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Proton transfer in ba3 cytochrome c oxidase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:650-7. [DOI: 10.1016/j.bbabio.2011.11.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 11/23/2022]
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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.
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53
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Porrini M, Daskalakis V, Farantos SC. Exploring the topography of free energy surfaces and kinetics of cytochrome c oxidases interacting with small ligands. RSC Adv 2012. [DOI: 10.1039/c2ra20625k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Näsvik Öjemyr L, von Ballmoos C, Gennis RB, Sligar SG, Brzezinski P. Reconstitution of respiratory oxidases in membrane nanodiscs for investigation of proton-coupled electron transfer. FEBS Lett 2011; 586:640-5. [PMID: 22209982 DOI: 10.1016/j.febslet.2011.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 12/31/2022]
Abstract
The function of membrane-bound transporters is commonly affected by the milieu of the hydrophobic, membrane-spanning part of the transmembrane protein. Consequently, functional studies of these proteins often involve incorporation into a native-like bilayer where the lipid components of the membrane can be controlled. The classical approach is to reconstitute the purified protein into liposomes. Even though the use of such liposomes is essential for studies of transmembrane transport processes in general, functional studies of the transporters themselves in liposomes suffer from several disadvantages. For example, transmembrane proteins can adopt two different orientations when reconstituted into liposomes, and one of these populations may be inaccessible to ligands, to changes in pH or ion concentration in the external solution. Furthermore, optical studies of proteins reconstituted in liposomes suffer from significant light scattering, which diminishes the signal-to-noise value of the measurements. One attractive approach to circumvent these problems is to use nanodiscs, which are phospholipid bilayers encircled by a stabilizing amphipathic helical membrane scaffold protein. These membrane nanodiscs are stable, soluble in aqueous solution without detergent and do not scatter light significantly. In the present study, we have developed a protocol for reconstitution of the aa(3)- and ba(3)-type cytochrome c oxidases into nanodiscs. Furthermore, we studied proton-coupled electron-transfer reactions in these enzymes with microsecond time resolution. The data show that the nanodisc membrane environment accelerates proton uptake in both oxidases.
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Affiliation(s)
- Linda Näsvik Öjemyr
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Kinetic studies of the reactions of O(2) and NO with reduced Thermus thermophilus ba(3) and bovine aa(3) using photolabile carriers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:672-9. [PMID: 22201543 DOI: 10.1016/j.bbabio.2011.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 11/20/2022]
Abstract
The reactions of molecular oxygen (O(2)) and nitric oxide (NO) with reduced Thermus thermophilus (Tt) ba(3) and bovine heart aa(3) were investigated by time-resolved optical absorption spectroscopy to establish possible relationships between the structural diversity of these enzymes and their reaction dynamics. To determine whether the photodissociated carbon monoxide (CO) in the CO flow-flash experiment affects the ligand binding dynamics, we monitored the reactions in the absence and presence of CO using photolabile O(2) and NO complexes. The binding of O(2)/NO to reduced ba(3) in the absence of CO occurs with a second-order rate constant of 1×10(9)M(-1)s(-1). This rate is 10-times faster than for the mammalian enzyme, and which is attributed to structural differences in the ligand channels of the two enzymes. Moreover, the O(2)/NO binding in ba(3) is 10-times slower in the presence of the photodissociated CO while the rates are the same for the bovine enzyme. This indicates that the photodissociated CO directly or indirectly impedes O(2) and NO access to the active site in Tt ba(3), and that traditional CO flow-flash experiments do not accurately reflect the O(2) and NO binding kinetics in ba(3). We suggest that in ba(3) the binding of O(2) (NO) to heme a(3)(2+) causes rapid dissociation of CO from Cu(B)(+) through steric or electronic effects or, alternatively, that the photodissociated CO does not bind to Cu(B)(+). These findings indicate that structural differences between Tt ba(3) and the bovine aa(3) enzyme are tightly linked to mechanistic differences in the functions of these enzymes. This article is part of a Special Issue entitled: Respiratory Oxidases.
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Egawa T, Chen Y, Fee JA, Yeh SR, Rousseau DL. The rate-limiting step in O(2) reduction by cytochrome ba(3) from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:666-71. [PMID: 22138627 DOI: 10.1016/j.bbabio.2011.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/10/2011] [Accepted: 11/11/2011] [Indexed: 11/15/2022]
Abstract
Cytochrome ba(3) (ba(3)) of Thermus thermophilus (T. thermophilus) is a member of the heme-copper oxidase family, which has a binuclear catalytic center comprised of a heme (heme a(3)) and a copper (Cu(B)). The heme-copper oxidases generally catalyze the four electron reduction of molecular oxygen in a sequence involving several intermediates. We have investigated the reaction of the fully reduced ba(3) with O(2) using stopped-flow techniques. Transient visible absorption spectra indicated that a fraction of the enzyme decayed to the oxidized state within the dead time (~1ms) of the stopped-flow instrument, while the remaining amount was in a reduced state that decayed slowly (k=400s(-1)) to the oxidized state without accumulation of detectable intermediates. Furthermore, no accumulation of intermediate species at 1ms was detected in time resolved resonance Raman measurements of the reaction. These findings suggest that O(2) binds rapidly to heme a(3) in one fraction of the enzyme and progresses to the oxidized state. In the other fraction of the enzyme, O(2) binds transiently to a trap, likely Cu(B), prior to its migration to heme a(3) for the oxidative reaction, highlighting the critical role of Cu(B) in regulating the oxygen reaction kinetics in the oxidase superfamily.
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Affiliation(s)
- Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
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57
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Abstract
Aerobic respiration in bacteria, Archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. These enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. The oxygen reductases can be divided into three main families based on evolutionary and structural analyses (A-, B- and C-families), with the B- and C-families evolving after the A-family. The A-family utilizes two proton input channels to transfer protons for pumping and chemistry, whereas the B- and C-families require only one. Generally, the B- and C-families also have higher apparent oxygen affinities than the A-family. Here we use whole cell proton pumping measurements to demonstrate differential proton pumping efficiencies between representatives of the A-, B-, and C-oxygen reductase families. The A-family has a coupling stoichiometry of 1 H(+)/e(-), whereas the B- and C-families have coupling stoichiometries of 0.5 H(+)/e(-). The differential proton pumping stoichiometries, along with differences in the structures of the proton-conducting channels, place critical constraints on models of the mechanism of proton pumping. Most significantly, it is proposed that the adaptation of aerobic respiration to low oxygen environments resulted in a concomitant reduction in energy conservation efficiency, with important physiological and ecological consequences.
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Tiefenbrunn T, Liu W, Chen Y, Katritch V, Stout CD, Fee JA, Cherezov V. High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment. PLoS One 2011; 6:e22348. [PMID: 21814577 PMCID: PMC3141039 DOI: 10.1371/journal.pone.0022348] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/20/2011] [Indexed: 11/26/2022] Open
Abstract
The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H+ and e- transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba3-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O2-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the CuB atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fea3 and CuB atoms that is best modeled as peroxide. The structure of ba3-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba3-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the door for systematic structure-function studies.
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Affiliation(s)
- Theresa Tiefenbrunn
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Wei Liu
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ying Chen
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Vsevolod Katritch
- Skaggs School of Pharmacy & Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America
| | - C. David Stout
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James A. Fee
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (VC); (JF)
| | - Vadim Cherezov
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (VC); (JF)
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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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Lipids in photosystem II: Multifunctional cofactors. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2011; 104:19-34. [DOI: 10.1016/j.jphotobiol.2011.02.025] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 11/21/2022]
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61
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Abstract
Energy conservation in all kingdoms of life involves electron transfer, through a number of membrane-bound proteins, associated with proton transfer across the membrane. In aerobic organisms, the last component of this electron-transfer chain is a respiratory heme-copper oxidase that catalyzes reduction of O(2) to H(2)O, linking this process to transmembrane proton pumping. So far, the molecular mechanism of proton pumping is not known for any system that is driven by electron transfer. Here, we show that this problem can be addressed and elucidated in a unique cytochrome c oxidase (cytochrome ba(3)) from a thermophilic bacterium, Thermus thermophilus. The results show that in this oxidase the electron- and proton-transfer reactions are orchestrated in time such that previously unresolved proton-transfer reactions could be directly observed. On the basis of these data we propose that loading of the proton pump occurs upon electron transfer, but before substrate proton transfer, to the catalytic site. Furthermore, the results suggest that the pump site alternates between a protonated and deprotonated state for every second electron transferred to the catalytic site, which would explain the noninteger pumping stoichiometry (0.5 H(+)/e(-)) of the ba(3) oxidase. Our studies of this variant of Nature's palette of mechanistic solutions to a basic problem offer a route toward understanding energy conservation in biological systems.
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62
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Affiliation(s)
- Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Beaverton, OR 97006, USA.
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63
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Chakrabarty S, Namslauer I, Brzezinski P, Warshel A. Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:413-26. [PMID: 21232525 DOI: 10.1016/j.bbabio.2011.01.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/22/2010] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
Abstract
Gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (CcO) is a problem of great current interest. Despite promising mechanistic proposals, so far, a physically consistent model that would reproduce all the relevant barriers needed to create a working pump has not been presented. In addition, there are major problems in elucidating the origin of key mutational effects and in understanding the nature of the apparent pK(a) values associated with the pH dependencies of specific proton transfer (PT) reactions in CcO. This work takes a key step in resolving the above problems, by considering mutations, such as the Asn139Asp replacement, that blocks proton pumping without affecting PT to the catalytic site. We first introduce a formulation that makes it possible to relate the apparent pK(a) of Glu286 to different conformational states of this residue. We then use the new formulation along with the calculated pK(a) values of Glu286 at these different conformations to reproduce the experimentally observed apparent pK(a) of the residue. Next, we take the X-ray structures of the native and Asn139Asp mutant of the Paracoccus denitrificans CcO (N131D in this system) and reproduce for the first time the change in the primary PT pathways (and other key features) based on simulations that start with the observed structural changes. We also consider the competition between proton transport to the catalytic site and the pump site, as a function of the bulk pH, as well as the H/D isotope effect, and use this information to explore the relative height of the two barriers. The paper emphasizes the crucial role of energy-based considerations that include the PT process, and the delicate control of PT in CcO.
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Affiliation(s)
- Suman Chakrabarty
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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64
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Lautier T, Ezanno P, Baffert C, Fourmond V, Cournac L, Fontecilla-Camps JC, Soucaille P, Bertrand P, Meynial-Salles I, Léger C. The quest for a functional substrate access tunnel in FeFe hydrogenase. Faraday Discuss 2011; 148:385-407; discussion 421-41. [DOI: 10.1039/c004099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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CO impedes superfast O2 binding in ba3 cytochrome oxidase from Thermus thermophilus. Proc Natl Acad Sci U S A 2010; 107:21010-5. [PMID: 21097703 DOI: 10.1073/pnas.1008603107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinetic studies of heme-copper terminal oxidases using the CO flow-flash method are potentially compromised by the fate of the photodissociated CO. In this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by ba(3) cytochrome c oxidase from Thermus thermophilus in the absence and presence of CO using a photolabile O(2)-carrier. A novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the O(2)-carrier with a 355 nm laser pulse and the fully reduced CO-bound ba(3) simultaneously with a second 532-nm laser pulse. A kinetic analysis reveals a sequential mechanism in which O(2) binding to heme a(3) at 90 μM O(2) occurs with lifetimes of 9.3 and 110 μs in the absence and presence of CO, respectively, followed by a faster cleavage of the dioxygen bond (4.8 μs), which generates the P intermediate with the concomitant oxidation of heme b. The second-order rate constant of 1 × 10(9) M(-1) s(-1) for O(2) binding to ba(3) in the absence of CO is 10 times greater than observed in the presence of CO as well as for the bovine heart enzyme. The O(2) bond cleavage in ba(3) of 4.8 μs is also approximately 10 times faster than in the bovine enzyme. These results suggest important structural differences between the accessibility of O(2) to the active site in ba(3) and the bovine enzyme, and they demonstrate that the photodissociated CO impedes access of dioxygen to the heme a(3) site in ba(3), making the CO flow-flash method inapplicable.
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Guskov A, Gabdulkhakov A, Broser M, Glöckner C, Hellmich J, Kern J, Frank J, Müh F, Saenger W, Zouni A. Recent Progress in the Crystallographic Studies of Photosystem II. Chemphyschem 2010; 11:1160-71. [DOI: 10.1002/cphc.200900901] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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67
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Satagopan S, Scott SS, Smith TG, Tabita FR. A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration. Biochemistry 2009; 48:9076-83. [PMID: 19705820 DOI: 10.1021/bi9006385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) is a globally significant biocatalyst that facilitates the removal and sequestration of CO2 from the biosphere. Rubisco-catalyzed CO2 reduction thus provides virtually all of the organic carbon utilized by living organisms. Despite catalyzing the rate-limiting step of photosynthetic and chemoautotrophic CO2 assimilation, Rubisco is markedly inefficient as the competition between O2 and CO2 for the same substrate limits the ability of aerobic organisms to obtain maximum amounts of organic carbon for CO2-dependent growth. Random and site-directed mutagenesis procedures were coupled with genetic selection to identify an "oxygen-insensitive" mutant cyanobacterial (Synechococcus sp. strain PCC 6301) Rubisco that allowed for CO2-dependent growth of a host bacterium at an oxygen concentration that inhibited growth of the host containing wild-type Synechococcus Rubisco. The mutant substitution, A375V, was identified as an intragenic suppressor of D103V, a negative mutant enzyme incapable of supporting autotrophic growth. Ala-375 (Ala-378 of spinach Rubisco) is a conserved residue in all form I (plant-like) Rubiscos. Structure-function analyses indicate that the A375V substitution decreased the enzyme's oxygen sensitivity (and not CO2/O2 specificity), possibly by rearranging a network of interactions in a fairly conserved hydrophobic pocket near the active site. These studies point to the potential of engineering plants and other significant aerobic organisms to fix CO2 unfettered by the presence of O2.
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Affiliation(s)
- Sriram Satagopan
- Department of Microbiology and the Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210-1292, USA
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Water-mediated signal multiplication with Y-shaped carbon nanotubes. Proc Natl Acad Sci U S A 2009; 106:18120-4. [PMID: 19815515 DOI: 10.1073/pnas.0902676106] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular scale signal conversion and multiplication is of particular importance in many physical and biological applications, such as molecular switches, nano-gates, biosensors, and various neural systems. Unfortunately, little is currently known regarding the signal processing at the molecular level, partly due to the significant noises arising from the thermal fluctuations and interferences between branch signals. Here, we use molecular dynamics simulations to show that a signal at the single-electron level can be converted and multiplied into 2 or more signals by water chains confined in a narrow Y-shaped nanochannel. This remarkable transduction capability of molecular signal by Y-shaped nanochannel is found to be attributable to the surprisingly strong dipole-induced ordering of such water chains, such that the concerted water orientations in the 2 branches of the Y-shaped nanotubes can be modulated by the water orientation in the main channel. The response to the switching of the charge signal is very rapid, from a few nanoseconds to a few hundred nanoseconds. Furthermore, simulations with various water models, including TIP3P, TIP4P, and SPC/E, show that the transduction capability of the Y-shaped carbon nanotubes is very robust at room temperature, with the interference between branch signals negligible.
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69
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The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping. Proc Natl Acad Sci U S A 2009; 106:16169-73. [PMID: 19805275 DOI: 10.1073/pnas.0905264106] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [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 that generate a proton motive force in both prokaryotes and mitochondria. These enzymes have been divided into 3 evolutionarily related groups: the A-, B- and C-families. Most experimental work on proton-pumping mechanisms has been performed with members of the A-family. These enzymes require 2 proton input pathways (D- and K-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the D-channel transporting all pumped protons. In this work we use site-directed mutagenesis to demonstrate that the ba(3) oxygen reductase from Thermus thermophilus, a representative of the B-family, does not contain a D-channel. Rather, it utilizes only 1 proton input channel, analogous to that of the A-family K-channel, and it delivers protons to the active site for both O2 chemistry and proton pumping. Comparison of available subunit I sequences reveals that the only structural elements conserved within the oxygen reductase families that could perform these functions are active-site components, namely the covalently linked histidine-tyrosine, the Cu(B) and its ligands, and the active-site heme and its ligands. Therefore, our data suggest that all oxygen reductases perform the same chemical reactions for oxygen reduction and comprise the essential elements of the proton-pumping mechanism (e.g., the proton-loading and kinetic-gating sites). These sites, however, cannot be located within the D-channel. These results along with structural considerations point to the A-propionate region of the active-site heme and surrounding water molecules as the proton-loading site.
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70
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Gabdulkhakov A, Guskov A, Broser M, Kern J, Müh F, Saenger W, Zouni A. Probing the Accessibility of the Mn4Ca Cluster in Photosystem II: Channels Calculation, Noble Gas Derivatization, and Cocrystallization with DMSO. Structure 2009; 17:1223-34. [DOI: 10.1016/j.str.2009.07.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/16/2009] [Accepted: 07/21/2009] [Indexed: 01/05/2023]
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71
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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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Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA. Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry 2009; 48:820-6. [PMID: 19140675 DOI: 10.1021/bi801759a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three paths for obtaining crystals of reduced (II-E4Q/I-K258R) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 A resolution. Microspectrophotometry of single crystals of Thermus ba(3) oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory), being nearly complete in 1 min. The previously reported structures of ba(3) (Protein Data Bank entries 1EHK and 1XME ), having a crystallographically detectable water between the Cu(B) and Fe(a3) metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite-reduced crystals or crystals formed from dithionite-reduced enzyme revealed the absence of the above-mentioned water and an increase in the Cu(B)-Fe(a3) distance of approximately 0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals.
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Affiliation(s)
- Bin Liu
- Department of Molecular Biology, The Scripps Research Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Kern J, Zouni A, Guskov A, Krauß N. Lipids in the Structure of Photosystem I, Photosystem II and the Cytochrome b 6 f Complex. LIPIDS IN PHOTOSYNTHESIS 2009. [DOI: 10.1007/978-90-481-2863-1_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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74
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Cytochrome c oxidase: exciting progress and remaining mysteries. J Bioenerg Biomembr 2008; 40:521-31. [PMID: 18975062 DOI: 10.1007/s10863-008-9181-7] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 08/15/2008] [Indexed: 10/21/2022]
Abstract
Cytochrome c oxidase generates a proton motive force by two separate mechanisms. The first mechanism is similar to that postulated by Peter Mitchell, and is based on electrons and protons used to generate water coming from opposite sides of the membrane. The second mechanism was not initially anticipated, but is now firmly established as a proton pump. A brief review of the current state of our understanding of the proton pump of cytochrome oxidase is presented. We have come a long way since the initial observation of the pump by Mårten Wikström in 1977, but a number of essential questions remain to be answered.
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75
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Fee JA, Case DA, Noodleman L. Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus. J Am Chem Soc 2008; 130:15002-21. [PMID: 18928258 DOI: 10.1021/ja803112w] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O 2 to the Fe-Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)- (-)O-O (-)-Cu(II) to form water and the active oxidized enzyme, Fe(III)- (-)OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba 3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O 2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O 2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with Cu B. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O 2 reduction in the heme a 3 -Cu B dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.
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Affiliation(s)
- James A Fee
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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76
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Renger G, Renger T. Photosystem II: The machinery of photosynthetic water splitting. PHOTOSYNTHESIS RESEARCH 2008; 98:53-80. [PMID: 18830685 DOI: 10.1007/s11120-008-9345-7] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 07/29/2008] [Indexed: 05/26/2023]
Abstract
This review summarizes our current state of knowledge on the structural organization and functional pattern of photosynthetic water splitting in the multimeric Photosystem II (PS II) complex, which acts as a light-driven water: plastoquinone-oxidoreductase. The overall process comprises three types of reaction sequences: (1) photon absorption and excited singlet state trapping by charge separation leading to the ion radical pair [Formula: see text] formation, (2) oxidative water splitting into four protons and molecular dioxygen at the water oxidizing complex (WOC) with P680+* as driving force and tyrosine Y(Z) as intermediary redox carrier, and (3) reduction of plastoquinone to plastoquinol at the special Q(B) binding site with Q(A)-* acting as reductant. Based on recent progress in structure analysis and using new theoretical approaches the mechanism of reaction sequence (1) is discussed with special emphasis on the excited energy transfer pathways and the sequence of charge transfer steps: [Formula: see text] where (1)(RC-PC)* denotes the excited singlet state (1)P680* of the reaction centre pigment complex. The structure of the catalytic Mn(4)O(X)Ca cluster of the WOC and the four step reaction sequence leading to oxidative water splitting are described and problems arising for the electronic configuration, in particular for the nature of redox state S(3), are discussed. The unravelling of the mode of O-O bond formation is of key relevance for understanding the mechanism of the process. This problem is not yet solved. A multistate model is proposed for S(3) and the functional role of proton shifts and hydrogen bond network(s) is emphasized. Analogously, the structure of the Q(B) site for PQ reduction to PQH(2) and the energetic and kinetics of the two step redox reaction sequence are described. Furthermore, the relevance of the protein dynamics and the role of water molecules for its flexibility are briefly outlined. We end this review by presenting future perspectives on the water oxidation process.
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Affiliation(s)
- Gernot Renger
- Max Volmer Laboratory for Biophysical Chemistry, Berlin Institute of Technology, Berlin, Germany.
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