-oxidase structure was published in 2000 and functional characterization is well-documented in the literature, we recently successfully solved the structure of the caa3-nature made enzyme-substrate complex. This chapter is dedicated to the purification and crystallization process of caa3-cytochrome c oxidase.
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24
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Structure and Functional Characterization of Membrane Integral Proteins in the Lipid Cubic Phase. J Mol Biol 2020; 432:5104-5123. [PMID: 32113953 DOI: 10.1016/j.jmb.2020.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
The lipid cubic phase (LCP) has been used extensively as a medium for crystallizing membrane proteins. It is an attractive environment in which to perform such studies because it incorporates a lipid bilayer. It is therefore considered a useful and a faithful biomembrane mimetic. Here, we bring together evidence that supports this view. Biophysical characterizations are described demonstrating that the cubic phase is a porous medium into and out of which water-soluble molecules can diffuse for binding to and reaction with reconstituted proteins. The proteins themselves are shown to be functionally reconstituted into and to have full mobility in the bilayered membrane, a prerequisite for LCP crystallogenesis. Spectroscopic methods have been used to characterize the conformation and disposition of proteins in the mesophase. Procedures for performing activity assays on enzymes directly in the cubic phase have been reported. Specific examples described here include a kinase and two transferases, where quantitative kinetics and mechanism-defining measurements were performed directly or via a coupled assay system. Finally, ligand-binding assays are described, where binding to proteins in the mesophase membrane was monitored directly by eye and indirectly by fluorescence quenching, enabling binding constant determinations for targets with affinity values in the micromolar and nanomolar range. These results make a convincing case that the lipid bilayer of the cubic mesophase is an excellent membrane mimetic and a suitable medium in which to perform not only crystallogenesis but also biochemical and biophysical characterizations of membrane proteins.
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25
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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Proc Natl Acad Sci U S A 2020; 117:5280-5290. [PMID: 32094184 DOI: 10.1073/pnas.1922133117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.
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26
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Cell Membrane and Electron Transfer Engineering for Improved Synthesis of Menaquinone-7 in Bacillus subtilis. iScience 2020; 23:100918. [PMID: 32109677 PMCID: PMC7044751 DOI: 10.1016/j.isci.2020.100918] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
The formation of biofilm facilitates the synthesis of valuable natural product menaquinone-7 (MK-7) in static culture of Bacillus subtilis, whereas the essential role and mechanism of biofilm in MK-7 synthesis have not been revealed. Herein, comparative transcriptomics show that the formation of biofilm affected MK-7 synthesis by changing the transcription levels of signal receptor (BSU02010), transmembrane transporter (BSU29340, BSU03070), and signal transduction (BSU02630). Moreover, we also found that oxalate decarboxylase OxdC has an important effect on electron generation and MK-7 synthesis, when the transcriptional level of NADH dehydrogenase decreases in static culture. Our results revealed that cell membrane and electron transfer are important factors in promoting MK-7 synthesis. Transcriptome analysis shows the relationship between biofilm and MK-7 synthesis Electron transfer significantly affects the synthesis of MK-7 Oxalate decarboxylase OxdC plays a role in electron generation and MK-7 synthesis
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27
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Morgada MN, Llases ME, Giannini E, Castro MA, Alzari PM, Murgida DH, Lisa MN, Vila AJ. Unexpected electron spin density on the axial methionine ligand in Cu A suggests its involvement in electron pathways. Chem Commun (Camb) 2020; 56:1223-1226. [PMID: 31897463 DOI: 10.1039/c9cc08883k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CuA center is a paradigm for the study of long-range biological electron transfer. This metal center is an essential cofactor for terminal oxidases like cytochrome c oxidase, the enzymatic complex responsible for cellular respiration in eukaryotes and in most bacteria. CuA acts as an electron hub by transferring electrons from reduced cytochrome c to the catalytic site of the enzyme where dioxygen reduction takes place. Different electron transfer pathways have been proposed involving a weak axial methionine ligand residue, conserved in all CuA sites. This hypothesis has been challenged by theoretical calculations indicating the lack of electron spin density in this ligand. Here we report an NMR study with selectively labeled methionine in a native CuA. NMR spectroscopy discloses the presence of net electron spin density in the methionine axial ligand in the two alternative ground states of this metal center. Similar spin delocalization observed on two second sphere mutants further supports this evidence. These data provide a novel view of the electronic structure of CuA centers and support previously neglected electron transfer pathways.
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Affiliation(s)
- Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario 2000, Argentina.
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28
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Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site. Proc Natl Acad Sci U S A 2019; 117:872-876. [PMID: 31888984 DOI: 10.1073/pnas.1915013117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Virtually all proton-pumping terminal respiratory oxygen reductases are members of the heme-copper oxidoreductase superfamily. Most of these enzymes use reduced cytochrome c as a source of electrons, but a group of enzymes have evolved to directly oxidize membrane-bound quinols, usually menaquinol or ubiquinol. All of the quinol oxidases have an additional transmembrane helix (TM0) in subunit I that is not present in the related cytochrome c oxidases. The current work reports the 3.6-Å-resolution X-ray structure of the cytochrome aa 3 -600 menaquinol oxidase from Bacillus subtilis containing 1 equivalent of menaquinone. The structure shows that TM0 forms part of a cleft to accommodate the menaquinol-7 substrate. Crystals which have been soaked with the quinol-analog inhibitor HQNO (N-oxo-2-heptyl-4-hydroxyquinoline) or 3-iodo-HQNO reveal a single binding site where the inhibitor forms hydrogen bonds to amino acid residues shown previously by spectroscopic methods to interact with the semiquinone state of menaquinone, a catalytic intermediate.
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29
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Abstract
X-ray crystallographic analyses of mitochondrial cytochrome c oxidase (CcO) have been based on its dimeric form. Recent cryo-electron microscopy structures revealed that CcO exists in its monomeric form in the respiratory supercomplex. This study, using amphipol-stabilized CcO, shows that the activity of monomer is higher than that of the dimer. The crystal structure of monomer determined here shows that the local structure of one of the proton transfer pathways differs from that in the dimer. The crystal structure also shows that cardiolipins are located at the interface region in the supercomplex. Taken together, these results suggest that CcO in the monomeric state, dimeric state, and supercomplex state depending on cardiolipins are involved in regulation of respiratory electron transport. Cytochrome c oxidase (CcO), a membrane enzyme in the respiratory chain, catalyzes oxygen reduction by coupling electron and proton transfer through the enzyme with a proton pump across the membrane. In all crystals reported to date, bovine CcO exists as a dimer with the same intermonomer contacts, whereas CcOs and related enzymes from prokaryotes exist as monomers. Recent structural analyses of the mitochondrial respiratory supercomplex revealed that CcO monomer associates with complex I and complex III, indicating that the monomeric state is functionally important. In this study, we prepared monomeric and dimeric bovine CcO, stabilized using amphipol, and showed that the monomer had high activity. In addition, using a newly synthesized detergent, we determined the oxidized and reduced structures of monomer with resolutions of 1.85 and 1.95 Å, respectively. Structural comparison of the monomer and dimer revealed that a hydrogen bond network of water molecules is formed at the entry surface of the proton transfer pathway, termed the K-pathway, in monomeric CcO, whereas this network is altered in dimeric CcO. Based on these results, we propose that the monomer is the activated form, whereas the dimer can be regarded as a physiological standby form in the mitochondrial membrane. We also determined phospholipid structures based on electron density together with the anomalous scattering effect of phosphorus atoms. Two cardiolipins are found at the interface region of the supercomplex. We discuss formation of the monomeric CcO, dimeric CcO, and supercomplex, as well as their role in regulation of CcO activity.
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30
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Canonica F, Klose D, Ledermann R, Sauer MM, Abicht HK, Quade N, Gossert AD, Chesnov S, Fischer HM, Jeschke G, Hennecke H, Glockshuber R. Structural basis and mechanism for metallochaperone-assisted assembly of the Cu A center in cytochrome oxidase. SCIENCE ADVANCES 2019; 5:eaaw8478. [PMID: 31392273 PMCID: PMC6669012 DOI: 10.1126/sciadv.aaw8478] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The mechanisms underlying the biogenesis of the structurally unique, binuclear Cu1.5+•Cu1.5+ redox center (CuA) on subunit II (CoxB) of cytochrome oxidases have been a long-standing mystery. Here, we reconstituted the CoxB•CuA center in vitro from apo-CoxB and the holo-forms of the copper transfer chaperones ScoI and PcuC. A previously unknown, highly stable ScoI•Cu2+•CoxB complex was shown to be rapidly formed as the first intermediate in the pathway. Moreover, our structural data revealed that PcuC has two copper-binding sites, one each for Cu1+ and Cu2+, and that only PcuC•Cu1+•Cu2+ can release CoxB•Cu2+ from the ScoI•Cu2+•CoxB complex. The CoxB•CuA center was then formed quantitatively by transfer of Cu1+ from a second equivalent of PcuC•Cu1+•Cu2+ to CoxB•Cu2+. This metalation pathway is consistent with all available in vivo data and identifies the sources of the Cu ions required for CuA center formation and the order of their delivery to CoxB.
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Affiliation(s)
- Fabia Canonica
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Maximilian M. Sauer
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Helge K. Abicht
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nick Quade
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alvar D. Gossert
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Serge Chesnov
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | | | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Hauke Hennecke
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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31
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Interfaces Between Alpha-helical Integral Membrane Proteins: Characterization, Prediction, and Docking. Comput Struct Biotechnol J 2019; 17:699-711. [PMID: 31303974 PMCID: PMC6603304 DOI: 10.1016/j.csbj.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/28/2022] Open
Abstract
Protein-protein interaction (PPI) is an essential mechanism by which proteins perform their biological functions. For globular proteins, the molecular characteristics of such interactions have been well analyzed, and many computational tools are available for predicting PPI sites and constructing structural models of the complex. In contrast, little is known about the molecular features of the interaction between integral membrane proteins (IMPs) and few methods exist for constructing structural models of their complexes. Here, we analyze the interfaces from a non-redundant set of complexes of α-helical IMPs whose structures have been determined to a high resolution. We find that the interface is not significantly different from the rest of the surface in terms of average hydrophobicity. However, the interface is significantly better conserved and, on average, inter-subunit contacting residue pairs correlate more strongly than non-contacting pairs, especially in obligate complexes. We also develop a neural network-based method, with an area under the receiver operating characteristic curve of 0.75 and a Pearson correlation coefficient of 0.70, for predicting interface residues and their weighted contact numbers (WCNs). We further show that predicted interface residues and their WCNs can be used as restraints to reconstruct the structure α-helical IMP dimers through docking for fourteen out of a benchmark set of sixteen complexes. The RMSD100 values of the best-docked ligand subunit to its native structure are <2.5 Å for these fourteen cases. The structural analysis conducted in this work provides molecular details about the interface between α-helical IMPs and the WCN restraints represent an efficient means to score α-helical IMP docking candidates.
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Key Words
- AUC, Area under the ROC curve
- IMP, Integral membrane protein
- MAE, Mean absolute error
- MSA, Multiple sequence alignment
- Membrane protein docking
- Membrane protein interfaces
- Neural networks
- OPM, Orientations of proteins in membranes
- PCC, Pearson correlation coefficient
- PDB, Protein data bank
- PPI, Protein-protein interaction
- PPM, Positioning of proteins in membrane.
- PPV, Positive predictive value
- PSSM, Position-specific scoring matrix
- RMSD, Root-mean-square distance
- ROC, Receiver operating characteristic curve
- RSA, Relative solvent accessibility
- TNR, True negative rate
- TPR, True positive rate
- WCN, Weighted contact number
- Weighted contact numbers
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Koutsoupakis C, Soulimane T, Varotsis C. Discrete Ligand Binding and Electron Transfer Properties of ba 3-Cytochrome c Oxidase from Thermus thermophilus: Evolutionary Adaption to Low Oxygen and High Temperature Environments. Acc Chem Res 2019; 52:1380-1390. [PMID: 31021078 DOI: 10.1021/acs.accounts.9b00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (C cO) couples the oxidation of cytochrome c to the reduction of molecular oxygen to water and links these electron transfers to proton translocation. The redox-driven C cO conserves part of the released free energy generating a proton motive force that leads to the synthesis of the main biological energy source ATP. Cytochrome ba3 oxidase is a B-type oxidase from the extremely thermophilic eubacterium Thermus thermophilus with high O2 affinity, expressed under elevated temperatures and limited oxygen supply and possessing discrete structural, ligand binding, and electron transfer properties. The origin and the cause of the peculiar, as compared to other C cOs, thermodynamic and kinetic properties remain unknown. Fourier transform infrared (FTIR) and time-resolved step-scan FTIR (TRS2-FTIR) spectroscopies have been employed to investigate the origin of the binding and electron transfer properties of cytochrome ba3 oxidase in both the fully reduced (FR) and mixed valence (MV) forms. Several independent and not easily separated factors leading to increased thermostability and high O2 affinity have been determined. These include (i) the increased hydrophobicity of the active center, (ii) the existence of a ligand input channel, (iii) the high affinity of CuB for exogenous ligands, (iv) the optimized electron transfer (ET) pathways, (v) the effective proton-input channel and water-exit pathway as well the proton-loading/exit sites, (vi) the specifically engineered protein structure, and (vii) the subtle thermodynamic and kinetic regulation. We correlate the unique ligand binding and electron transfer properties of cytochrome ba3 oxidase with the existence of an adaption mechanism which is necessary for efficient function. These results suggest that a cascade of structural factors have been optimized by evolution, through protein architecture, to ensure the conversion of cytochrome ba3 oxidase into a high O2-affinity enzyme that functions effectively in its extreme native environment. The present results show that ba3-cytochrome c oxidase uses a unique structural pattern of energy conversion that has taken into account all the extreme environmental factors that affect the function of the enzyme and is assembled in such a way that its exclusive functions are secured. Based on the available data of CcOs, we propose possible factors including the rigidity and nonpolar hydrophobic interactions that contribute to the behavior observed in cytochrome ba3 oxidase.
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Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department and Materials & Surface Science Institute (MSSI), University of Limerick, Limerick, Ireland
| | - Constantinos Varotsis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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Krishnan A, Degnan BM, Degnan SM. The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains. BMC Evol Biol 2019; 19:96. [PMID: 31023220 PMCID: PMC6485061 DOI: 10.1186/s12862-019-1418-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/31/2019] [Indexed: 11/25/2022] Open
Abstract
Background Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicellularity. However, the genomes of sponges and ctenophores – non-bilaterian basal animals – typically encode no, or far fewer, recognisable signalling ligands compared to bilaterians and cnidarians. For instance, the largest subclass of receptor tyrosine kinases (RTKs) in bilaterians, the Eph receptors (Ephs), are present in sponges and ctenophores, but their cognate ligands, the ephrins, have not yet been detected. Results Here, we use an iterative HMM analysis to identify for the first time membrane-bound ephrins in sponges and ctenophores. We also expand the number of Eph-receptor subtypes identified in these animals and in cnidarians. Both sequence and structural analyses are consistent with the Eph ligand binding domain (LBD) and the ephrin receptor binding domain (RBD) having evolved via the co-option of ancient galactose-binding (discoidin-domain)-like and monodomain cupredoxin domains, respectively. Although we did not detect a complete Eph-ephrin signalling pathway in closely-related unicellular holozoans or in other non-metazoan eukaryotes, truncated proteins with Eph receptor LBDs and ephrin RBDs are present in some choanoflagellates. Together, these results indicate that Eph-ephrin signalling was present in the last common ancestor of extant metazoans, and perhaps even in the last common ancestor of animals and choanoflagellates. Either scenario pushes the origin of Eph-ephrin signalling back much earlier than previously reported. Conclusions We propose that the Eph-LBD and ephrin-RBD, which were ancestrally localised in the cytosol, became linked to the extracellular parts of two cell surface proteins before the divergence of sponges and ctenophores from the rest of the animal kingdom. The ephrin-RBD lost the ancestral capacity to bind copper, and the Eph-LBD became linked to an ancient RTK. The identification of divergent ephrin ligands in sponges and ctenophores suggests that these ligands evolve faster than their cognate receptors. As this may be a general phenomena, we propose that the sequence-structure approach used in this study may be usefully applied to other signalling systems where no, or a small number of, ligands have been identified. Electronic supplementary material The online version of this article (10.1186/s12862-019-1418-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arunkumar Krishnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Present Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sandie M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.
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35
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Degli Esposti M, Mentel M, Martin W, Sousa FL. Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments. Front Microbiol 2019; 10:499. [PMID: 30936856 PMCID: PMC6431628 DOI: 10.3389/fmicb.2019.00499] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/27/2019] [Indexed: 01/24/2023] Open
Abstract
Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well.
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Affiliation(s)
| | - Marek Mentel
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Bratislava, Slovakia
| | - William Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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36
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Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
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Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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37
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Abstract
Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-containing integral membrane protein, and its structure and reaction mechanisms have remained unknown. Thus, little is known about HAS despite of its importance. Here we report the crystal structure of HAS from Bacillus subtilis at 2.2-Å resolution. The N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant. Many water molecules are found in the transmembrane region and around the substrate-binding site, and some of them interact with the main chain of transmembrane helix. Comparison of these two domain structures enables us to construct a substrate-heme binding state structure. This structure implies that a completely conserved glutamate, Glu57 in B. subtilis, is the catalytic residue for the formylation reaction. These results provide valuable suggestions of the substrate-heme binding mechanism. Our results present significant insight into the heme A biosynthesis.
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38
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Kaur H, Singh P. Rationally designed molecules for resurgence of cyanide mitigated cytochrome c oxidase activity. Bioorg Chem 2018; 82:229-240. [PMID: 30391853 DOI: 10.1016/j.bioorg.2018.10.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/26/2022]
Abstract
Cytochrome c oxidase (CcOX) containing binuclear heme a3-Cu B centre (BNC) mechanises the process of electron transfer in the last phase of cellular respiration. The molecular modelling based structural analysis of CcOX - heme a3-Cu B complex was performed and the disturbance to this complex under cyanide poisoning conditions was investigated. Taking into consideration the results of molecular docking studies, new chemical entities were developed for clipping cyanide from the enzyme and restoring its normal function. It was found that the molecules obtained by combining syringaldehyde, oxindole and chrysin moieties bearing propyl/butyl spacing groups occupy the BNC region and effectively remove cyanide bound to the enzyme. The binding constant of compound 2 with CN- was 2.3 × 105 M-1 and its ED50 for restoring the cyanide bound CcOX activity in 10 min was 16 µM. The compound interacted with CN- over the pH range 5-10. The comparison of the loss of enzymatic activity in the presence of CN- and resumption of enzymatic activity by compound 2 mediated removal of CN- indicated the efficacy of the compound as antidote of cyanide.
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Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar 143005, India
| | - Palwinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar 143005, India.
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39
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Kardos J, Héja L, Simon Á, Jablonkai I, Kovács R, Jemnitz K. Copper signalling: causes and consequences. Cell Commun Signal 2018; 16:71. [PMID: 30348177 PMCID: PMC6198518 DOI: 10.1186/s12964-018-0277-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Copper-containing enzymes perform fundamental functions by activating dioxygen (O2) and therefore allowing chemical energy-transfer for aerobic metabolism. The copper-dependence of O2 transport, metabolism and production of signalling molecules are supported by molecular systems that regulate and preserve tightly-bound static and weakly-bound dynamic cellular copper pools. Disruption of the reducing intracellular environment, characterized by glutathione shortage and ambient Cu(II) abundance drives oxidative stress and interferes with the bidirectional, copper-dependent communication between neurons and astrocytes, eventually leading to various brain disease forms. A deeper understanding of of the regulatory effects of copper on neuro-glia coupling via polyamine metabolism may reveal novel copper signalling functions and new directions for therapeutic intervention in brain disorders associated with aberrant copper metabolism.
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Affiliation(s)
- Julianna Kardos
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, Budapest, 1117 Hungary
| | - László Héja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, Budapest, 1117 Hungary
| | - Ágnes Simon
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, Budapest, 1117 Hungary
| | - István Jablonkai
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, Budapest, 1117 Hungary
| | - Richard Kovács
- Institute of Neurophysiology, Charité-Universitätsmedizin, Berlin, Germany
| | - Katalin Jemnitz
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, Budapest, 1117 Hungary
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40
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Hayes K, Noor M, Djeghader A, Armshaw P, Pembroke T, Tofail S, Soulimane T. The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Sci Rep 2018; 8:13327. [PMID: 30190503 PMCID: PMC6127216 DOI: 10.1038/s41598-018-31724-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved architecture of three domains: the catalytic domain, NAD(P)+ binding domain, and the oligomerization domain. Here, we describe the structure and function of the ALDH from Thermus thermophilus (ALDHTt) which exhibits non-canonical features of both dimeric and tetrameric ALDH and a previously uncharacterized C-terminal arm extension forming novel interactions with the N-terminus in the quaternary structure. This unusual tail also interacts closely with the substrate entry tunnel in each monomer providing further mechanistic detail for the recent discovery of tail-mediated activity regulation in ALDH. However, due to the novel distal extension of the tail of ALDHTt and stabilizing termini-interactions, the current model of tail-mediated substrate access is not apparent in ALDHTt. The discovery of such a long tail in a deeply and early branching phylum such as Deinococcus-Thermus indicates that ALDHTt may be an ancestral or primordial metabolic model of study. This structure provides invaluable evidence of how metabolic regulation has evolved and provides a link to early enzyme regulatory adaptations.
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Affiliation(s)
- Kevin Hayes
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Mohamed Noor
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Patricia Armshaw
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tony Pembroke
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Syed Tofail
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.,Physics Department, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland. .,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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41
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:712-724. [PMID: 29883591 DOI: 10.1016/j.bbabio.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/05/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O2 reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze an intermediate step of denitrification by reducing nitric oxide (NO) to nitrous oxide (N2O). They are structurally similar to heme‑copper oxygen reductases (HCOs), which reduce O2 to water. The experimentally observed apparent bimolecular rate constant of NO delivery to the deeply buried catalytic site of NORs was previously reported to approach the diffusion-controlled limit (108-109 M-1 s-1). Using the crystal structure of cytochrome-c dependent NOR (cNOR) from Pseudomonas aeruginosa, we employed several protocols of molecular dynamics (MD) simulation, which include flooding simulations of NO molecules, implicit ligand sampling and umbrella sampling simulations, to elucidate how NO in solution accesses the catalytic site of this cNOR. The results show that NO partitions into the membrane, enters the enzyme from the lipid bilayer and diffuses to the catalytic site via a hydrophobic tunnel that is resolved in the crystal structures. This is similar to what has been found for O2 diffusion through the closely related O2 reductases. The apparent second order rate constant approximated using the simulation data is ~5 × 108 M-1 s-1, which is optimized by the dynamics of the amino acid side chains lining in the tunnel. It is concluded that both NO and O2 reductases utilize well defined hydrophobic tunnels to assure that substrate diffusion to the buried catalytic sites is not rate limiting under physiological conditions.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
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42
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Structural basis for energy transduction by respiratory alternative complex III. Nat Commun 2018; 9:1728. [PMID: 29712914 PMCID: PMC5928083 DOI: 10.1038/s41467-018-04141-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/02/2018] [Indexed: 01/30/2023] Open
Abstract
Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron–sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump. Some prokaryotes use alternative respiratory chain complexes, such as the alternative complex III (ACIII), to generate energy. Here authors provide the cryoEM structure of ACIII from Rhodothermus marinus which shows the arrangement of cofactors and provides insights into the mechanism for energy transduction.
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43
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Cytochrome aa 3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O 2 for Catalysis. Biochemistry 2018; 57:2150-2161. [PMID: 29546752 DOI: 10.1021/acs.biochem.7b01194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome aa3 is the terminal respiratory enzyme of all eukaryotes and many bacteria and archaea, reducing O2 to water and harnessing the free energy from the reaction to generate the transmembrane electrochemical potential. The diffusion of O2 to the heme-copper catalytic site, which is buried deep inside the enzyme, is the initiation step of the reaction chemistry. Our previous molecular dynamics (MD) study with cytochrome ba3, a homologous enzyme of cytochrome aa3 in Thermus thermophilus, demonstrated that O2 diffuses from the lipid bilayer to its reduction site through a 25 Å long tunnel inferred by Xe binding sites detected by X-ray crystallography [Mahinthichaichan, P., Gennis, R., and Tajkhorshid, E. (2016) Biochemistry 55, 1265-1278]. Although a similar tunnel is observed in cytochrome aa3, this putative pathway appears partially occluded between the entrances and the reduction site. Also, the experimentally determined second-order rate constant for O2 delivery in cytochrome aa3 (∼108 M-1 s-1) is 10 times slower than that in cytochrome ba3 (∼109 M-1 s-1). A question to be addressed is whether cytochrome aa3 utilizes this X-ray-inferred tunnel as the primary pathway for O2 delivery. Using complementary computational methods, including multiple independent flooding MD simulations and implicit ligand sampling calculations, we probe the O2 delivery pathways in cytochrome aa3 of Rhodobacter sphaeroides. All of the O2 molecules that arrived in the reduction site during the simulations were found to diffuse through the X-ray-observed tunnel, despite its apparent constriction, supporting its role as the main O2 delivery pathway in cytochrome aa3. The rate constant for O2 delivery in cytochrome aa3, approximated using the simulation results, is 10 times slower than in cytochrome ba3, in agreement with the experimentally determined rate constants.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert B Gennis
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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44
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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45
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Sandri F, Musiani F, Selamoglu N, Daldal F, Zannoni D. Pseudomonas pseudoalcaligenes KF707 grown with biphenyl expresses a cytochrome caa 3 oxidase that uses cytochrome c 4 as electron donor. FEBS Lett 2018; 592:901-915. [PMID: 29427514 DOI: 10.1002/1873-3468.13001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/09/2022]
Abstract
Combining peroxidase activity-based heme staining (TMBZ/SDS/PAGE) with mass spectrometry analyses (Nano LC-MS/MS) of protein extracts from wild-type and appropriate mutants, we provide evidence that the polychlorinated biphenyl degrader Pseudomonas pseudoalcaligenes KF707 primarily expresses a caa3 -type cytochrome c oxidase (caa3 -Cox) using cytochrome (cyt) c4 as an electron donor in cells grown with biphenyl versus glucose as the sole carbon source. Homology modeling of KF707 caa3 -Cox using the three-dimensional structure of that from Thermus thermophilus highlights multiple similarities and differences between the proton channels in subunit I of the aa3 - and caa3 -Cox of Paracoccus and Thermus spp., respectively. To our knowledge, this is the first report demonstrating the presence of a caa3 -Cox using cyt c4 as an electron donor in a Pseudomonas species.
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Affiliation(s)
- Federica Sandri
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
| | - Francesco Musiani
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
| | - Nur Selamoglu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Davide Zannoni
- Department of Pharmacy and BioTechnology, University of Bologna, Italy
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46
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Wikström M, Krab K, Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem Rev 2018; 118:2469-2490. [PMID: 29350917 PMCID: PMC6203177 DOI: 10.1021/acs.chemrev.7b00664] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
This review focuses on the type
A cytochrome c oxidases (CcO), which
are found in all mitochondria
and also in several aerobic bacteria. CcO catalyzes
the respiratory reduction of dioxygen (O2) to water by
an intriguing mechanism, the details of which are fairly well understood
today as a result of research for over four decades. Perhaps even
more intriguingly, the membrane-bound CcO couples
the O2 reduction chemistry to translocation of protons
across the membrane, thus contributing to generation of the electrochemical
proton gradient that is used to drive the synthesis of ATP as catalyzed
by the rotary ATP synthase in the same membrane. After reviewing the
structure of the core subunits of CcO, the active
site, and the transfer paths of electrons, protons, oxygen, and water,
we describe the states of the catalytic cycle and point out the few
remaining uncertainties. Finally, we discuss the mechanism of proton
translocation and the controversies in that area that still prevail.
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Affiliation(s)
- Mårten Wikström
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland
| | - Klaas Krab
- Department of Molecular Cell Physiology , Vrije Universiteit , P.O. Box 7161 , Amsterdam 1007 MC , The Netherlands
| | - Vivek Sharma
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland.,Department of Physics , University of Helsinki , P.O. Box 64 , Helsinki FI-00014 , Finland
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47
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Melin F, Schoepp-Cothenet B, Abdulkarim S, Noor MR, Soulimane T, Hellwig P. Electrochemical study of an electron shuttle diheme protein: The cytochrome c from T. thermophilus. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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48
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Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies. Biochem Soc Trans 2017; 45:813-829. [PMID: 28620043 DOI: 10.1042/bst20160139] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/04/2023]
Abstract
Mitochondrial cytochrome c oxidase is a member of a diverse superfamily of haem-copper oxidases. Its mechanism of oxygen reduction is reviewed in terms of the cycle of catalytic intermediates and their likely chemical structures. This reaction cycle is coupled to the translocation of protons across the inner mitochondrial membrane in which it is located. The likely mechanism by which this occurs, derived in significant part from studies of bacterial homologues, is presented. These mechanisms of catalysis and coupling, together with current alternative proposals of underlying mechanisms, are critically reviewed.
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The cubicon method for concentrating membrane proteins in the cubic mesophase. Nat Protoc 2017; 12:1745-1762. [DOI: 10.1038/nprot.2017.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tadokoro M, Hosoda H, Inoue T, Murayama A, Noguchi K, Iioka A, Nishimura R, Itoh M, Sugaya T, Kamebuchi H, Haga MA. Synchronized Collective Proton-Assisted Electron Transfer in Solid State by Hydrogen-Bonding Ru(II)/Ru(III) Mixed-Valence Molecular Crystals. Inorg Chem 2017; 56:8513-8526. [PMID: 28682602 DOI: 10.1021/acs.inorgchem.7b01256] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A proton-coupled electron transfer (PCET) reaction was widely studied with isolated organic molecules and metal complexes in solution in view of the biological catalytic reaction, while studying this reaction in the crystalline or solid-state phase, which has a novel example, would give insight into the rather internal environment of proteins without solvation and a creation of new molecular materials. We tried to crystallize a hydrogen-bonded (H-bonded) coordination polymer with one-dimensional nanoporous channels, formed from redox-active RuIII complexes, [RuIII(Hbim)3] (Hbim- = 2,2'-biimidazolate monoanion). As a result, a synchronized collective PCET phenomenon was observed for the molecular nanoporous crystal by novel solid-state cyclic voltammetry (CV), which could be measured by only setting some crystals on the electrode surface. The nanoporous crystals, {[RuIII(Hbim)3]}n (1), are simultaneously induced to a synchronized collective RuIIRuIII mixed-valence state, {RuIIRuIII}n, with alternating arrays of RuII and RuIII complexes by PCET in a way of the reductive state of {RuIIRuII}n. Further, a new crystal with {RuIIRuIII}n, {[RuII(H2bim)(Hbim)2][RuIII(bim) (Hbim)2][K(MeOBz)6]}n (2), was also prepared, and the solid-state CV revealed the same electrochemical behavior of {RuIIRuIII}n with 1. The single crystal with {RuIIRuIII}n of 2 was unusually a semiconductor with 5.12 × 10-6 S/cm conductivity at 298 K by an impedance method (8.01 × 10-6 S/cm by a direct-current method at 277 K). Thus, an unprecedented electron-hopping conductor driven by a low-barrier proton transfer through a PCET mechanism (Ea = 0.30 eV) was realized in the H-bonding molecular crystal with {RuIIRuIII}n. Such studies on a PCET reaction in the crystalline state is not only worthwhile as a model of essential biological reactions without solvation, but also proposed to a new design of molecular materials to occur an electron transfer by using an intermolecular H-bond.
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Affiliation(s)
- Makoto Tadokoro
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan.,Department of Chemistry, Graduate School of Science, Osaka City University , Sugimoto-cho 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hiroyuki Hosoda
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Tomonori Inoue
- Department of Chemistry, Graduate School of Science, Osaka City University , Sugimoto-cho 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Akira Murayama
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Koichiro Noguchi
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Atsushi Iioka
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Ryota Nishimura
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Masaki Itoh
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Tomoaki Sugaya
- Education Center, Faculty of Engineering, Chiba Institute of Technology , Shibazono 2-1-1, Narashino, Chiba 275-0023, Japan
| | - Hajime Kamebuchi
- Department of Chemistry, Faculty of Science, Tokyo University of Science , Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Masa-Aki Haga
- Department of Applied Chemistry, Faculty of Science and Technology, Chuo University , Korakuen, Chuo-ku, Tokyo 112-8551, Japan
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