1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Nicolaides A, Soulimane T, Varotsis C. Reversible temperature-dependent high- to low-spin transition in the heme Fe–Cu binuclear center of cytochrome ba3 oxidase. RSC Adv 2019; 9:4776-4780. [PMID: 35514640 PMCID: PMC9060599 DOI: 10.1039/c8ra09954e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/31/2019] [Indexed: 12/03/2022] Open
Abstract
A reversible temperature-dependent high-spin to low-spin transition with T1/2 = −60 °C has been observed in the resonance Raman spectra of the equilibrium reduced and photoreduced heme a3 of the thermophilic ba3 heme–copper oxidoreductase. The transition is based on the frequency shifts of the spin-state marker bands ν2 (CbCb) and ν10 (CaCm) and is attributed to the displacement of the heme iron along the heme normal as a consequence of the Fe–Np repulsion at temperature below −40 °C which will increase the ligand field strength forcing the pairing of d electrons into the lower energy orbitals. A reversible temperature-dependent high- to low-spin transition with T1/2 = −60 °C has been observed in the resonance Raman spectra of the equilibrium reduced and photoreduced heme a3 of the thermophilic ba3 heme–copper oxidoreductase.![]()
Collapse
Affiliation(s)
- Antonis Nicolaides
- Cyprus University of Technology
- Department of Environmental Science and Technology
- 3603 Lemesos
- Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department
- Materials & Surface Science Institute
- University of Limerick
- Limerick
- Ireland
| | - Constantinos Varotsis
- Cyprus University of Technology
- Department of Environmental Science and Technology
- 3603 Lemesos
- Cyprus
| |
Collapse
|
4
|
Boschetto F, Toyama N, Horiguchi S, Bock RM, McEntire BJ, Adachi T, Marin E, Zhu W, Mazda O, Bal BS, Pezzotti G. In vitroantibacterial activity of oxide and non-oxide bioceramics for arthroplastic devices: II. Fourier transform infrared spectroscopy. Analyst 2018; 143:2128-2140. [DOI: 10.1039/c8an00234g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metabolic response of Gram-positiveStaphylococcus epidermidisbacteria to bioceramic substrates was probed by Fourier transform infrared spectroscopy.
Collapse
Affiliation(s)
- Francesco Boschetto
- Ceramic Physics Laboratory
- Kyoto Institute of Technology
- Kyoto
- Japan
- Department of Immunology
| | - Nami Toyama
- Ceramic Physics Laboratory
- Kyoto Institute of Technology
- Kyoto
- Japan
| | - Satoshi Horiguchi
- Department of Dental Medicine
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Kyoto 602-8566
- Japan
| | | | | | - Tetsuya Adachi
- Department of Dental Medicine
- Graduate School of Medical Science
- Kyoto Prefectural University of Medicine
- Kyoto 602-8566
- Japan
| | - Elia Marin
- Ceramic Physics Laboratory
- Kyoto Institute of Technology
- Kyoto
- Japan
- Department of Dental Medicine
| | - Wenliang Zhu
- Ceramic Physics Laboratory
- Kyoto Institute of Technology
- Kyoto
- Japan
| | - Osam Mazda
- Department of Immunology
- Kyoto Prefectural University of Medicine
- Kyoto 602-8566
- Japan
| | - B. Sonny Bal
- Amedica Corporation
- Salt Lake City
- USA
- Department of Orthopaedic Surgery
- University of Missouri
| | - Giuseppe Pezzotti
- Ceramic Physics Laboratory
- Kyoto Institute of Technology
- Kyoto
- Japan
- Department of Immunology
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Koutsoupakis C, Soulimane T, Varotsis C. Photobiochemical production of carbon monoxide by Thermus thermophilus ba3 -cytochrome c oxidase. Chemistry 2015; 21:4958-61. [PMID: 25689606 DOI: 10.1002/chem.201406239] [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: 11/26/2014] [Indexed: 11/08/2022]
Abstract
We report the photobiochemical production of carbon monoxide by a terminal ba3 -cytochrome c oxidase from T. thermophilus HB8. FTIR and time-resolved step-scan FTIR spectroscopies were combined to probe this process and also monitor the concomitant binding of the produced gas to other intact ba3 molecules forming the ba3 -CO complex. The activation of this mechanism by ba3 -oxidase under visible excitation raises the question as to whether such a mechanism is physiologically relevant to the extreme environment in which it operates.
Collapse
Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P.O. Box 50329, 3603 Lemesos (Cyprus)
| | | | | |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Pavlou A, Martínková M, Shimizu T, Kitanishi K, Stranava M, Loullis A, Pinakoulaki E. Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy. Phys Chem Chem Phys 2015; 17:17007-15. [DOI: 10.1039/c5cp01708d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present time-resolved step-scan FTIR evidence for the role of the distal Y43 and L65 residues in controlling the ligand dynamics in the signal transducer protein YddV.
Collapse
Affiliation(s)
- Andrea Pavlou
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Martin Stranava
- Department of Biochemistry
- Faculty of Science
- Charles University in Prague
- 128 43 Prague 2
- Czech Republic
| | - Andreas Loullis
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
| | | |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Irina Smirnova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University , SE-106 91 Stockholm, Sweden
| | | | | | | | | | | |
Collapse
|
14
|
Koutsoupakis C, Soulimane T, Varotsis C. Spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from Thermus thermophilus: a Fourier transform infrared (FTIR) and time-resolved step-scan FTIR study. J Biol Chem 2012; 287:37495-507. [PMID: 22927441 DOI: 10.1074/jbc.m112.403600] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The complete understanding of a molecular mechanism of action requires the thermodynamic and kinetic characterization of different states and intermediates. Cytochrome c oxidase reduces O(2) to H(2)O, a reaction coupled to proton translocation across the membrane. Therefore, it is necessary to undertake a thorough characterization of the reduced form of the enzyme and the determination of the electron transfer processes and pathways between the redox-active centers. In this study Fourier transform infrared (FTIR) and time-resolved step-scan FTIR spectroscopy have been applied to study the fully reduced and mixed valence states of cytochrome ba(3) from Thermus thermophilus. We used as probe carbon monoxide (CO) to characterize both thermodynamically and kinetically the cytochrome ba(3)-CO complex in the 5.25-10.10 pH/pD range and to study the reverse intramolecular electron transfer initiated by the photolysis of CO in the two-electron reduced form. The time-resolved step-scan FTIR data revealed no pH/pD dependence in both the decay of the transient Cu(B)(1+)-CO complex and rebinding to heme a(3) rates, suggesting that no structural change takes place in the vicinity of the binuclear center. Surprisingly, photodissociation of CO from the mixed valence form of the enzyme does not lead to reverse electron transfer from the reduced heme a(3) to the oxidized low-spin heme b, as observed in all the other aa(3) and bo(3) oxidases previously examined. The heme b-heme a(3) electron transfer is guaranteed, and therefore, there is no need for structural rearrangements and complex synchronized cooperativities. Comparison among the available structures of ba(3)- and aa(3)-cytochrome c oxidases identifies possible active pathways involved in the electron transfer processes and key structural elements that contribute to the different behavior observed in cytochrome ba(3).
Collapse
Affiliation(s)
- Constantinos Koutsoupakis
- Department of Environmental Science and Technology, Cyprus University of Technology, P. O. Box 50329, 3603 Lemesos, Cyprus
| | | | | |
Collapse
|
15
|
Loullis A, Noor MR, Soulimane T, Pinakoulaki E. Observation of ligand transfer in ba3 oxidase from Thermus thermophilus: simultaneous FTIR detection of photolabile heme a3(2+)-CN and transient Cu(B)(2+)-CN complexes. J Phys Chem B 2012; 116:8955-60. [PMID: 22765881 DOI: 10.1021/jp305096y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
FTIR and light-minus-dark FTIR spectroscopy have been employed to investigate the reaction of oxidized and fully reduced ba(3) oxidase with cyanide. The characterization of the structures of the bound CN(-) in the binuclear heme Fe-Cu(B) center is essential, given that a central issue in the function of ba(3) oxidase is the extent to which the partially reduced substrates interact with the two metals. In the reaction of oxidized ba(3) oxidase with cyanide the initially formed heme a(3)(3+)-C≡N-Cu(B)(2+) species with ν(CN) frequency at 2152 cm(-1) was replaced by a photolabile complex with a frequency at 2075 cm(-1) characteristic of heme a(3)(2+)-CN(-). Photolysis of the heme a(3)(2+)-CN(-) adduct produced a band at 2146 cm(-1) attributed to the formation of a transient Cu(B)(2+)-CN(-) complex. All forms are pH independent between pH 5.5-9.5 and at pD 7.5 indicating the absence of ionizable groups that influence the properties of the cyanide complexes. In contrast to previous reports, our results show that CN(-) does not bind simultaneously to both heme a(3)(2+) and Cu(B)(2+) to form the mixed valence a(3)(2+)-CN·Cu(B)(2+)CN species. The photolysis products of the heme a(3)(2+)-CN(-)/Cu(B)(2+) and heme a(3)(2+)-CN(-)/Cu(B)(1+) species are different suggesting that relaxation dynamics in the binuclear center following ligand photodissociation are dependent on the oxidation state of Cu(B).
Collapse
Affiliation(s)
- Andreas Loullis
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | | | | |
Collapse
|
16
|
The origin of the FeIV=O intermediates in cytochrome aa3 oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:552-7. [DOI: 10.1016/j.bbabio.2011.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 11/17/2022]
|
17
|
Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus. Proc Natl Acad Sci U S A 2012; 109:5259-64. [PMID: 22431640 DOI: 10.1073/pnas.1107345109] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heme-copper oxygen reductases are redox-driven proton pumps. In the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from Thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits I and II. Recent studies have proposed important roles for His376 and Asp372, both of which are hydrogen-bonded to propionate-A of heme a(3), and for Glu126(II) (subunit II), which is hydrogen-bonded to His376. Based on the current results, His376, Glu126(II), and Asp372 are not essential for either oxidase activity or proton pumping. In addition, Tyr133, which is hydrogen-bonded to propionate-D of heme a(3), was also shown not to be essential for function. However, two mutations of the residues hydrogen-bonded to propionate-A, Asp372Ile and His376Asn, retain high electron transfer activity and normal spectral features but, in different preparations, either do not pump protons or exhibit substantially diminished proton pumping. It is concluded that either propionate-A of heme a(3) or possibly the cluster of groups centered about the conserved water molecule that hydrogen-bonds to both propionates-A and -D of heme a(3) is a good candidate to be the proton loading site.
Collapse
|
18
|
Pinakoulaki E, Koutsoupakis C, Sawai H, Pavlou A, Kato Y, Asano Y, Aono S. Aldoxime Dehydratase: Probing the Heme Environment Involved in the Synthesis of the Carbon–Nitrogen Triple Bond. J Phys Chem B 2011; 115:13012-8. [DOI: 10.1021/jp205944e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Hitomi Sawai
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Andrea Pavlou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shigetoshi Aono
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Farantos SC, Schinke R, Guo H, Joyeux M. Energy Localization in Molecules, Bifurcation Phenomena, and Their Spectroscopic Signatures: The Global View. Chem Rev 2009; 109:4248-71. [DOI: 10.1021/cr900069m] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stavros C. Farantos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, and Department of Chemistry, University of Crete, Iraklion 711 10, Crete, Greece, Max-Planck-Institut für Dynamik und Selbstorganisation, D-37073 Göttingen, Germany, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, and Laboratoire de Spectrométrie Physique, Université Joseph Fourier—Grenoble I, BP 87, F-38402, St. Martin d’Heres Cedex, France
| | - Reinhard Schinke
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, and Department of Chemistry, University of Crete, Iraklion 711 10, Crete, Greece, Max-Planck-Institut für Dynamik und Selbstorganisation, D-37073 Göttingen, Germany, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, and Laboratoire de Spectrométrie Physique, Université Joseph Fourier—Grenoble I, BP 87, F-38402, St. Martin d’Heres Cedex, France
| | - Hua Guo
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, and Department of Chemistry, University of Crete, Iraklion 711 10, Crete, Greece, Max-Planck-Institut für Dynamik und Selbstorganisation, D-37073 Göttingen, Germany, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, and Laboratoire de Spectrométrie Physique, Université Joseph Fourier—Grenoble I, BP 87, F-38402, St. Martin d’Heres Cedex, France
| | - Marc Joyeux
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, and Department of Chemistry, University of Crete, Iraklion 711 10, Crete, Greece, Max-Planck-Institut für Dynamik und Selbstorganisation, D-37073 Göttingen, Germany, Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, and Laboratoire de Spectrométrie Physique, Université Joseph Fourier—Grenoble I, BP 87, F-38402, St. Martin d’Heres Cedex, France
| |
Collapse
|
22
|
Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
23
|
Abstract
The enzymatic activity of Paracoccus denitrificans cytochrome c oxidase (COX) and Escherichia coli cytochrome b(o) ubiquinol oxidase (QOX) was determined in the presence of formamide, N,N-dimethyl formamide and N,N-dimethyl acetamide. Formamide was found to inhibit the enzyme activity of the oxidases most significantly, whereas the other two compounds inhibited the activity to a lesser extent. The effects of formamide and analogs on enzyme activity were very similar for COX and QOX, indicating that the mechanism of inhibition might be the same for both of these oxidases. The inhibition kinetics followed a non-competitive mechanism. Studies using proteoliposomes of COX and QOX containing the electron entry site of the enzyme directed towards the outside of the vesicles showed that the effect of inhibition by formamide was higher when the inhibitor was present on the outside of the proteoliposome compared to when it was present only in the aqueous core. This indicates that inhibition of enzyme activity by formamide possibly predominantly involves blocking of the water exit pathway in the oxidases.
Collapse
Affiliation(s)
- Sayan Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | | |
Collapse
|
24
|
Nitric oxide activation and reduction by heme–copper oxidoreductases and nitric oxide reductase. J Inorg Biochem 2008; 102:1277-87. [DOI: 10.1016/j.jinorgbio.2008.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 11/18/2022]
|
25
|
Spectroscopic study on the communication between a heme a3 propionate, Asp399 and the binuclear center of cytochrome c oxidase from Paracoccus denitrificans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1777:220-6. [PMID: 18078804 DOI: 10.1016/j.bbabio.2007.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Revised: 11/01/2007] [Accepted: 11/02/2007] [Indexed: 11/27/2022]
Abstract
The proton pumping mechanism of cytochrome c oxidase on a molecular level is highly disputed. Recently theoretical calculations and real time electron transfer measurements indicated the involvement of residues in the vicinity of the ring A propionate of heme a3, including Asp399 and the CuB ligands His 325, 326. In this study we probed the interaction of Asp399 with the binuclear center and characterize the protonation state of its side chain. Redox induced FTIR difference spectra of mutations at the site in direct comparison to wild type, indicate that below pH 5 Asp 399 displays signals typical for the deprotonation of the acidic residue with reduction of the enzyme. Interestingly at a pH higher than 5, no contributions from Asp 399 are evident. In order to probe the interaction of the site with the binuclear center we followed the rebinding of CO by infrared spectroscopy for mutations on residue Asp399 to Glu, Asn and Leu. Previously different CO conformers have been identified for bacterial cytochrome c oxidases, and its pH dependent behaviour discussed to be relevant for catalysis. Interestingly we observe the lack of this pH dependency and a strong influence on the observable conformers for all mutants studied here, clearly suggesting a communication of the site with the heme-copper center and the nearby histidine residues.
Collapse
|
26
|
Daskalakis V, Pinakoulaki E, Stavrakis S, Varotsis C. Probing the Environment of CuB in Heme−Copper Oxidases. J Phys Chem B 2007; 111:10502-9. [PMID: 17696387 DOI: 10.1021/jp0718597] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved step-scan FTIR (TRS2-FTIR) and density functional theory have been applied to probe the structural dynamics of CuB in heme-copper oxidases at room temperature. The TRS2-FTIR data of cbb3 from Pseudomonas stutzeri indicate a small variation in the frequency of the transient CO bound to CuB in the pH/pD 7-9 range. This observation in conjunction with density functional theory calculations, in which significant frequency shifts of the nu(CO) are observed upon deprotonation and/or detachment of the CuB ligands, demonstrates that the properties of the CuB ligands including the cross-linked tyrosine, in contrast to previous reports, remain unchanged in the pH 7-9 range. We attribute the small variations in the nu(CO) of CuB to protein conformational changes in the vicinity of CuB. Consequently, the split of the heme Fe-CO vibrations (alpha-, beta-, and gamma-forms) is not due to changes in the ligation and/or protonation states of the CuB ligands or to the presence of one or more ionizable groups, as previously suggested, but the result of global protein conformational changes in the vicinity of CuB which, in turn, affect the position of CuB with respect to the heme Fe.
Collapse
Affiliation(s)
- Vangelis Daskalakis
- Department of Chemistry, University of Crete, 71003 Voutes, Heraklion, Crete, Greece
| | | | | | | |
Collapse
|
27
|
Pinakoulaki E, Ohta T, Soulimane T, Kitagawa T, Varotsis C. Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus. J Am Chem Soc 2006; 127:15161-7. [PMID: 16248657 DOI: 10.1021/ja0539490] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a(3)(2+)-NO species formed in the reaction of ba(3)-oxidase with NO from resonance Raman spectroscopy. We have identified the His-heme a(3)(2+)-NO/Cu(B)(1+) species by its characteristic Fe-NO and N-O stretching frequencies at 539 and 1620 cm(-)(1), respectively. The Fe-NO and N-O frequencies in ba(3)-oxidase are 21 and 7 cm(-)(1) lower and higher, respectively, than those observed in Mb-NO. From these results and earlier Raman and FTIR measurements, we demonstrate that the protein environment of the proximal His384 that is part of the Q-proton pathway controls the strength of the Fe-His384 bond upon ligand (CO vs NO) binding. We also show by time-resolved FTIR spectroscopy that Cu(B)(1+) has a much lower affinity for NO than for CO. We suggest that the reduction of NO to N(2)O by ba(3)-oxidase proceeds by the fast binding of the first NO molecule to heme a(3) with high-affinity, and the second NO molecule binds to Cu(B) with low-affinity, producing the temporal co-presence of two NO molecules in the heme-copper center. The low-affinity of Cu(B) for NO binding also explains the NO reductase activity of the ba(3)-oxidase as opposed to other heme-copper oxidases. With the identification of the His-heme a(3)(2+)-NO/Cu(B)(1+) species, the structure of the binuclear heme a(3)-Cu(B)(1+) center in the initial step of the NO reduction mechanism is known.
Collapse
|
28
|
Nie B, Stutzman J, Xie A. A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Biophys J 2005; 88:2833-47. [PMID: 15653739 PMCID: PMC1305378 DOI: 10.1529/biophysj.104.047639] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: approximately 1759-1776 cm(-1) for zero, approximately 1733-1749 cm(-1) for one, and 1703-1710 cm(-1) for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins.
Collapse
Affiliation(s)
- Beining Nie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | | | | |
Collapse
|
29
|
Victor BL, Baptista AM, Soares CM. Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens. Biophys J 2004; 87:4316-25. [PMID: 15377522 PMCID: PMC1304938 DOI: 10.1529/biophysj.104.049353] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 09/08/2004] [Indexed: 11/18/2022] Open
Abstract
Heme-copper oxidases are membrane proteins found in the respiratory chain of aerobic organisms. They are the terminal electron acceptors coupling the translocation of protons across the membrane with the reduction of oxygen to water. Because the catalytic process occurs in the heme cofactors positioned well inside the protein matrix, proton channels must exist. However, due to the high structural divergence among this kind of proteins, the proton channels previously described are not necessarily conserved. In this work we modeled the structure of the quinol oxidase from Acidianus ambivalens using comparative modeling techniques for identifying proton channels. Additionally, given the high importance that water molecules may have in this process, we have developed a methodology, within the context of comparative modeling, to identify high water probability zones and to deconvolute them into chains of ordered water molecules. From our results, and from the existent information from other proteins from the same superfamily, we were able to suggest three possible proton channels: one K-, one D-, and one Q-spatial homologous proton channels. This methodology can be applied to other systems where water molecules are important for their biological function.
Collapse
Affiliation(s)
- Bruno L Victor
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal
| | | | | |
Collapse
|
30
|
Pinakoulaki E, Ohta T, Soulimane T, Kitagawa T, Varotsis C. Simultaneous Resonance Raman Detection of the Heme a3-Fe-CO and CuB-CO Species in CO-bound ba3-Cytochrome c Oxidase from Thermus thermophilus. J Biol Chem 2004; 279:22791-4. [PMID: 15066990 DOI: 10.1074/jbc.c400124200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding of the chemical nature of the dioxygen and nitric oxide moiety of ba3-cytochrome c oxidase from Thermus thermophilus is crucial for elucidation of its physiological function. In the present work, direct resonance Raman (RR) observation of the Fe-C-O stretching and bending modes and the C-O stretching mode of the CuB-CO complex unambiguously establishes the vibrational characteristics of the heme-copper moiety in ba3-oxidase. We assigned the bands at 507 and 568 cm(-1) to the Fe-CO stretching and Fe-C-O bending modes, respectively. The frequencies of these modes in conjunction with the C-O mode at 1973 cm(-1) showed, despite the extreme values of the Fe-CO and C-O stretching vibrations, the presence of the alpha-conformation in the catalytic center of the enzyme. These data, distinctly different from those observed for the caa3-oxidase, are discussed in terms of the proposed coupling of the alpha-and beta-conformations that occur in the binuclear center of heme-copper oxidases with enzymatic activity. The CuB-CO complex was identified by its nu(CO) at 2053 cm(-1) and was strongly enhanced with 413.1 nm excitation indicating the presence of a metal-to-ligand charge transfer transition state near 410 nm. These findings provide, for the first time, RR vibrational information on the EPR silent CuB(I) that is located at the O2 delivery channel and has been proposed to play a crucial role in both the catalytic and proton pumping mechanisms of heme-copper oxidases.
Collapse
|
31
|
Ohta T, Pinakoulaki E, Soulimane T, Kitagawa T, Varotsis C. Detection of a Photostable Five-Coordinate Heme a3-Fe−CO Species and Functional Implications of His384/α10 in CO-Bound ba3-Cytochrome c Oxidase from Thermus thermophilus. J Phys Chem B 2004. [DOI: 10.1021/jp049259k] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Takehiro Ohta
- Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece, Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585 Japan, and Paul Scherrer Institute, Life Sciences, OSRA/008,CH-5232 Villigen PSI, Switzerland
| | - Eftychia Pinakoulaki
- Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece, Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585 Japan, and Paul Scherrer Institute, Life Sciences, OSRA/008,CH-5232 Villigen PSI, Switzerland
| | - Tewfik Soulimane
- Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece, Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585 Japan, and Paul Scherrer Institute, Life Sciences, OSRA/008,CH-5232 Villigen PSI, Switzerland
| | - Teizo Kitagawa
- Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece, Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585 Japan, and Paul Scherrer Institute, Life Sciences, OSRA/008,CH-5232 Villigen PSI, Switzerland
| | - Constantinos Varotsis
- Department of Chemistry, University of Crete, 71409 Heraklion, Crete, Greece, Center for Integrative Bioscience, Okazaki National Research Institutes, Myodaiji, Okazaki, Aichi 444-8585 Japan, and Paul Scherrer Institute, Life Sciences, OSRA/008,CH-5232 Villigen PSI, Switzerland
| |
Collapse
|