1
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Murali R, Pace LA, Sanford RA, Ward LM, Lynes MM, Hatzenpichler R, Lingappa UF, Fischer WW, Gennis RB, Hemp J. Diversity and evolution of nitric oxide reduction in bacteria and archaea. Proc Natl Acad Sci U S A 2024; 121:e2316422121. [PMID: 38900790 PMCID: PMC11214002 DOI: 10.1073/pnas.2316422121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/22/2024] Open
Abstract
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four of which (eNOR, sNOR, gNOR, and nNOR) appear to perform NO reduction. These families have novel active-site structures and several have conserved proton channels, suggesting that they might be able to couple NO reduction to energy conservation. We isolated and biochemically characterized a member of the eNOR family from the bacterium Rhodothermus marinus and found that it performs NO reduction. These recently identified NORs exhibited broad phylogenetic and environmental distributions, greatly expanding the diversity of microbes in nature capable of NO reduction. Phylogenetic analyses further demonstrated that NORs evolved multiple times independently from oxygen reductases, supporting the view that complete denitrification evolved after aerobic respiration.
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Affiliation(s)
- Ranjani Murali
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV89154
| | - Laura A. Pace
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
- meliora.bio, Salt Lake City, UT84103
| | - Robert A. Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - L. M. Ward
- Department of Geosciences, Smith College, Northampton, MA01063
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Mackenzie M. Lynes
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT59717
- Center for Biofilm Enginering, Montana State University, Bozeman, MT59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT59717
| | - Usha F. Lingappa
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
| | - Woodward W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL61801
| | - James Hemp
- meliora.bio, Salt Lake City, UT84103
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
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2
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Noodleman L, Götz AW, Han Du WG, Hunsicker-Wang L. Reaction pathways, proton transfer, and proton pumping in ba3 class cytochrome c oxidase: perspectives from DFT quantum chemistry and molecular dynamics. Front Chem 2023; 11:1186022. [PMID: 38188931 PMCID: PMC10766771 DOI: 10.3389/fchem.2023.1186022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
After drawing comparisons between the reaction pathways of cytochrome c oxidase (CcO, Complex 4) and the preceding complex cytochrome bc1 (Complex 3), both being proton pumping complexes along the electron transport chain, we provide an analysis of the reaction pathways in bacterial ba3 class CcO, comparing spectroscopic results and kinetics observations with results from DFT calculations. For an important arc of the catalytic cycle in CcO, we can trace the energy pathways for the chemical protons and show how these pathways drive proton pumping of the vectorial protons. We then explore the proton loading network above the Fe heme a3-CuB catalytic center, showing how protons are loaded in and then released by combining DFT-based reaction energies with molecular dynamics simulations over states of that cycle. We also propose some additional reaction pathways for the chemical and vector protons based on our recent work with spectroscopic support.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, United States
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
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3
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Yang X, Liu S, Yin Z, Chen M, Song J, Li P, Yang L. New insights into the proton pumping mechanism of ba 3 cytochrome c oxidase: the functions of key residues and water. Phys Chem Chem Phys 2023; 25:25105-25115. [PMID: 37461851 DOI: 10.1039/d3cp01334k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
As the terminal oxidase of cell respiration in mitochondria and aerobic bacteria, the proton pumping mechanism of ba3-type cytochrome c oxidase (CcO) of Thermus thermophiles is still not fully understood. Especially, the functions of key residues which were considered as the possible proton loading sites (PLSs) above the catalytic center, as well as water located above and within the catalytic center, remain unclear. In this work, molecular dynamic simulations were performed on a set of designed mutants of key residues (Asp287, Asp372, His376, and Glu126II). The results showed that Asp287 may not be a PLS, but it could modulate the ability of the proton transfer pathway to transfer protons through its salt bridge with Arg225. Maintaining the closed state of the water pool above the catalytic center is necessary for the participation of inside water molecules in proton transfer. Water molecules inside the water pool can form hydrogen bond chains with PLS to facilitate proton transfer. Additional quantum cluster models of the Fe-Cu metal catalytic center are established, indicating that when the proton is transferred from Tyr237, it is more likely to reach the OCu atom directly through only one water molecule. This work provides a more profound understanding of the functions of important residues and specific water molecules in the proton pumping mechanism of CcO.
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Affiliation(s)
- Xiaoyue Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Shaohui Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Zhili Yin
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Mengguo Chen
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Illinois 60660, USA
| | - Longhua Yang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan 450001, China.
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4
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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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5
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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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6
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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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7
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Probing the Proton-Loading Site of Cytochrome C Oxidase Using Time-Resolved Fourier Transform Infrared Spectroscopy. Molecules 2020; 25:molecules25153393. [PMID: 32727022 PMCID: PMC7435947 DOI: 10.3390/molecules25153393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023] Open
Abstract
Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the “fast” kinetic spectra were found based on the following three requirements: (1) they are present in the “fast” phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the “slow” kinetic spectra in these mutants, and (3) they are absent in “fast” kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).
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8
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Cai X, Son CY, Mao J, Kaur D, Zhang Y, Khaniya U, Cui Q, Gunner MR. Identifying the proton loading site cluster in the ba 3 cytochrome c oxidase that loads and traps protons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148239. [PMID: 32531221 DOI: 10.1016/j.bbabio.2020.148239] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022]
Abstract
Cytochrome c Oxidase (CcO) is the terminal electron acceptor in aerobic respiratory chain, reducing O2 to water. The released free energy is stored by pumping protons through the protein, maintaining the transmembrane electrochemical gradient. Protons are held transiently in a proton loading site (PLS) that binds and releases protons driven by the electron transfer reaction cycle. Multi-Conformation Continuum Electrostatics (MCCE) was applied to crystal structures and Molecular Dynamics snapshots of the B-type Thermus thermophilus CcO. Six residues are identified as the PLS, binding and releasing protons as the charges on heme b and the binuclear center are changed: the heme a3 propionic acids, Asp287, Asp372, His376 and Glu126B. The unloaded state has one proton and the loaded state two protons on these six residues. Different input structures, modifying the PLS conformation, show different proton distributions and result in different proton pumping behaviors. One loaded and one unloaded protonation states have the loaded/unloaded states close in energy so the PLS binds and releases a proton through the reaction cycle. The alternative proton distributions have state energies too far apart to be shifted by the electron transfers so are locked in loaded or unloaded states. Here the protein can use active states to load and unload protons, but has nearby trapped states, which stabilize PLS protonation state, providing new ideas about the CcO proton pumping mechanism. The distance between the PLS residues Asp287 and His376 correlates with the energy difference between loaded and unloaded states.
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Affiliation(s)
- Xiuhong Cai
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Chang Yun Son
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Chemistry and Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Junjun Mao
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Qiang Cui
- Department of Chemistry & Department of Biomedical Engineering & Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - M R Gunner
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Department of Physics, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA; Department of Chemistry, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
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9
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Wang Y, Wang J, Pang J, Zhang L, Xu W, Shao C. Introduction of protonic potential of Brønsted−Lowry acids and bases to the quantification of the energy of proton translocation and elucidation of oxidative phosphorylation. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.113909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Han Du WG, Götz AW, Noodleman L. A Water Dimer Shift Activates a Proton Pumping Pathway in the P R → F Transition of ba 3 Cytochrome c Oxidase. Inorg Chem 2018; 57:1048-1059. [PMID: 29308889 DOI: 10.1021/acs.inorgchem.7b02461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2-···CuB2+, in which the H2O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+═O2- stretching modes in P (804 cm-1) and F (785 cm-1) identified by resonance Raman experiments. In this F state, the CuB2+···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea33+-OH--CuB2+] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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11
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Carvalheda CA, Pisliakov AV. Insights into proton translocation in cbb 3 oxidase from MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:396-406. [PMID: 28259641 DOI: 10.1016/j.bbabio.2017.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/03/2017] [Accepted: 02/27/2017] [Indexed: 01/18/2023]
Abstract
Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb3) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337.
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Affiliation(s)
- Catarina A Carvalheda
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom; Physics, School of Sciences and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN, United Kingdom.
| | - Andrei V Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom; Physics, School of Sciences and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN, United Kingdom.
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12
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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13
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ns-μs Time-Resolved Step-Scan FTIR of ba₃ Oxidoreductase from Thermus thermophilus: Protonic Connectivity of w941-w946-w927. Int J Mol Sci 2016; 17:ijms17101657. [PMID: 27690021 PMCID: PMC5085690 DOI: 10.3390/ijms17101657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/13/2016] [Accepted: 09/21/2016] [Indexed: 02/07/2023] Open
Abstract
Time-resolved step-scan FTIR spectroscopy has been employed to probe the dynamics of the ba3 oxidoreductase from Thermus thermophilus in the ns-μs time range and in the pH/pD 6–9 range. The data revealed a pH/pD sensitivity of the D372 residue and of the ring-A propionate of heme a3. Based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the D372 and the ring-A propionate of heme a3 is described.
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14
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:1594-1606. [PMID: 27317965 PMCID: PMC4995112 DOI: 10.1016/j.bbabio.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/21/2016] [Accepted: 06/14/2016] [Indexed: 01/22/2023]
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA.
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15
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Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proc Natl Acad Sci U S A 2016; 113:7420-5. [PMID: 27339133 DOI: 10.1073/pnas.1601982113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.
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16
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Nicolaides A, Soulimane T, Varotsis C. Nanosecond ligand migration and functional protein relaxation in ba3 oxidoreductase: Structures of the B0, B1 and B2 intermediate states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1534-1540. [PMID: 27207588 DOI: 10.1016/j.bbabio.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/13/2016] [Accepted: 05/15/2016] [Indexed: 11/28/2022]
Abstract
Nanosecond time-resolved step-scan FTIR spectroscopy (nTRS (2) -FTIR) has been applied to literally probe the active site of the carbon monoxide (CO)-bound thermophilic ba3 heme-copper oxidoreductase as it executes its function. The nTRS (2) - snapshots of the photolysed heme a3 Fe-CO/CuB species captured a "transition state" whose side chains prevent the photolysed CO to enter the docking cavity. There are three sets of ba3 photoproduct bands of docked CO with different orientation exhibiting different kinetics. The trajectories of the "docked" CO at 2122, 2129 and 2137cm(-1) is referred to in the literature as B2, B1 and B0 intermediate states, respectively. The present data provided direct evidence for the role of water in controlling ligand orientation in an intracavity protein environment.
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Affiliation(s)
- Antonis Nicolaides
- Cyprus University of Technology, Department of Environmental Science and Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department, University of Limerick, Limerick, Ireland; Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Constantinos Varotsis
- Cyprus University of Technology, Department of Environmental Science and Technology, P.O. Box 50329, 3603 Lemesos, Cyprus.
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17
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Han Du WG, Götz AW, Yang L, Walker RC, Noodleman L. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus. Phys Chem Chem Phys 2016; 18:21162-71. [PMID: 27094074 DOI: 10.1039/c6cp00349d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans. PLoS One 2016; 11:e0152745. [PMID: 27030968 PMCID: PMC4816578 DOI: 10.1371/journal.pone.0152745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/18/2016] [Indexed: 01/22/2023] Open
Abstract
Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed.
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19
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Han Du WG, Noodleman L. Broken Symmetry DFT Calculations/Analysis for Oxidized and Reduced Dinuclear Center in Cytochrome c Oxidase: Relating Structures, Protonation States, Energies, and Mössbauer Properties in ba3 Thermus thermophilus. Inorg Chem 2015; 54:7272-90. [PMID: 26192749 PMCID: PMC4525772 DOI: 10.1021/acs.inorgchem.5b00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/22/2022]
Abstract
The Fea3(3+)···CuB(2+) dinuclear center (DNC) structure of the as-isolated oxidized ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt) is still not fully understood. When the proteins are initially crystallized in the oxidized state, they typically become radiolyticly reduced through X-ray irradiation. Several X-ray crystal structures of reduced ba3 CcO from Tt are available. However, depending on whether the crystals were prepared in a lipidic cubic phase environment or in detergent micelles, and whether the CcO's were chemically or radiolyticly reduced, the X-ray diffraction analysis of the crystals showed different Fea3(2+)···CuB(+) DNC structures. On the other hand, Mössbauer spectroscopic experiments on reduced and oxidized ba3 CcOs from Tt (Zimmermann et al., Proc. Natl. Acad. Sci. USA 1988, 85, 5779-5783) revealed multiple (57)Fea3(2+) and (57)Fea3(3+) components. Moreover, one of the (57)Fea3(3+) components observed at 4.2 K transformed from a proposed "low-spin" state to a different high-spin species when the temperature was increased above 190 K, whereas the other high-spin (57)Fea3(3+) component remained unchanged. In the current Article, in order to understand the heterogeneities of the DNC in both Mössbauer spectra and X-ray crystal structures, the spin crossover of one of the (57)Fea3(3+) components, and how the coordination and spin states of the Fea3(3+/2+) and Cu(2+/1+) sites relate to the heterogeneity of the DNC structures, we have applied density functional OLYP calculations to the DNC clusters established based on the different X-ray crystal structures of ba3 CcO from Tt. As a result, specific oxidized and reduced DNC structures related to the observed Mössbauer spectra and to spectral changes with temperature have been proposed. Our calculations also show that, in certain intermediate states, the His233 and His283 ligand side chains may dissociate from the CuB(+) site, and they may become potential proton loading sites during the catalytic cycle.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational
Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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20
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Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus. Biophys J 2015; 107:2177-84. [PMID: 25418102 DOI: 10.1016/j.bpj.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/03/2014] [Accepted: 09/11/2014] [Indexed: 01/08/2023] Open
Abstract
A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.
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21
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Mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site. Proc Natl Acad Sci U S A 2015; 112:3397-402. [PMID: 25733886 DOI: 10.1073/pnas.1422434112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ba3-type cytochrome c oxidase from Thermus thermophilus is a membrane-bound protein complex that couples electron transfer to O2 to proton translocation across the membrane. To elucidate the mechanism of the redox-driven proton pumping, we investigated the kinetics of electron and proton transfer in a structural variant of the ba3 oxidase where a putative "pump site" was modified by replacement of Asp372 by Ile. In this structural variant, proton pumping was uncoupled from internal electron transfer and O2 reduction. The results from our studies show that proton uptake to the pump site (time constant ∼65 μs in the wild-type cytochrome c oxidase) was impaired in the Asp372Ile variant. Furthermore, a reaction step that in the wild-type cytochrome c oxidase is linked to simultaneous proton uptake and release with a time constant of ∼1.2 ms was slowed to ∼8.4 ms, and in Asp372Ile was only associated with proton uptake to the catalytic site. These data identify reaction steps that are associated with protonation and deprotonation of the pump site, and point to the area around Asp372 as the location of this site in the ba3 cytochrome c oxidase.
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22
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Nicolaides A, Soulimane T, Varotsis C. Detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba3-oxidoreductase. Phys Chem Chem Phys 2015; 17:8113-9. [DOI: 10.1039/c5cp00043b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we report FTIR data on the detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba3-oxidoreductase.
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Affiliation(s)
- Antonis Nicolaides
- Department of Environmental Science and Technology
- Cyprus University of Technology
- 3603 Lemesos
- Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department and Materials & Surface Science Institute
- University of Limerick
- Limerick
- Ireland
| | - Constantinos Varotsis
- Department of Environmental Science and Technology
- Cyprus University of Technology
- 3603 Lemesos
- Cyprus
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23
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Goyal P, Yang S, Cui Q. Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci 2015; 6:826-841. [PMID: 25678950 PMCID: PMC4321873 DOI: 10.1039/c4sc01674b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps.
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. For the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. Here we carry out extensive QM/MM free energy simulations to probe the kinetics of relevant proton transfer steps and analyze the effects of local structure and hydration level. We show that protonation of the proton loading site (PLS, taken to be a propionate of heme a3) requires a concerted process in which a key glutamic acid (Glu286H) delivers the proton to the PLS while being reprotonated by an excess proton coming from the D-channel. The concerted nature of the mechanism is a crucial feature that enables the loading of the PLS before the cavity containing Glu286 is better hydrated to lower its pKa to experimentally measured range; the charged rather than dipolar nature of the process also ensures a tight coupling with heme a reduction, as emphasized by Siegbahn and Blomberg. In addition, we find that rotational flexibility of the PLS allows its protonation before that of the binuclear center (the site where oxygen gets reduced to water). Together with our recent study (P. Goyal, et al., Proc. Natl. Acad. Sci. U. S. A., 2013, 110, 18886–18891) that focused on the modulation of Glu286 pKa, the current work suggests a mechanism that builds in a natural sequence for the protonation of the PLS prior to that of the binuclear center. This provides microscopic support to the kinetic constraints revealed by kinetic network analysis as essential elements that ensure an efficient vectorial proton transport in cytochrome c oxidase.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Shuo Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
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24
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Noodleman L, Han Du WG, Fee J, Götz AW, Walker RC. Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex. Inorg Chem 2014; 53:6458-72. [PMID: 24960612 PMCID: PMC4095914 DOI: 10.1021/ic500363h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 12/23/2022]
Abstract
After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment.
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Affiliation(s)
- Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - Wen-Ge Han Du
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - James
A. Fee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - Andreas W. Götz
- San Diego Supercomputer
Center and Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, MC0505, La Jolla, California 92093, United States
| | - Ross C. Walker
- San Diego Supercomputer
Center and Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, MC0505, La Jolla, California 92093, United States
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25
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Horton JS, Stokes AJ. The transmembrane channel-like protein family and human papillomaviruses: Insights into epidermodysplasia verruciformis and progression to squamous cell carcinoma. Oncoimmunology 2014; 3:e28288. [PMID: 24800179 PMCID: PMC4006860 DOI: 10.4161/onci.28288] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 12/25/2022] Open
Abstract
Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by increased sensitivity to infection by the β-subtype of human papillomaviruses (β-HPVs), causing persistent, tinea versicolor-like dermal lesions. In a majority of affected individuals, these macular lesions progress to invasive cutaneous squamous cell carcinoma (CSCC) in sun-exposed areas. While mutations in transmembrane channel-like 6 (TMC6 / EVER1) and 8 (TMC8 / EVER2) have been causally linked to EV, their molecular functions are unclear. It is likely that their protective effects involve regulation of the β-HPV life cycle, host keratinocyte apoptosis vs. survival balance and/or T-cell interaction with infected host cells.
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Affiliation(s)
- Jaime S Horton
- Laboratory of Experimental Medicine; John A. Burns School of Medicine; Honolulu, HI USA ; Department of Cell and Molecular Biology; John A. Burns School of Medicine; Honolulu, HI USA
| | - Alexander J Stokes
- Laboratory of Experimental Medicine; John A. Burns School of Medicine; Honolulu, HI USA ; Department of Cell and Molecular Biology; John A. Burns School of Medicine; Honolulu, HI USA ; Chaminade University; Honolulu, HI USA
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Rauhamäki V, Wikström M. The causes of reduced proton-pumping efficiency in type B and C respiratory heme-copper oxidases, and in some mutated variants of type A. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:999-1003. [PMID: 24583065 DOI: 10.1016/j.bbabio.2014.02.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 01/27/2014] [Accepted: 02/17/2014] [Indexed: 12/11/2022]
Abstract
The heme-copper oxidases may be divided into three categories, A, B, and C, which include cytochrome c and quinol-oxidising enzymes. All three types are known to be proton pumps and are found in prokaryotes, whereas eukaryotes only contain A-type cytochrome c oxidase in their inner mitochondrial membrane. However, the bacterial B- and C-type enzymes have often been reported to pump protons with an H(+)/e(-) ratio of only one half of the unit stoichiometry in the A-type enzyme. We will show here that these observations are likely to be the result of difficulties with the measuring technique together with a higher sensitivity of the B- and C-type enzymes to the protonmotive force that opposes pumping. We find that under optimal conditions the H(+)/e(-) ratio is close to unity in all the three heme-copper oxidase subfamilies. A higher tendency for proton leak in the B- and C-type enzymes may result from less efficient gating of a proton pump mechanism that we suggest evolved before the so-called D-channel of proton transfer. There is also a discrepancy between results using whole bacterial cells vs. phospholipid vesicles inlaid with oxidase with respect to the observed proton pumping after modification of the D-channel residue asparagine-139 (Rhodobacter sphaeroides numbering) to aspartate in A-type cytochrome c oxidase. This discrepancy might also be explained by a higher sensitivity of proton pumping to protonmotive force in the mutated variant. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Virve Rauhamäki
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, 00014 Helsinki, Finland
| | - Mårten Wikström
- Institute of Biotechnology, University of Helsinki, Viikinkaari 1, 00014 Helsinki, Finland.
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The K(C) channel in the cbb3-type respiratory oxygen reductase from Rhodobacter capsulatus is required for both chemical and pumped protons. J Bacteriol 2014; 196:1825-32. [PMID: 24563037 DOI: 10.1128/jb.00005-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The heme-copper superfamily of proton-pumping respiratory oxygen reductases are classified into three families (A, B, and C families) based on structural and phylogenetic analyses. Most studies have focused on the A family, which includes the eukaryotic mitochondrial cytochrome c oxidase as well as many bacterial homologues. Members of the C family, also called the cbb3-type oxygen reductases, are found only in prokaryotes and are of particular interest because of their presence in a number of human pathogens. All of the heme-copper oxygen reductases require proton-conducting channels to convey chemical protons to the active site for water formation and to convey pumped protons across the membrane. Previous work indicated that there is only one proton-conducting input channel (the K(C) channel) present in the cbb3-type oxygen reductases, which, if correct, must be utilized by both chemical protons and pumped protons. In this work, the effects of mutations in the K(C) channel of the cbb3-type oxygen reductase from Rhodobacter capsulatus were investigated by expressing the mutants in a strain lacking other respiratory oxygen reductases. Proton pumping was evaluated by using intact cells, and catalytic oxygen reductase activity was measured in isolated membranes. Two mutations, N346M and Y374F, severely reduced catalytic activity, presumably by blocking the chemical protons required at the active site. One mutation, T272A, resulted in a substantially lower proton-pumping stoichiometry but did not inhibit oxygen reductase activity. These are the first experimental data in support of the postulate that pumped protons are taken up from the bacterial cytoplasm through the K(C) channel.
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Cerda JF, Malloy MC, Werkheiser BO, Stockhausen AT, Gallagher MF, Lawler AC. Evaluation of Heme Peripheral Group Interactions in Extremely Low-Dielectric Constant Media and Their Contributions to the Heme Reduction Potential. Inorg Chem 2013; 53:182-8. [DOI: 10.1021/ic401986n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jose F. Cerda
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
| | - Mary C. Malloy
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
| | - Brady O. Werkheiser
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
| | - Alaina T. Stockhausen
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
| | - Michael F. Gallagher
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
| | - Andrew C. Lawler
- Department of Chemistry, Saint Joseph’s University, Philadelphia, Pennsylvania 19131, United States
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Du WGH, Noodleman L. Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus. Inorg Chem 2013; 52:14072-88. [PMID: 24262070 DOI: 10.1021/ic401858s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, TPC15, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Smirnova I, Chang HY, von Ballmoos C, Ädelroth P, Gennis RB, Brzezinski P. Single mutations that redirect internal proton transfer in the ba3 oxidase from Thermus thermophilus. Biochemistry 2013; 52:7022-30. [PMID: 24004023 DOI: 10.1021/bi4008726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ba3-type cytochrome c oxidase from Thermus thermophilus is a membrane-bound proton pump. Results from earlier studies have shown that with the aa3-type oxidases proton uptake to the catalytic site and "pump site" occurs simultaneously. However, with ba3 oxidase the pump site is loaded before proton transfer to the catalytic site because the proton transfer to the latter is slower than that with the aa3 oxidases. In addition, the timing of formation and decay of catalytic intermediates is different in the two types of oxidases. In the present study, we have investigated two mutant ba3 CytcOs in which residues of the proton pathway leading to the catalytic site as well as the pump site were exchanged, Thr312Val and Tyr244Phe. Even though ba3 CytcO uses only a single proton pathway for transfer of the substrate and "pumped" protons, the amino-acid residue substitutions had distinctly different effects on the kinetics of proton transfer to the catalytic site and the pump site. The results indicate that the rates of these reactions can be modified independently by replacement of single residues within the proton pathway. Furthermore, the data suggest that the Thr312Val and Tyr244Phe mutations interfere with a structural rearrangement in the proton pathway that is rate limiting for proton transfer to the catalytic site.
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Affiliation(s)
- Irina Smirnova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University , SE-106 91 Stockholm, Sweden
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Ter Beek J, Krause N, Reimann J, Lachmann P, Ädelroth P. The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway. J Biol Chem 2013; 288:30626-30635. [PMID: 24014024 DOI: 10.1074/jbc.m113.497347] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.
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Affiliation(s)
- Josy Ter Beek
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nils Krause
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Joachim Reimann
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Lachmann
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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32
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Current advances in research of cytochrome c oxidase. Amino Acids 2013; 45:1073-87. [PMID: 23999646 DOI: 10.1007/s00726-013-1585-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/21/2013] [Indexed: 12/13/2022]
Abstract
The function of cytochrome c oxidase as a biomolecular nanomachine that transforms energy of redox reaction into protonmotive force across a biological membrane has been subject of intense research, debate, and controversy. The structure of the enzyme has been solved for several organisms; however details of its molecular mechanism of proton pumping still remain elusive. Particularly, the identity of the proton pumping site, the key element of the mechanism, is still open to dispute. The pumping mechanism has been for a long time one of the key unsolved issues of bioenergetics and biochemistry, but with the accelerating progress in this field many important details and principles have emerged. Current advances in cytochrome oxidase research are reviewed here, along with a brief discussion of the most complete proton pumping mechanism proposed to date, and a molecular basis for control of its efficiency.
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