Perfusion‐induced redox differences in cytochrome <i>c</i> oxidase: ATR/FT‐IR spectroscopy

Nyquist, Rebecca M.; Heitbrink, Dirk; Bolwien, Carsten; Wells, Todd A.; Gennis, Robert B.; Heberle, Joachim

doi:10.1016/s0014-5793(01)02769-7

Cited by 63 publications

(91 citation statements)

References 31 publications

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“…Similar, but simpler, changes occur in the same frequency range in redox spectra of CcO from P. denitrificans, Rb. sphaeroides, and Escherichia coli (22)(23)(24) and have been assigned to their E242 equivalent (E278, E286, and E286, respectively). The bovine CcO 1;749 cm −1 component, which also appears in the ferrous state of bovine CcO after CO photolysis, most likely also arises from E242, which undergoes a downshift because of increased H bonding to its immediate environment (25).…”

Section: Resultsmentioning

confidence: 99%

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

Maréchal

Rich

2011

Proc. Natl. Acad. Sci. U.S.A.

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Although internal electron transfer and oxygen reduction chemistry in cytochrome c oxidase are fairly well understood, the associated groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. Several possible pathways have been identified from crystallographic structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle. To date, however, comparisons of atomic structures of different oxidases in different redox or ligation states have not provided a consistent answer as to which pathways are operative or the details of their dynamic changes during catalysis. In order to provide an experimental means to address this issue, FTIR spectroscopy in the 3,560-3,800 cm −1 range has been used to detect weakly H-bonded water molecules in bovine cytochrome c oxidase that might change during catalysis. Full redox spectra exhibited at least four signals at 3,674(+), 3,638(+), 3,620(−), and 3,607(+) cm −1 . A more complex set of signals was observed in spectra of photolysis of the ferrous-CO compound, a reaction that mimics the catalytic oxygen binding step, and their D 2 O and H 2 18 O sensitivities confirmed that they arose from water molecule rearrangements. Fitting with Gaussian components indicated the involvement of up to eight waters in the photolysis transition. Similar signals were also observed in photolysis spectra of the ferrous-CO compound of bacterial CcO from Paracoccus denitrificans. Such water changes are discussed in relation to roles in hydrophilic channels and proton/electron coupling mechanism.energy coupling | mitochondria | respiratory chain | complex IV M itochondrial cytochrome c oxidase (CcO) catalyses electron transfer from cytochrome c to molecular oxygen, conserving the released energy as coupled transmembrane proton transfers. It is a member of a homologous "superfamily" of oxidases that includes diverse bacterial forms; all types in the CcO subgroup contain a common "catalytic core" of subunits I, II, and III with equivalent metal centers of Cu A , heme a. and a binuclear center (BNC) that is formed from heme a 3 and Cu B (1, 2). Structures of bovine mitochondrial (3, 4) and various bacterial (5-7) CcOs have been solved at atomic resolution and show common details in the binuclear heme a 3 ∕Cu B catalytic site, other cofactors, key amino acids, and several unusual structural features. These structural data, coupled with a substantial body of biophysical and spectroscopic studies, have provided detailed information on internal electron transfer and the chemical catalytic cycle of oxygen reduction.Crucially, however, these structural data have not provided a single picture for all forms of CcO of the pathway(s) for coupled proton transfer and, therefore, the interplay between electron transfer/oxygen chemistry and the intraprotein proton transfer reactions that result in proton-motive action. Crystal structures of bacteri...

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Section: Resultsmentioning

confidence: 99%

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

Maréchal

Rich

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…An attenuated total reflection accessory was used with a diamond disc as the internal reflection element (26). 10 l of the protein solution was put on the diamond surface and concentrated by a stream of nitrogen.…”

Section: Sample Preparation-r-pyp Was Heterologously Overexpressed Inmentioning

confidence: 99%

The Two Photocycles of Photoactive Yellow Protein fromRhodobacter sphaeroides

Haker

Hendriks

Stokkum

et al. 2003

Journal of Biological Chemistry

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Photoactive yellow protein (PYP)1 is a photoreceptor that has been found in several purple bacteria (1). The first, and so far best studied example for this group of blue light receptors, was found in Ectothiorhodospira halophila (E-PYP) (2). The chromophore, responsible for the photophysical properties of PYP, is 4-hydroxy-cinnamic acid that is bound to Cys-69 via a thiolester linkage (3, 4). The crystal structure of this small protein, consisting of 125 amino acids, has been solved to 1.4-Å resolution (5) and shows an ␣/␤-fold, which has become the prototype for the folding of the Per-Arnt-Sim domain superfamily (6, 7). In the ground state the chromophore is deprotonated and buried in a hydrophobic pocket of the protein where its negative charge is stabilized via a hydrogen bonding network. Absorption of light induces a photocycle in E-PYP, in which isomerization of the chromophore is the initial step, which leads to the formation of several transient intermediates on the femtosecond to nanosecond timescale (8, 9 (14,15).In contrast to the detailed knowledge available for PYP from E. halophila, other photoactive yellow proteins are biophysically poorly investigated. So far, proteins from three other species were purified and basically characterized: (i) PYP from Rhodospirillum salexigens (16), which shares 71% amino acid sequence identity with E-PYP and has virtually the same ground state absorption spectrum ( max ϭ 445 nm) and similar kinetics of photobleaching and recovery (with time constants for pB formation and pG recovery of 85 s and 210 ms, respectively); (ii) PYP-phytochrome-related protein from Rhodospirillum centenum (17), a hybrid-protein, consisting of 884 amino acids, with an N-terminal PYP domain fused to a central phytochrome-like domain and a C-terminal histidine kinase domain. When heterologously expressed and reconstituted with 4-hydroxy-cinnamic acid, Ppr displays an absorbance maximum at 434 nm and is photoactive; bleaching at 434 nm is accompanied by the initial formation of a red-shifted intermediate with a difference absorption maximum at ϳ470 nm, and subsequently a blue-shifted intermediate is formed with a difference absorption maximum at ϳ330 nm. The recovery to the ground state is biphasic with a fast and a very slow component (lifetimes of 0.21 ms and 46 s, respectively); and (iii) PYP from Rhodobacter sphaeroides (R-PYP), which has been characterized in some more detail (18) and is also the subject of this study.Heterologously expressed R-PYP, reconstituted in vitro with 4-hydroxy-cinnamic acid, is a yellow-colored and photoactive protein (18). The main absorption band with a maximum at 446

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“…Application of spectro-electrochemical cells (47)(48)(49)(50)(51)(52), attenuated total reflection FTIR apparatus (41,42,(53)(54)(55)(56), and a photochemical reduction technique (57-60) enabled us to examine protein structural changes upon reduction of the redox metal centers of respiratory terminal oxidases. Alternatively, photodissociation of CO from the reduced enzyme revealed the local structural change surrounding the heme-copper binuclear center of the E. coli cytochrome bo (61,62).…”

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Redox-induced Protein Structural Changes in Cytochrome bo Revealed by Fourier Transform Infrared Spectroscopy and [13C]Tyr Labeling

Kandori

Nakamura

Yamazaki

et al. 2005

Journal of Biological Chemistry

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Cytochrome bo is a heme-copper terminal ubiquinol oxidase of Escherichia coli under highly aerated growth conditions. Tyr-288 present at the end of the K-channel forms a C ⑀ -N ⑀ covalent bond with one of the Cu B ligand histidines and has been proposed to be an acid-base catalyst essential for the O-O bond cleavage at the Oxyto-P transition of the dioxygen reduction cycle (Uchida, T., Mogi, T., and Kitagawa, T. Cytochrome bo is a four-subunit ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli and belongs to the heme-copper terminal oxidase superfamily (1-3). Subunit I binds all four redox centers, the high affinity ubiquinone binding site (Q H 1 ), low spin heme b, high spin heme o, and Cu B ; the latter two centers form the heme o-Cu B binuclear center. Quinols are oxidized at the low affinity quinol oxidation site (Q L ) in subunit II, and electrons are sequentially transferred through Q H and heme b to the heme o-Cu B binuclear metal center, where dioxygen reduction takes place (4 -10). The two-electron oxidation of ubiquinol-8 at the periplasmic side of the cytoplasmic membrane is coupled to the four-electron reduction of dioxygen at the cytoplasmic side. Accordingly, four chemical protons are apparently translocated from the cytoplasm to the periplasm, generating an electrochemical proton gradient across the membrane. In addition, the enzyme can vectorially translocate four other protons per dioxygen reduction by a pump mechanism (11). Mutagenesis (12-16) and x-ray crystallographic (17-22) studies on the heme-copper terminal oxidases suggest that the D-and K-channels in subunit I are operative during redox-coupled proton pumping (Fig. 1A). Iwata et al. (18) identified two putative proton channels in cytochrome c oxidase from Paracoccus denitrificans, the D-channel characterized by a conserved Asp residue at the entry site and the K-channel characterized by a conserved Lys residue in the middle of the channel. They proposed that the D-channel translocates four pumped protons, whereas the K-channel delivers four chemical protons to the binuclear center (18). However, it is now assumed that the K-channel delivers one or two chemical protons to the binuclear center at the initial reductive phase of dioxygen reduction and that the D-channel translocates all other chemical and pumped protons (12,(25)(26)(27)(28).In the vicinity of the binuclear center, Tyr-288 (the E. coli cytochrome bo numbering: Tyr-280 in the soil bacterium P. denitrificans and Tyr-244 in bovine cytochrome c oxidase) is highly conserved in the SoxMtype terminal oxidase and has been proposed to be involved in dioxygen reduction (25, 26, 29 -32). Upon two-electron reduction of the enzyme, two chemical protons are taken up from the cytoplasm to compensate for an increased negative charge at the binuclear center (12,33), and at least the first proton is delivered to the binuclear center by Tyr-288 at the end of the K-channel (27). If deprotonated at the oxidized (O) state (20), Tyr-288 serves as one of proton acceptors (26). ...

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Perfusion‐induced redox differences in cytochrome c oxidase: ATR/FT‐IR spectroscopy

Cited by 63 publications

References 31 publications

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy

The Two Photocycles of Photoactive Yellow Protein fromRhodobacter sphaeroides

Redox-induced Protein Structural Changes in Cytochrome bo Revealed by Fourier Transform Infrared Spectroscopy and [13C]Tyr Labeling

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