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Koutsoupakis C, Soulimane T, Varotsis C. Discrete Ligand Binding and Electron Transfer Properties of ba 3-Cytochrome c Oxidase from Thermus thermophilus: Evolutionary Adaption to Low Oxygen and High Temperature Environments. Acc Chem Res 2019; 52:1380-1390. [PMID: 31021078 DOI: 10.1021/acs.accounts.9b00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (C cO) couples the oxidation of cytochrome c to the reduction of molecular oxygen to water and links these electron transfers to proton translocation. The redox-driven C cO conserves part of the released free energy generating a proton motive force that leads to the synthesis of the main biological energy source ATP. Cytochrome ba3 oxidase is a B-type oxidase from the extremely thermophilic eubacterium Thermus thermophilus with high O2 affinity, expressed under elevated temperatures and limited oxygen supply and possessing discrete structural, ligand binding, and electron transfer properties. The origin and the cause of the peculiar, as compared to other C cOs, thermodynamic and kinetic properties remain unknown. Fourier transform infrared (FTIR) and time-resolved step-scan FTIR (TRS2-FTIR) spectroscopies have been employed to investigate the origin of the binding and electron transfer properties of cytochrome ba3 oxidase in both the fully reduced (FR) and mixed valence (MV) forms. Several independent and not easily separated factors leading to increased thermostability and high O2 affinity have been determined. These include (i) the increased hydrophobicity of the active center, (ii) the existence of a ligand input channel, (iii) the high affinity of CuB for exogenous ligands, (iv) the optimized electron transfer (ET) pathways, (v) the effective proton-input channel and water-exit pathway as well the proton-loading/exit sites, (vi) the specifically engineered protein structure, and (vii) the subtle thermodynamic and kinetic regulation. We correlate the unique ligand binding and electron transfer properties of cytochrome ba3 oxidase with the existence of an adaption mechanism which is necessary for efficient function. These results suggest that a cascade of structural factors have been optimized by evolution, through protein architecture, to ensure the conversion of cytochrome ba3 oxidase into a high O2-affinity enzyme that functions effectively in its extreme native environment. The present results show that ba3-cytochrome c oxidase uses a unique structural pattern of energy conversion that has taken into account all the extreme environmental factors that affect the function of the enzyme and is assembled in such a way that its exclusive functions are secured. Based on the available data of CcOs, we propose possible factors including the rigidity and nonpolar hydrophobic interactions that contribute to the behavior observed in cytochrome ba3 oxidase.
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Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department and Materials & Surface Science Institute (MSSI), University of Limerick, Limerick, Ireland
| | - Constantinos Varotsis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
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Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:79-85. [PMID: 25117435 DOI: 10.1016/j.bbabio.2014.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
The catalytic site of heme-copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Liu B, Zhang Y, Sage JT, Soltis SM, Doukov T, Chen Y, Stout CD, Fee JA. Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: a combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1817:658-65. [PMID: 22226917 PMCID: PMC3294259 DOI: 10.1016/j.bbabio.2011.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/09/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022]
Abstract
The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a(3) moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba(3)-oxidase from Thermus thermophilus, determined at ~2.8-3.2Å resolution, reveal a Fe-C distance of ~2.0Å, a Cu-O distance of 2.4Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100K, X-ray structures indicate loss of Fe(a3)-CO and appearance of Cu(B)-CO having a Cu-C distance of ~1.9Å and an O-Fe distance of ~2.3Å. Absolute FTIR spectra recorded from single crystals of reduced ba(3)-CO that had not been exposed to X-ray radiation, showed several peaks around 1975cm(-1); after photolysis at 100K, the absolute FTIR spectra also showed a significant peak at 2050cm(-1). Analysis of the 'light' minus 'dark' difference spectra showed four very sharp CO stretching bands at 1970cm(-1), 1977cm(-1), 1981cm(-1), and 1985cm(-1), previously assigned to the Fe(a3)-CO complex, and a significantly broader CO stretching band centered at ~2050cm(-1), previously assigned to the CO stretching frequency of Cu(B) bound CO. As expected for light propagating along the tetragonal axis of the P4(3)2(1)2 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba(3) crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO(2) at 2337cm(-1) and one from traces of CO at 2133cm(-1); while bands associated with CO bound to either Fe(a3) or to Cu(B) in "light" minus "dark" FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2Å and FTIR spectra support the long-held position that photolysis of Fe(a3)-CO in cytochrome c oxidases leads to significant trapping of the CO on the Cu(B) atom; Fe(a3) and Cu(B) ligation, at the resolutions reported here, are otherwise unaltered.
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Affiliation(s)
- Bin Liu
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Yang Zhang
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 110 Forsyth St., Boston MA 02115
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 110 Forsyth St., Boston MA 02115
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park CA 94025
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park CA 94025
| | - Ying Chen
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - C. David Stout
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - James A. Fee
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
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Pavlou A, Soulimane T, Pinakoulaki E. Evidence for the Presence of Two Conformations of the Heme a3-CuB Pocket of Cytochrome caa3 from Thermus thermophilus. J Phys Chem B 2011; 115:11455-61. [DOI: 10.1021/jp2033356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Pavlou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Sciences Department and Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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Koutsoupakis C, Kolaj-Robin O, Soulimane T, Varotsis C. Probing protonation/deprotonation of tyrosine residues in cytochrome ba3 oxidase from Thermus thermophilus by time-resolved step-scan Fourier transform infrared spectroscopy. J Biol Chem 2011; 286:30600-30605. [PMID: 21757723 DOI: 10.1074/jbc.m111.252213] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elucidating the properties of the heme Fe-Cu(B) binuclear center and the dynamics of the protein response in cytochrome c oxidase is crucial to understanding not only the dioxygen activation and bond cleavage by the enzyme but also the events related to the release of the produced water molecules. The time-resolved step-scan FTIR difference spectra show the ν(7a)(CO) of the protonated form of Tyr residues at 1247 cm(-1) and that of the deprotonated form at 1301 cm(-1). By monitoring the intensity changes of the 1247 and 1301 cm(-1) modes as a function of pH, we measured a pK(a) of 7.8 for the observed tyrosine. The FTIR spectral changes associated with the tyrosine do not belong to Tyr-237 but are attributed to the highly conserved in heme-copper oxidases Tyr-136 and/or Tyr-133 residue (Koutsoupakis, K., Stavrakis, S., Pinakoulaki, E., Soulimane, T., and Varotsis, C. (2002) J. Biol. Chem. 277, 32860-32866). The oxygenation of CO by the mixed-valence form of the enzyme revealed the formation of the ∼607 nm P (Fe(IV)=O) species in the pH 6-9 range and the return to the oxidized form without the formation of the 580 nm F form. The data indicate that Tyr-237 is not involved in the proton transfer pathway in the oxygenation of CO by the mixed-valence form of the enzyme. The implication of these results with respect to the role of Tyr-136 and Tyr-133 in proton transfer/gating along with heme a(3) ring D propionate-H(2)O-ring A propionate-Asp-372 site to the exit/output proton channel (H(2)O pool) is discussed.
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Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, 3603 Lemesos, Cyprus
| | - Olga Kolaj-Robin
- Chemical and Environmental Science Department and Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - 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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Siegbahn PEM, Blomberg MRA. Quantum Chemical Studies of Proton-Coupled Electron Transfer in Metalloenzymes. Chem Rev 2010; 110:7040-61. [DOI: 10.1021/cr100070p] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Per E. M. Siegbahn
- Department of Physics, AlbaNova University Center and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Margareta R. A. Blomberg
- Department of Physics, AlbaNova University Center and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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Blomberg MR, Siegbahn PE. Quantum chemistry as a tool in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:129-42. [DOI: 10.1016/j.bbabio.2009.10.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 11/16/2022]
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Daskalakis V, Varotsis C. Binding and docking interactions of NO, CO and O₂in heme proteins as probed by density functional theory. Int J Mol Sci 2009; 10:4137-4156. [PMID: 19865536 PMCID: PMC2769150 DOI: 10.3390/ijms10094137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 08/30/2009] [Accepted: 09/15/2009] [Indexed: 11/28/2022] Open
Abstract
Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O(2) with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O(2) molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O(2) molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm(-1), respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed.
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Affiliation(s)
- Vangelis Daskalakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, P.O. Box 1527,GR-711 10 Heraklion, Greece; E-Mail: (V.D.)
| | - Constantinos Varotsis
- Department of Chemistry, University of Crete, P.O. Box 2208, 71003, Voutes – Heraklion, Greece
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Porrini M, Daskalakis V, Farantos SC, Varotsis C. Heme Cavity Dynamics of Photodissociated CO from ba3-Cytochrome c Oxidase: The Role of Ring-D Propionate. J Phys Chem B 2009; 113:12129-35. [DOI: 10.1021/jp904466n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Massimiliano Porrini
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Vangelis Daskalakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Stavros C. Farantos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
| | - Constantinos Varotsis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, Vasilika Vouton, Heraklion 71110, Crete, Greece, and Department of Chemistry, University of Crete, P.O. Box 2208, Vasilika Vouton, Heraklion 71305, Crete, Greece
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Kaila VRI, Johansson MP, Sundholm D, Laakkonen L, Wiström M. The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:221-33. [PMID: 19388139 DOI: 10.1016/j.bbabio.2009.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The CuB metal center is at the core of the active site of the heme-copper oxidases, comprising a copper atom ligating three histidine residues one of which is covalently bonded to a tyrosine residue. Using quantum chemical methodology, we have studied the CuB site in several redox and ligand states proposed to be intermediates of the catalytic cycle. The importance of the His-Tyr crosslink was investigated by comparing energetics, charge, and spin distributions between systems with and without the crosslink. The His-Tyr bond was shown to decrease the proton affinity and increase the electron affinity of both Tyr-244 and the copper. A previously unnoticed internal electronic equilibrium between the copper atom and the tyrosine was observed, which seems to be coupled to the unique structure of the system. In certain states the copper and Tyr-244 compete for the unpaired electron, the localization of which is determined by the oxygenous ligand of the copper. This electronic equilibrium was found to be sensitive to the presence of a positive charge 10 A away from the center, simulating the effect of Lys-319 in the K-pathway of proton transfer. The combined results provide an explanation for why the heme-copper oxidases need two pathways of proton uptake, and why the K-pathway is active only in the second half of the reaction cycle.
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Affiliation(s)
- Ville R I Kaila
- Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Lucas HR, Karlin KD. Copper-Carbon Bonds in Mechanistic and Structural Probing of Proteins as well as in Situations where Copper is a Catalytic or Receptor Site. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00295] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
While copper-carbon bonds are well appreciated in organometallic synthetic chemistry, such occurrences are less known in biological settings. By far, the greatest incidence of copper-carbon moieties is in bioinorganic research aimed at probing copper protein active site structure and mechanism; for example, carbon monoxide (CO) binding as a surrogate for O2. Using infrared (IR) spectroscopy, CO coordination to cuprous sites has proven to be an extremely useful tool for determining active site copper ligation (e.g., donor atom number and type). The coupled (hemocyanin, tyrosinase, catechol oxidase) and non-coupled (peptidylglycine α-hydroxylating monooxygenase, dopamine β-monooxygenase) binuclear copper proteins as well as the heme-copper oxidases (HCOs) have been studied extensively via this method. In addition, environmental changes within the vicinity of the active site have been determined based on shifts in the CO stretching frequencies, such as for copper amine oxidases, nitrite reductases and again in the binuclear proteins and HCOs. In many situations, spectroscopic monitoring has provided kinetic and thermodynamic data on CuI-CO formation and CO dissociation from copper(I); recently, processes occurring on a femtosecond timescale have been reported. Copper-cyano moieties have also been useful for obtaining insights into the active site structure and mechanisms of copper-zinc superoxide dismutase, azurin, nitrous oxide reductase, and multi-copper oxidases. Cyanide is a good ligand for both copper(I) and copper(II), therefore multiple physical-spectroscopic techniques can be applied. A more obvious occurrence of a “Cu-C” moiety was recently described for a CO dehydrogenase which contains a novel molybdenum-copper catalytic site. A bacterial copper chaperone (CusF) was recently established to have a novel d-π interaction comprised of copper(I) with the arene containing side-chain of a tryptophan amino acid residue. Meanwhile, good evidence exists that a plant receptor site (ETR1) utilizes copper(I) to sense ethylene, a growth hormone. A copper olfactory receptor has also been suggested. All of the above mentioned occurrences or uses of carbon-containing substrates and/or probes are reviewed and discussed within the framework of copper proteins and other relevant systems.
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Affiliation(s)
- Heather R. Lucas
- Department of Chemistry, The Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
| | - Kenneth D. Karlin
- Department of Chemistry, The Johns Hopkins University 3400 N. Charles Street Baltimore MD 21218 USA
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