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Shimada A, Baba J, Nagao S, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J Biol Chem 2023; 299:105277. [PMID: 37742916 PMCID: PMC10598403 DOI: 10.1016/j.jbc.2023.105277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
Cytochrome c oxidase (CcO) reduces O2 in the O2-reduction site by sequential four-electron donations through the low-potential metal sites (CuA and Fea). Redox-coupled X-ray crystal structural changes have been identified at five distinct sites including Asp51, Arg438, Glu198, the hydroxyfarnesyl ethyl group of heme a, and Ser382, respectively. These sites interact with the putative proton-pumping H-pathway. However, the metal sites responsible for each structural change have not been identified, since these changes were detected as structural differences between the fully reduced and fully oxidized CcOs. Thus, the roles of these structural changes in the CcO function are yet to be revealed. X-ray crystal structures of cyanide-bound CcOs under various oxidation states showed that the O2-reduction site controlled only the Ser382-including site, while the low-potential metal sites induced the other changes. This finding indicates that these low-potential site-inducible structural changes are triggered by sequential electron-extraction from the low-potential sites by the O2-reduction site and that each structural change is insensitive to the oxidation and ligand-binding states of the O2-reduction site. Because the proton/electron coupling efficiency is constant (1:1), regardless of the reaction progress in the O2-reduction site, the structural changes induced by the low-potential sites are assignable to those critically involved in the proton pumping, suggesting that the H-pathway, facilitating these low-potential site-inducible structural changes, pumps protons. Furthermore, a cyanide-bound CcO structure suggests that a hypoxia-inducible activator, Higd1a, activates the O2-reduction site without influencing the electron transfer mechanism through the low-potential sites, kinetically confirming that the low-potential sites facilitate proton pump.
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Affiliation(s)
- Atsuhiro Shimada
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Jumpei Baba
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Shuhei Nagao
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kazumasa Muramoto
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
| | - Tomitake Tsukihara
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| | - Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Akoh, Hyogo, Japan.
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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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3
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Palese LL. Explaining leak states in the proton pump of heme-copper oxidases observed in single-molecule experiments. Biophys Chem 2019; 256:106276. [PMID: 31731070 DOI: 10.1016/j.bpc.2019.106276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 11/28/2022]
Abstract
Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Generally, these models associate, more or less directly, all translocation events with redox transitions. Although they can account for many phenomenological aspects of the pump, evidences from single-molecules experiments about leak states of the pump represent a formidable challenge. Disconnecting the redox-linked pKa shifts of the proton loading site from the external barriers, we obtain a simple stochastic mechanism which behaves similarly to the real enzyme, able to reverse the flow of the proton transfer.
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4
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Capitanio G, Palese LL, Papa F, Papa S. Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase. J Mol Biol 2019; 432:534-551. [PMID: 31626808 DOI: 10.1016/j.jmb.2019.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/06/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome c oxidase (CcO), the CuA, heme a, heme a3, CuB enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH+). ΔμH+ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH+.
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Affiliation(s)
- Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", 70124 Bari, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.
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5
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Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase. Proc Natl Acad Sci U S A 2019; 116:3572-3577. [PMID: 30808749 DOI: 10.1073/pnas.1814526116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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 dioxygen to water and harnesses the chemical energy to drive proton translocation across the inner mitochondrial membrane by an unresolved mechanism. By using time-resolved serial femtosecond crystallography, we identified a key oxygen intermediate of bovine CcO. It is assigned to the PR-intermediate, which is characterized by specific redox states of the metal centers and a distinct protein conformation. The heme a 3 iron atom is in a ferryl (Fe4+ = O2-) configuration, and heme a and CuB are oxidized while CuA is reduced. A Helix-X segment is poised in an open conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a distinct structure. These data offer insights into the mechanism by which the oxygen chemistry is coupled to unidirectional proton translocation.
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6
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Palese LL. Cytochrome c oxidase structures suggest a four-state stochastic pump mechanism. Phys Chem Chem Phys 2019; 21:4822-4830. [DOI: 10.1039/c8cp07365a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A simple stochastic model for a cytochrome c oxidase proton pump.
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Affiliation(s)
- Luigi Leonardo Palese
- University of Bari “Aldo Moro”
- Department of Basic Medical Sciences
- Neurosciences and Sense Organs (SMBNOS)
- Bari
- Italy
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7
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Vygodina TV, Kaminskaya OP, Konstantinov AA, Ptushenko VV. Effect of Ca 2+ on the redox potential of heme a in cytochrome c oxidase. Biochimie 2018; 149:71-78. [PMID: 29635042 DOI: 10.1016/j.biochi.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 04/04/2018] [Indexed: 11/19/2022]
Abstract
Subunit I of cytochrome c oxidase (CcO) from mitochondria and many bacteria contains a cation binding site (CBS) located at the outer positively charged aqueous phase not far from heme a. Binding of Ca2+ with the CBS in bovine CcO inhibits activity of the enzyme 2-3 -fold [Vygodina, T., Kirichenko, A. & Konstantinov A.A. (2013) Direct Regulation of Cytochrome c Oxidase by Calcium Ions, PLoS One.8 e74436]. Here we show that binding of Ca2+ at CBS of bovine CcO shifts Em of heme a to the positive by 15-20 mV. Na+ ions that bind to the same site and compete with Ca2+ do not affect Em of heme a and also prevent and reverse the effect of Ca2+. No effect of Ca2+ or EGTA is observed on Em of heme a with the wild type bacterial oxidases from R.sphaeroides or P.denitrificans that contain tightly-bound calcium at the site. In the D477A mutant CcO from P. denitrificans that binds Ca2+ reversibly like the mitochondrial CcO, calcium shifts redox titration curve of heme a to the positive by ∼35-50 mV that is in good agreement with the results of electrostatic calculations; however, as shown earlier, it does not inhibit CcO activity of the mutant enzyme. Therefore the data do not support the proposal that the inhibitory effect of Ca2+ on CcO activity may be explained by the Ca2+-induced shift of Em of heme a. Rather, Ca2+ retards electron transfer by inhibition of charge dislocation in the exit part of the proton channel H in mammalian CcO, that is absent in the bacterial oxidases.
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Affiliation(s)
- Tatiana V Vygodina
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Olga P Kaminskaya
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | | | - Vasily V Ptushenko
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia; N.M.Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.
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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: 233] [Impact Index Per Article: 38.8] [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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Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Proc Natl Acad Sci U S A 2017; 114:8011-8016. [PMID: 28698372 DOI: 10.1073/pnas.1705628114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.
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10
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Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:103-108. [PMID: 27810193 DOI: 10.1016/j.bbabio.2016.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/18/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a3 have been proposed to act as a proton loading site (PLS) in the proton pumping pathway, yet this proposal could not be verified by experimental data so far. We have set up an experiment where the redox states of the two hemes in CcO can be controlled via external electrical potential. Surface enhanced resonance Raman (SERR) spectroscopy was applied to simultaneously monitor the redox state of the hemes and the protonation state of the heme propionates. Simulated spectra based on QM/MM calculations were used to assign the resonant enhanced CH2 twisting modes of the propionates to the protonation state of the individual heme a and heme a3 propionates respectively. The comparison between calculated and measured H2OD2O difference spectra allowed a sound band assignment. In the fully reduced enzyme at least three of the four heme propionates were found to be protonated whereas in the presence of a reduced heme a and an oxidized heme a3 only protonation of one heme a3 propionates was observed. Our data supports the postulated scenario where the heme a3 propionates are involved in the proton pathway.
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11
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Yano N, Muramoto K, Shimada A, Takemura S, Baba J, Fujisawa H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Tsukihara T, Yoshikawa S. The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. J Biol Chem 2016; 291:23882-23894. [PMID: 27605664 DOI: 10.1074/jbc.m115.711770] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 08/26/2016] [Indexed: 11/06/2022] Open
Abstract
Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H3O+ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O2 bound to heme a3 To block backward proton movement, the water channel remains closed after O2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu198, which bridges the Mg2+ and CuA (the initial electron acceptor from cytochrome c) sites, suggest that the CuA-Glu198-Mg2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg2+-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.
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Affiliation(s)
| | - Kazumasa Muramoto
- the Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297
| | | | | | | | | | | | | | - Eiki Yamashita
- the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, and
| | - Tomitake Tsukihara
- From the Picobiology Institute and.,the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, and.,JSJT, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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12
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Calcium ions inhibit reduction of heme a in bovine cytochrome c oxidase. FEBS Lett 2015; 589:3853-8. [PMID: 26611345 DOI: 10.1016/j.febslet.2015.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/15/2015] [Accepted: 11/16/2015] [Indexed: 01/14/2023]
Abstract
The effect of Ca(2+) on the rate of heme a reduction by dithionite and hexaammineruthenium (RuAm) was studied in the cyanide-complexed bovine cytochrome oxidase (CcO). The rate of heme a reduction is proportional to RuAm concentration below 300 μM with kv of 0.53×10(6) M(-1) s(-1). Ca(2+) inhibits the rate of heme a reduction by dithionite by ∼25%. As the reaction speeds up with increased concentrations of RuAm, the inhibition by Ca(2+) disappears. The inhibition of heme a reduction may contribute to recently described partial inhibition of CcO by Ca(2+) in the enzymatic assays. The inhibitory effect of Ca(2+) on heme a reduction indicates that ET through heme a may be coupled to proton movement in the exit part of the proton channel H.
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Yoshikawa S, Shimada A, Shinzawa-Itoh K. Respiratory conservation of energy with dioxygen: cytochrome C oxidase. Met Ions Life Sci 2015; 15:89-130. [PMID: 25707467 DOI: 10.1007/978-3-319-12415-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cytochrome c oxidase (CcO) is the terminal oxidase of cell respiration which reduces molecular oxygen (O₂) to H2O coupled with the proton pump. For elucidation of the mechanism of CcO, the three-dimensional location and chemical reactivity of each atom composing the functional sites have been extensively studied by various techniques, such as crystallography, vibrational and time-resolved electronic spectroscopy, since the X-ray structures (2.8 Å resolution) of bovine and bacterial CcO have been published in 1995.X-ray structures of bovine CcO in different oxidation and ligand binding states showed that the O₂reduction site, which is composed of Fe (heme a 3) and Cu (CuB), drives a non-sequential four-electron transfer for reduction of O₂to water without releasing any reactive oxygen species. These data provide the crucial structural basis to solve a long-standing problem, the mechanism of the O₂reduction.Time-resolved resonance Raman and charge translocation analyses revealed the mechanism for coupling between O₂reduction and the proton pump: O₂is received by the O₂reduction site where both metals are in the reduced state (R-intermediate), giving the O₂-bound form (A-intermediate). This is spontaneously converted to the P-intermediate, with the bound O₂fully reduced to 2 O²⁻. Hereafter the P-intermediate receives four electron equivalents from the second Fe site (heme a), one at a time, to form the three intermediates, F, O, and E to regenerate the R-intermediate. Each electron transfer step from heme a to the O₂reduction site is coupled with the proton pump.X-ray structural and mutational analyses of bovine CcO show three possible proton transfer pathways which can transfer pump protons (H) and chemical (water-forming) protons (K and D). The structure of the H-pathway of bovine CcO indicates that the driving force of the proton pump is the electrostatic repulsion between the protons on the H-pathway and positive charges of heme a, created upon oxidation to donate electrons to the O₂reduction site. On the other hand, mutational and time-resolved electrometric findings for the bacterial CcO strongly suggest that the D-pathway transfers both pump and chemical protons. However, the structure for the proton-gating system in the D-pathway has not been experimentally identified. The structural and functional diversities in CcO from various species suggest a basic proton pumping mechanism in which heme a pumps protons while heme a 3 reduces O₂as proposed in 1978.
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan,
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14
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Affiliation(s)
- Shinya Yoshikawa
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
| | - Atsuhiro Shimada
- Picobiology Institute, Graduate
School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan
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15
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Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:98-108. [PMID: 25268561 DOI: 10.1016/j.bbabio.2014.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/11/2014] [Accepted: 09/20/2014] [Indexed: 11/19/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Izumi Ishigami
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Masahide Hikita
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Denis L Rousseau
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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16
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Weidinger IM. Analysis of structure-function relationships in cytochrome c oxidase and its biomimetic analogs via resonance Raman and surface enhanced resonance Raman spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:119-25. [PMID: 25223590 DOI: 10.1016/j.bbabio.2014.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023]
Abstract
Cytochrome c oxidase (CcO) catalyzes the four electron reduction of molecular oxygen to water while avoiding the formation of toxic peroxide; a quality that is of high relevance for the development of oxygen-reducing catalysts. Resonance Raman spectroscopy has been used since many years as a technique to identify electron transfer pathways in cytochrome c oxidase and to identify the key intermediates in the catalytic cycle. This information can be compared to artificial systems such as modified heme-copper enzymes, molecular heme-copper catalysts or CcO/electrode complexes in order to shed light into the reaction mechanism of these non-natural systems. Understanding the structural commonalities and differences of CcO with its non-natural analogs is of great value for designing efficient oxygen-reducing catalysts. In this review therefore Raman spectroscopic measurements on artificial heme-copper enzymes and model complexes are summarized and compared to the natural enzyme cytochrome c oxidase. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Inez M Weidinger
- Department of Chemistry PC 14, Technische Universitaet Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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17
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Bhagi-Damodaran A, Petrik ID, Marshall NM, Robinson H, Lu Y. Systematic tuning of heme redox potentials and its effects on O2 reduction rates in a designed oxidase in myoglobin. J Am Chem Soc 2014; 136:11882-5. [PMID: 25076049 PMCID: PMC4151708 DOI: 10.1021/ja5054863] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 11/28/2022]
Abstract
Cytochrome c Oxidase (CcO) is known to catalyze the reduction of O2 to H2O efficiently with a much lower overpotential than most other O2 reduction catalysts. However, methods by which the enzyme fine-tunes the reduction potential (E°) of its active site and the corresponding influence on the O2 reduction activity are not well understood. In this work, we report systematic tuning of the heme E° in a functional model of CcO in myoglobin containing three histidines and one tyrosine in the distal pocket of heme. By removing hydrogen-bonding interactions between Ser92 and the proximal His ligand and a heme propionate, and increasing hydrophobicity of the heme pocket through Ser92Ala mutation, we have increased the heme E° from 95 ± 2 to 123 ± 3 mV. Additionally, replacing the native heme b in the CcO mimic with heme a analogs, diacetyl, monoformyl, and diformyl hemes, that posses electron-withdrawing groups, resulted in higher E° values of 175 ± 5, 210 ± 6, and 320 ± 10 mV, respectively. Furthermore, O2 consumption studies on these CcO mimics revealed a strong enhancement in O2 reduction rates with increasing heme E°. Such methods of tuning the heme E° through a combination of secondary sphere mutations and heme substitutions can be applied to tune E° of other heme proteins, allowing for comprehensive investigations of the relationship between E° and enzymatic activity.
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Affiliation(s)
- Ambika Bhagi-Damodaran
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Igor D. Petrik
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Nicholas M. Marshall
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Howard Robinson
- Department
of Biology, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yi Lu
- Department
of Chemistry, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
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18
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Nakashima S, Ogura T, Kitagawa T. Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:86-97. [PMID: 25135480 DOI: 10.1016/j.bbabio.2014.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Satoru Nakashima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Department of Life Science, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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19
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Morrill GA, Kostellow AB, Gupta RK. The pore-lining regions in cytochrome c oxidases: A computational analysis of caveolin, cholesterol and transmembrane helix contributions to proton movement. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2838-51. [PMID: 25037006 DOI: 10.1016/j.bbamem.2014.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/19/2014] [Accepted: 07/08/2014] [Indexed: 11/30/2022]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain. CcO catalyzes a four electron reduction of O2 to water at a catalytic site formed by high-spin heme (a3) and copper atoms (CuB). While it is recognized that proton movement is coupled to oxygen reduction, the proton channel(s) have not been well defined. Using computational methods developed to study protein topology, membrane channels and 3D packing arrangements within transmembrane (TM) helix arrays, we find that subunit-1 (COX-1), subunit-2 (COX-2) and subunit-3 (COX-3) contribute 139, 46 and 25 residues, respectively, to channel formation between the mitochondrial matrix and intermembrane space. Nine of 12 TM helices in COX-1, both helices in COX-2 and 5 of the 6 TM helices in COX-3 are pore-lining regions (possible channel formers). Heme a3 and the CuB sites (as well as the CuA center of COX-2) are located within the channel that includes TM-6, TM-7, TM-10 and TM-11 of COX-1 and are associated with multiple cholesterol and caveolin-binding (CB) motifs. Sequence analysis identifies five CB motifs within COX-1, two within COX-2 and four within COX-3; each caveolin containing a pore-lining helix C-terminal to a TM helix-turn-helix. Channel formation involves interaction between multiple pore-lining regions within protein subunits and/or dimers. PoreWalker analysis lends support to the D-channel model of proton translocation. Under physiological conditions, caveolins may introduce channel formers juxtaposed to those in COX-1, COX-2 and COX-3, which together with cholesterol may form channel(s) essential for proton translocation through the inner mitochondrial membrane.
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Affiliation(s)
- Gene A Morrill
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA.
| | - Adele B Kostellow
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Raj K Gupta
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
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20
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Bagkos G, Koufopoulos K, Piperi C. A new model for mitochondrial membrane potential production and storage. Med Hypotheses 2014; 83:175-81. [PMID: 24907229 DOI: 10.1016/j.mehy.2014.05.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/10/2014] [Indexed: 02/05/2023]
Abstract
Mitochondrial membrane potential (MMP) is the most reliable indicator of mitochondrial function. The MMP value range of -136 to -140mV has been considered optimal for maximum ATP production for all living organisms. Even small changes from the above range result in a large fall in ATP production and a large increase in ROS production. The resulting bioenergetic deregulation is considered as the causative agent for numerous major human diseases. Normalization of MMP value improves mitochondrial function and gives excellent therapeutic results. In order for a systematic effective treatment of these diseases to be developed, a detailed knowledge of the mechanism of MMP production is absolutely necessary. However, despite the long-standing research efforts, a concrete mechanism for MMP production has not been found yet. The present paper proposes a novel mechanism of MMP production based on new considerations underlying the function of the two basic players of MMP production, the electron transport chain (ETC) and the F1F0 ATP synthase. Under normal conditions, MMP is almost exclusively produced by the electron flow through ETC complexes I-IV, creating a direct electric current that stops in subunit II of complex IV and gradually charges MMP. However, upon ETC dysfunction F1F0 ATP synthase reverses its action and starts to hydrolyze ATP. ATP hydrolysis further produces electric energy which is transferred, in the form of a direct electric current, from F1 to F0 where is used to charge MMP. This new model is expected to redirect current experimental research on mitochondrial bioenergetics and indicate new therapeutic schemes for mitochondrial disorders.
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Affiliation(s)
- Georgios Bagkos
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece
| | - Kostas Koufopoulos
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, University of Athens Medical School, Athens, Greece.
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21
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Rottenberg H. Exceptional longevity and exceptionally high metabolic rates in anthropoid primates are linked to a major modification of the ubiquinone reduction site of cytochrome b. J Bioenerg Biomembr 2014; 46:435-45. [PMID: 24827527 DOI: 10.1007/s10863-014-9552-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/07/2014] [Indexed: 11/26/2022]
Abstract
The maximal lifespan of Anthropoid primates (monkeys, apes and humans) exceed the lifespan of most other mammals of equal body mass. Unexpectedly, their exceptional longevity is associated with exceptionally high metabolic rates, in apparent contradiction to the Free Radical Theory of Aging. It was therefore suggested that in anthropoid primates (and several other taxa of mammals and birds) the mitochondrial electron transport complexes evolved to modify the relationship between basal electron transport and superoxide generation to allow for the evolution of exceptional longevity. Cytochrome b, the core protein of the bc1 complex is a major source of superoxide. The amino-acid sequence of cytochrome b evolved much faster in anthropoid than in prosimian primates, and most other mammals, resulting in a large change in the amino-acids composition of the protein. As a result of these changes cytochrome b in anthropoid primates is significantly less hydrophobic and contains more polar residues than other primates and most other mammals. Most of these changes are clustered around the reduction site of uboiquinone. In particular a key positively charged residue, arginine 313, that interacts with propionate D of heme bH, and thus raises its redox potential, is substituted in anthropoid primates with the neutral residue glutamine, most likely resulting in a lower redox potential of heme bH and faster reduction of ubiquinone at high proton motive force. It is suggested that these changes contribute to the observed increased rates of basal metabolism and reduce the rates of superoxide production, thus allowing for increased lifespan.
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Affiliation(s)
- Hagai Rottenberg
- New Hope Biomedical R&D, 23 W. Bridge Street, New Hope, PA, 18938, USA,
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22
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1129] [Impact Index Per Article: 112.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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23
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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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24
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Vygodina T, Kirichenko A, Konstantinov AA. Direct regulation of cytochrome c oxidase by calcium ions. PLoS One 2013; 8:e74436. [PMID: 24058566 PMCID: PMC3769247 DOI: 10.1371/journal.pone.0074436] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/01/2013] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c oxidase from bovine heart binds Ca2+ reversibly at a specific Cation Binding Site located near the outer face of the mitochondrial membrane. Ca2+ shifts the absorption spectrum of heme a, which allowed previously to determine the kinetics and equilibrium characteristics of the binding. However, no effect of Ca2+ on the functional characteristics of cytochrome oxidase was revealed earlier. Here we report that Ca2+ inhibits cytochrome oxidase activity of isolated bovine heart enzyme by 50–60% with Ki of ∼1 µM, close to Kd of calcium binding with the oxidase determined spectrophotometrically. The inhibition is observed only at low, but physiologically relevant, turnover rates of the enzyme (∼10 s−1 or less). No inhibitory effect of Ca2+ is observed under conventional conditions of cytochrome c oxidase activity assays (turnover number >100 s−1 at pH 8), which may explain why the effect was not noticed earlier. The inhibition is specific for Ca2+ and is reversed by EGTA. Na+ ions that compete with Ca2+ for binding with the Cation Binding Site, do not affect significantly activity of the enzyme but counteract the inhibitory effect of Ca2+. The Ca2+-induced inhibition of cytochrome c oxidase is observed also with the uncoupled mitochondria from several rat tissues. At the same time, calcium ions do not inhibit activity of the homologous bacterial cytochrome oxidases. Possible mechanisms of the inhibition are discussed as well as potential physiological role of Ca2+ binding with cytochrome oxidase. Ca2+- binding at the Cation Binding Site is proposed to inhibit proton-transfer through the exit part of the proton conducting pathway H in the mammalian oxidases.
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Affiliation(s)
- Tatiana Vygodina
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna Kirichenko
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A. Konstantinov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail:
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25
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Sun F, Zhou Q, Pang X, Xu Y, Rao Z. Revealing various coupling of electron transfer and proton pumping in mitochondrial respiratory chain. Curr Opin Struct Biol 2013; 23:526-38. [DOI: 10.1016/j.sbi.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 01/23/2023]
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