Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus

Overview of protein structural and functional folds

This overview provides an illustrated, comprehensive survey of some commonly observed protein‐fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web‐based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein‐structure databases, protein‐structure‐classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon‐diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.

Looking for the minimum common denominator in haem-copper oxygen reductases: towards a unified catalytic mechanism

Haem-copper oxygen reductases are transmembrane protein complexes that reduce dioxygen to water and pump protons across the mitochondrial or periplasmatic membrane, contributing to the transmembrane difference of electrochemical potential. Seven years ago we proposed a classification of these enzymes into three different families (A, B and C), based on the amino acid residues of their proton channels and amino acid sequence comparison, later supported by the so far identified characteristics of the catalytic centre of members from each family. The three families have in common the same general structural fold of the catalytic subunit, which contains the same or analogous prosthetic groups, and proton channels. These observations raise the hypothesis that the mechanisms for dioxygen reduction, proton pumping and the coupling of the two processes may be the same for all these enzymes. Under this hypothesis, they should be performed and controlled by the same or equivalent elements/events, and the identification of retained elements in all families will reveal their importance and may prompt the definition of the enzyme operating mode. Thus, we believe that the search for a minimum common denominator has a crucial importance, and in this article we highlight what is already established for the haem-copper oxygen reductases and emphasize the main questions still unanswered in a comprehensive basis.

Solution structure of At3g28950 from Arabidopsis thaliana

We determined the solution structure of At3g28950 from A. thaliana, a homolog of At5g39720, whose structure we solved earlier. The secondary structure of the 165-aa protein consists of a 5-strand antiparallel beta-barrel domain flanked by two alpha-helices and a 2-strand beta-sheet; an additional free C-terminal alpha-helix extends into solution. Bioinformatic searches and analyses suggest that members of this growing set of structurally related proteins have been recruited to serve a wide variety of functions ranging from gamma-glutamyl cyclotransferase activity to participation in plant responses to chemical and biotic stimuli. Expression of a human homolog is elevated in bladder cancer tissues. Expression patterns for At3g28950 and its Arabidopsis paralogs suggest that each one evolved a different physiological role. The At3g28950 structure was solved as part of a structural genomics effort, and the results demonstrate how such a project can further understanding of genome evolution in addition to sequence-structure and structure-function relationships. Proteins 2008. (c) 2008 Wiley-Liss, Inc.

Carboxyl group functions in the heme-copper oxidases: information from mid-IR vibrational spectroscopy

Carboxyl groups of possible functional importance in bovine and bacterial cytochrome c oxidases (CcO) are reviewed and assessed. A critical analysis is presented of available mid-infrared vibrational data that pertain to these functional carboxyl groups. These data and their interpretations are discussed in relation to current models of the mechanism of proton and electron coupling in the protonmotive CcO superfamily.

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase

Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. The membrane-bound cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water in mitochondria and many bacteria. The energy released in this reaction is conserved by pumping protons across the mitochondrial or bacterial membrane, creating an electrochemical proton gradient that drives production of ATP. A crucial question is how the protons pumped by CcO are prevented from flowing backwards during the process. Here, we show by molecular dynamics simulations that the conserved glutamic acid 242 near the active site of CcO undergoes a protonation state-dependent conformational change, which provides a valve in the pumping mechanism. The valve ensures that at any point in time, the proton pathway across the membrane is effectively discontinuous, thereby preventing thermodynamically favorable proton back-leakage while maintaining an overall high efficiency of proton translocation. Suppression of proton leakage is particularly important in mitochondria under physiological conditions, where production of ATP takes place in the presence of a high electrochemical proton gradient.

Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: structural analysis and role of oxygen transport channels in the heme-Cu oxidases

Cytochrome ba3 is a cytochrome c oxidase from the plasma membrane of Thermus thermophilus and is the preferred terminal enzyme of cellular respiration at low dioxygen tensions. Using cytochrome ba 3 crystals pressurized at varying conditions under Xe or Kr gas, and X-ray data for six crystals, we identify the relative affinities of Xe and Kr atoms for as many as seven distinct binding sites. These sites track a continuous, Y-shaped channel, 18-20 A in length, lined by hydrophobic residues, which leads from the surface of the protein where two entrance holes, representing the top of the Y, connect the bilayer to the a3-CuB center at the base of the Y. Considering the increased affinity of O2 for hydrophobic environments, the hydrophobic nature of the channel, its orientation within the bilayer, its connection to the active site, its uniform diameter, its virtually complete occupation by Xe, and its isomorphous presence in the native enzyme, we infer that the channel is a diffusion pathway for O2 into the dinuclear center of cytochrome ba3. These observations provide a basis for analyzing similar channels in other oxidases of known structure, and these structures are discussed in terms of mechanisms of O2 transport in biological systems, details of CO binding to and egress from the dinuclear center, the bifurcation of the oxygen-in and water-out pathways, and the possible role of the oxygen channel in aerobic thermophily.

Molecular mechanism of proton translocation by cytochrome c oxidase

Cytochrome c oxidase (CcO) is a terminal protein of the respiratory chain in eukaryotes and some bacteria. It catalyzes most of the biologic oxygen consumption on earth done by aerobic organisms. During the catalytic reaction, CcO reduces dioxygen to water and uses the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-linked proton pump. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. Thus, additional extensive studies of CcO by varieties of biophysical and biochemical approaches are involved to shed light on the mechanism of proton translocation. In this review, we summarize the current level of knowledge about CcO, including the latest model developed to explain the CcO proton-pumping mechanism.

Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling

Recent advances in DNA sequencing technologies have provided unprecedented access into the diversity of the microbial world. Herein we use the comparative genomic analysis of microbial genomes and environmental metagenomes coupled with structural modelling to explore the diversity of aerobic respiration in Archaea. We focus on the heme-copper oxidoreductase superfamily which is responsible for catalyzing the terminal reaction in aerobic respiration-the reduction of molecular oxygen to water. Sequence analyses demonstrate that there are at least eight heme-copper oxygen reductase families: A-, B-, C-, D-, E-, F-, G-, and H-families. Interestingly, five of these oxygen reductase families (D-, E-, F-, G-, and H-families) are currently found exclusively in Archaea. We review the structural properties of all eight families focusing on the members found within Archaea. Structural modelling coupled with sequence analysis suggests that many of the oxygen reductases identified from thermophilic Archaea have modified proton channel properties compared to the currently studied mesophilic bacterial oxygen reductases. These structural differences may be due to adaptation to the specific environments in which these enzymes function. We conclude with a brief analysis of the phylogenetic distribution and evolution of Archaeal heme-copper oxygen reductases.

Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases?

A comprehensive study of the thermodynamic redox behavior of the hemes of the ba3 enzyme from Thermus thermophilus, a B-type heme-copper oxygen reductase, is presented. This enzyme, in contrast to those having a single type of heme, allows the B- and A-type hemes to be monitored separately by visible spectroscopy and the reduction potential of each heme to be determined unequivocally. The relative order of the midpoint reduction potentials of each center changed in the pH range from 6 to 8.4, and both hemes present a significant redox-Bohr effect. For instance, at pH 7, the midpoint reduction potentials of the hemes B and A3 are 213 mV and 285 mV, respectively, whereas at pH 8.4, the order is reversed: 246 mV for heme B and 199 mV for heme A3. The existence of redox anticooperativity was established by introducing a redox interaction parameter in a model of pairwise interacting redox centers.

An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus

Past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. Described here is a successful application of this approach to the integral membrane protein Thermus thermophilus cytochrome ba(3) oxidase. Two mutant forms of this enzyme (I-K258R and I-K258R/II-E4Q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. These mutant proteins had greatly shortened crystallization times, decreasing from approximately 30 d for the wild type to 1-3 d for the mutants, and crystallization was highly reproducible. Native-like proteins crystallize in space group P4(3)2(1)2, whereas the mutant proteins crystallize in space group P4(1)2(1)2 with a different packing arrangement. Crystals of the P4(3)2(1)2 form occasionally diffracted to 2.4-2.3 A resolution following controlled dehydration, while those of the P4(1)2(1)2 form routinely diffracted to between 3.0 and 2.6 A for crystals that had been cryoprotected but not dehydrated.

Spectroscopic study on the communication between a heme a3 propionate, Asp399 and the binuclear center of cytochrome c oxidase from Paracoccus denitrificans

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.

Fourier transform infrared characterization of a CuB-nitrosyl complex in cytochrome ba3 from Thermus thermophilus: relevance to NO reductase activity in heme-copper terminal oxidases

The two heme-copper terminal oxidases of Thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (NO) to nitrous oxide (N2O) [Giuffre, A.; Stubauer, G.; Sarti, P.; Brunori, M.; Zumft, W. G.; Buse, G.; Soulimane, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14718-14723]. While it is well-established that NO binds to the reduced heme a3 to form a low-spin heme {FeNO}7 species, the role CuB plays in the binding of the second NO remains unclear. Here we present low-temperature FTIR photolysis experiments carried out on the NO complex formed by addition of NO to fully reduced cytochrome ba3. Low-temperature UV-vis, EPR, and RR spectroscopies confirm the binding of NO to the heme a3 and the efficiency of the photolysis at 30 K. The nu(NO) modes from the light-induced FTIR difference spectra are isolated from other perturbed vibrations using 15NO and 15N18O. The nu(N-O)a3 is observed at 1622 cm-1, and upon photolysis, it is replaced by a new nu(N-O) at 1589 cm-1 assigned to a CuB-nitrosyl complex. This N-O stretching frequency is more than 100 cm-1 lower than those reported for Cu-NO models with three N-ligands and for CuB+-NO in bovine aa3. Because the UV-vis and RR data do not support a bridging configuration between CuB and heme a3 for the photolyzed NO, we assign the exceptionally low nu(NO) to an O-bound (eta1-O) or a side-on (eta2-NO) CuB-nitrosyl complex. From this study, we propose that, after binding of a first NO molecule to the heme a3 of fully reduced Tt ba3, the formation of an N-bound {CuNO}11 is prevented, and the addition of a second NO produces an O-bond CuB-hyponitrite species bridging CuB and Fea3. In contrast, bovine cytochrome c oxidase is believed to form an N-bound CuB-NO species; the [{FeNO}7{CuNO}11] complex is suggested here to be an inhibitory complex.

Characterization of the phenoxyl radical in model complexes for the Cu(B) site of cytochrome c oxidase: steady-state and transient absorption measurements, UV resonance raman spectroscopy, EPR spectroscopy, and DFT calculations for M-BIAIP

Physicochemical properties of the covalently cross-linked tyrosine-histidine-Cu(B) (Tyr-His-Cu(B)) unit, which is a minimal model complex [M(II)-BIAIPBr]Br (M = Cu(II), Zn(II)) for the Cu(B) site of cytochrome c oxidase, were investigated with steady-state and transient absorption measurements, UV resonance Raman (UVRR) spectroscopy, X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy, and DFT calculations. The pH dependency of the absorption spectra reveals that the pK(a) of the phenolic hydroxyl is ca. 10 for the Cu(II) model complex (Cu(II)-BIAIP) in the ground state, which is similar to that of p-cresol (tyrosine), contrary to expectations. The bond between Cu(II) and nitrogen of cross-linked imidazole cleaves at pH 4.9. We have successfully obtained UVRR spectra of the phenoxyl radical form of BIAIPs and have assigned bands based on the previously reported isotope shifts of Im-Ph (2-(1-imidazoyl)-4-methylphenol) (Aki, M.; Ogura, T.; Naruta, Y.; Le, T. H.; Sato, T.; Kitagawa, T. J. Phys. Chem. A 2002, 106, 3436-3444) in combination with DFT calculations. The upshifts of the phenoxyl vibrational frequencies for 8a (C-C stretching), 7a' (C-O stretching), and 19a, and the Raman-intensity enhancements of 19b, 8b, and 14 modes indicate that UVRR spectra are highly sensitive to imidazole-phenol covalent linkage. Both transient absorption measurements and EPR spectra suggest that the Tyr-His-Cu(B) unit has only a minor effect on the electronic structure of the phenoxyl radical form, although our experimental results appear to indicate that the cross-linked Tyr radical exhibits no EPR. The role of the Tyr-His-Cu(B) unit in the enzyme is discussed in terms of the obtained spectroscopic parameters of the model complex.

Cytochrome bd from Azotobacter vinelandii: Evidence for High-Affinity Oxygen Binding

Cytochrome bd from Azotobacter vinelandii is a respiratory quinol oxidase that is highly efficient in reducing intracellular oxygen concentration, thus enabling nitrogen fixation under ambient aerobic conditions. Equilibrium measurements of O2 binding to ferrous heme d in the one-electron-reduced form of the A. vinelandii enzyme give Kd(O2) = 0.5 microM, close to the value for the Escherichia coli cytochrome bd (ca. 0.3 microM); thus, both enzymes have similar, high affinity for oxygen. The reaction of the A. vinelandii cytochrome bd in the one-electron-reduced and fully reduced states with O2 is extremely fast approaching the diffusion-controlled limit in water. In the fully reduced state, the rate of O2 binding depends linearly on the oxygen concentration consistently with a simple, single-step process. In contrast, in the one-electron-reduced state the rate of oxygen binding is hyperbolic, implying a more complex binding pattern. Two possible explanations for the saturation kinetics are considered: (A) There is a spectroscopically silent prebinding of oxygen to an unidentified low-affinity saturatable site followed by the oxygen transfer to heme d. (B) Oxygen binding to heme d requires an "activated" state of the enzyme in which an oxygen channel connecting heme d to the bulk is open. This channel is permanently open in the fully reduced enzyme (hence no saturation behavior) but flickers between the open and closed states in the one-electron-reduced enzyme.

Probing the Environment of CuB in Heme−Copper Oxidases

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.

Comparative Genomics and Site-Directed Mutagenesis Support the Existence of Only One Input Channel for Protons in the C-Family (cbb3 Oxidase) of Heme−Copper Oxygen Reductases

Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.

Mechanism and energetics of proton translocation by the respiratory heme-copper oxidases

Recent time-resolved optical and electrometric experiments have provided a sequence of events for the proton-translocating mechanism of cytochrome c oxidase. These data also set limits for the mechanistic, kinetic, and thermodynamic parameters of the proton pump, which are analysed here in some detail. The analysis yields limit values for the pK of the "pump site", its modulation during the proton-pumping process, and suggests its identity in the structure. Special emphasis is made on side-reactions that may short-circuit the pump, and the means by which these may be avoided. We will also discuss the most prominent proton pumping mechanisms proposed to date in relation to these data.

Kinetics of the electron transfer reaction of Cytochrome c 552 adsorbed on biomimetic electrode studied by time-resolved surface-enhanced resonance Raman spectroscopy and electrochemistry

Cytochrome c (552) (Cyt-c (552)) and its redox partner ba ( 3 )-oxidase from Thermus thermophilus possess structural differences compared with Horse heart cytochrome c (cyt-c)/cytochrome c oxidase (CcO) system, where the recognition between partners and the electron transfer (ET) process is initiated via electrostatic interactions. We demonstrated in a previous study by surface-enhanced resonance Raman (SERR) spectroscopy that roughened silver electrodes coated with uncharged mixed self-assembled monolayers HS-(CH(2))( n )-CH(3)/HS-(CH(2))( n + 1)-OH 50/50, n = 5, 10 or 15, was a good model to mimic the Cyt-c (552) redox partner. All the adsorbed molecules are well oriented on such biomimetic electrodes and transfer one electron during the redox process. The present work focuses on the kinetic part of the heterogeneous ET process of Cyt-c (552) adsorbed onto electrodes coated with such mixed SAMs of different alkyl chain length. For that purpose, two complementary methods were combined. Firstly cyclic voltammetry shows that the ET between the adsorbed Cyt-c (552) and the biomimetic electrode is direct and reversible. Furthermore, it allows the estimation of both the density surface coverage of adsorbed Cyt-c (552) and the kinetic constants values. Secondly, time-resolved SERR (TR-SERR) spectroscopy showed that the ET process occurs without conformational change of the Cyt-c (552) heme group and allows the determination of kinetic constants. Results show that the kinetic constant values obtained by TR-SERR spectroscopy could be compared to those obtained from cyclic voltammetry. They are estimated at 200, 150 and 40 s(-1) for the ET of Cyt-c (552) adsorbed onto electrodes coated with mixed SAMs HS-(CH(2))( n )-CH(3)/HS-(CH(2))( n + 1)-OH 50/50, n = 5, 10 or 15, respectively.

Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins

Nitric oxide (NO) plays an important role in cell signalling and in the mammalian immune response to infection. On its own, NO is a relatively inert radical, and when it is used as a signalling molecule, its concentration remains within the picomolar range. However, at infection sites, the NO concentration can reach the micromolar range, and reactions with other radical species and transition metals lead to a broad toxicity. Under aerobic conditions, microorganisms cope with this nitrosative stress by oxidizing NO to nitrate (NO3−). Microbial hemoglobins play an essential role in this NO-detoxifying process. Under anaerobic conditions, detoxification occurs via a 2-electron reduction of two NO molecules to N2O. In many bacteria and archaea, this NO-reductase reaction is catalyzed by diiron proteins. Despite the importance of this reaction in providing microorganisms with a resistance to the mammalian immune response, its mechanism remains ill-defined. Because NO is an obligatory intermediate of the denitrification pathway, respiratory NO reductases also provide resistance to toxic concentrations of NO. This family of enzymes is the focus of this review. Respiratory NO reductases are integral membrane protein complexes that contain a norB subunit evolutionarily related to subunit I of cytochrome c oxidase (Cc O). NorB anchors one high-spin heme b3 and one non-heme iron known as FeB, i.e ., analogous to CuB in Cc O. A second group of diiron proteins with NO-reductase activity is comprised of the large family of soluble flavoprotein A found in strict and facultative anaerobic bacteria and archaea. These soluble detoxifying NO reductases contain a non-heme diiron cluster with a Fe–Fe distance of 3.4 Å and are only briefly mentioned here as a promising field of research. This article describes possible mechanisms of NO reduction to N2O in denitrifying NO-reductase (NOR) proteins and critically reviews recent experimental results. Relevant theoretical model calculations and spectroscopic studies of the NO-reductase reaction in heme/copper terminal oxidases are also overviewed.

A pathway for protons in nitric oxide reductase from Paracoccus denitrificans

Nitric oxide reductase (NOR) from P. denitrificans is a membrane-bound protein complex that catalyses the reduction of NO to N(2)O (2NO+2e(-)+2H(+)-->N(2)O+H(2)O) as part of the denitrification process. Even though NO reduction is a highly exergonic reaction, and NOR belongs to the superfamily of O(2)-reducing, proton-pumping heme-copper oxidases (HCuOs), previous measurements have indicated that the reaction catalyzed by NOR is non-electrogenic, i.e. not contributing to the proton electrochemical gradient. Since electrons are provided by donors in the periplasm, this non-electrogenicity implies that the substrate protons are also taken up from the periplasm. Here, using direct measurements in liposome-reconstituted NOR during reduction of both NO and the alternative substrate O(2), we demonstrate that protons are indeed consumed from the 'outside'. First, multiple turnover reduction of O(2) resulted in an increase in pH on the outside of the NOR-vesicles. Second, comparison of electrical potential generation in NOR-liposomes during oxidation of the reduced enzyme by either NO or O(2) shows that the proton transfer signals are very similar for the two substrates proving the usefulness of O(2) as a model substrate for these studies. Last, optical measurements during single-turnover oxidation by O(2) show electron transfer coupled to proton uptake from outside the NOR-liposomes with a tau=15 ms, similar to results obtained for net proton uptake in solubilised NOR [U. Flock, N.J. Watmough, P. Adelroth, Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen, Biochemistry 44 (2005) 10711-10719]. NOR must thus contain a proton transfer pathway leading from the periplasmic surface into the active site. Using homology modeling with the structures of HCuOs as templates, we constructed a 3D model of the NorB catalytic subunit from P. denitrificans in order to search for such a pathway. A plausible pathway, consisting of conserved protonatable residues, is suggested.

Tryptophan-scanning mutagenesis in the alphaM3 transmembrane domain of the muscle-type acetylcholine receptor. A spring model revealed

Membrane proteins constitute a large fraction of all proteins, yet very little is known about their structure and conformational transitions. A fundamental question that remains obscure is how protein domains that are in direct contact with the membrane lipids move during the conformational change of the membrane protein. Important structural and functional information of several lipid-exposed transmembrane domains of the acetylcholine receptor (AChR) and other ion channel membrane proteins have been provided by the tryptophan-scanning mutagenesis. Here, we use the tryptophan-scanning mutagenesis to monitor the conformational change of the alphaM3 domain of the muscle-type AChR. The perturbation produced by the systematic tryptophan substitution along the alphaM3 domain were characterized through two-electrode voltage clamp and 125I-labeled alpha-bungarotoxin binding. The periodicity profiles of the changes in AChR expression (closed state) and ACh EC50 (open-channel state) disclose two different helical structures; a thinner-elongated helix for the closed state and a thicker-shrunken helix for the open-channel state. The existence of two different helical structures suggest that the conformational transition of the alphaM3 domain between both states resembles a spring motion and reveals that the lipid-AChR interface plays a key role in the propagation of the conformational wave evoked by agonist binding. In addition, the present study also provides evidence about functional and structural differences between the alphaM3 domains of the Torpedo and muscle-type receptors AChR.

The inhibitory binding site(s) of Zn2+in cytochromecoxidase

EXAFS analysis of Zn binding site(s) in bovine-heart cytochrome c oxidase and characterization of the inhibitory effect of internal zinc on respiratory activity and proton pumping of the liposome reconstituted oxidase are presented. EXAFS identifies tetrahedral coordination site(s) for Zn(2+) with two N-histidine imidazoles, one N-histidine imidazol or N-lysine and one O-COOH (glutamate or aspartate), possibly located at the entry site of the proton conducting D pathway in the oxidase and involved in inhibition of the oxygen reduction catalysis and proton pumping by internally trapped zinc.

Three-dimensional crystallization of membrane proteins

Although the examination of the protein data bank reveals an important backlog in the number of three-dimensional structures of membrane proteins, several recent successes are serving as preludes to what will become a very prosperous decade in this field. Systematic investigations of various factors affecting the stability of membrane proteins, as well as their potential to crystallize three dimensionally, have paved the way for such achievements. The importance of the role of detergents both at the level of purification and crystallization is now well established. In addition, the recognition of the protein-detergent complex as the entity to crystallize, as well as the understanding of its physical-chemical properties and discovery of factors affecting these, have permitted the design of better crystallization strategies. As a consequence of the various efforts in the field, new crystallization methods for membrane proteins are being implemented. These have already been successful and are expected to contribute significantly to the future successes. This chapter will review some basic principles in membrane protein crystallization and give an overview of the current state of the art in the field. Some practical guidelines to help the novice approach the problem of membrane protein crystallization from the initial step of protein purification to crystallogenesis will also be given.

Metals in membranes

In this critical review we discuss recent advances in understanding the modes of interaction of metal ions with membrane proteins, including channels, pumps, transporters, ATP-binding cassette proteins, G-protein coupled receptors, kinases and respiratory enzymes. Such knowledge provides a basis for elucidating the mechanism of action of some classes of metallodrugs, and a stimulus for the further exploration of the coordination chemistry of metal ions in membranes. Such research offers promise for the discovery of new drugs with unusual modes of action. The article will be of interest to bioinorganic chemists, chemical biologists, biochemists, pharmacologists and medicinal chemists. (247 references).

A new dinuclear heme-copper complex derived from functionalized protoporphyrin IX

A new biomimetic model for the heterodinuclear heme/copper center of respiratory oxidases is described. It is derived from iron(III) protoporphyrin IX by covalent attachment of a Gly-L-His-OMe residue to one propionic acid substituent and an amino-bis(benzimidazole) residue to the other propionic acid substituent of the porphyrin ring, yielding the Fe(III) complex 1, and subsequent addition of a copper(II) or copper(I) ion, according to needs. The fully oxidized Fe(III)/Cu(II) complex, 2, binds azide more strongly than 1, and likely contains azide bound as a bridging ligand between Fe(III) and Cu(II). The two metal centers also cooperate in the reaction with hydrogen peroxide, as the peroxide adducts obtained at low temperature for 1 and 2 display different optical features. Support to this interpretation comes from the investigation of the peroxidase activity of the complexes, where the activation of hydrogen peroxide has been studied through the phenol coupling reaction of p-cresol. Here the presence of Cu(II) improves the catalytic performance of complex 2 with respect to 1 at acidic pH, where the positive charge of the Cu(II) ion is useful to promote O-O bond cleavage of the iron-bound hydroperoxide, but it depresses the activity at basic pH because it can stabilize an intramolecular hydroxo bridge between Fe(III) and Cu(II). The reactivity to dioxygen of the reduced complexes has been studied at low temperature starting from the carbonyl adducts of the Fe(II) complex, 3, and Fe(II)/Cu(I) complex, 4. Also in this case the adducts derived from the Fe(II) and Fe(II)/Cu(I) complexes, that we formulate as Fe(III)-superoxo and Fe(III)/Cu(II)-peroxo exhibit slightly different spectral properties, showing that the copper center participates in a weak interaction with the dioxygen moiety.

Synthesis and structural characterization of cross-linked histidine–phenol Cu(ii) complexes as cytochrome c oxidase active site models

Tridentate cross-linked histidine-phenol Cu(ii) ether and ester complexes, chemical analogs of the active site of several heme-copper oxidases, have been synthesized and crystallized.

Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases

In the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the reduction of O2 to proton pumping, generating an electrochemical gradient. There are three distinct families of heme-copper oxygen reductases: A, B, and C types. The A- and B-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine has recently been predicted by molecular modeling to be located within a different transmembrane helix in comparison to the A- and B-type oxygen reductases. In this work, Fourier-transform mass spectrometry is used to show that the predicted tyrosine forms a histidine-tyrosine cross-linked cofactor in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique cofactor in all three families of proton-pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism and that the histidine-tyrosine cofactor may be a required component for proton pumping.

Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism

L-Amino acid oxidase is a dimeric glycosylated flavoenzyme, a major constituent of the venom-from the snake Calloselasma rhodostoma. The enzyme exhibits apoptosis inducing effects as well as antibacterial and anti-HIV activities. The structure of l-amino acid oxidase with its substrate (L-phenylalanine) has been refined to a resolution of 1.8 A. The complex structure reveals the substrate bound to the reduced flavin (FADred). Alternative conformations for the key residues His223 and Arg322 are evident, suggesting a dynamic active site. Furthermore, conformational changes are apparent for the isoalloxazine ring; the three-ring system exhibits more bending around the N5-N10 axis compared to the oxidized flavin. The implications of the observed dynamics on the mechanism of catalysis are discussed. Inspection of buried surfaces in the enzyme reveals a Y-shaped channel system extending from the external surface of the protein to the active site. One portion of this channel may serve as the entry path for O2 during the oxidative half-reaction. The second region, separated from the proposed O2 channel by the N terminus (residues 8-16) of the protein, may play a role in H2O2 release. Interestingly, the latter portion of the channel would direct the H2O2 product to the exterior surface of the protein, near the glycan moiety, thought to anchor the enzyme to the host cell. This channel location may explain the ability of the enzyme to localize H2O2 to the targeted cell and thus induce the apoptotic effect.

A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power

The evolution of carnivorous plants has been modeled as a selective tradeoff between photosynthetic costs and benefits in nutrient-poor habitats. Although possibly applicable for pitfall and flypaper trappers, more variables may be required for active trapping systems. Bladderwort (utricularia) suction traps react to prey stimuli with an extremely rapid release of elastic instability. Trap setting requires considerable energy to engage an active ion transport process whereby water is pumped out through the thin bladder walls to create negative internal pressure. Accordingly, empirical estimates have shown that respiratory rates in bladders are far greater than in leafy structures. Cytochrome C oxidase (COX) is a multi-subunit enzyme that catalyzes the respiratory reduction of oxygen to water and couples this reaction to translocation of protons, generating a transmembrane electrochemical gradient that is used for the synthesis of adenosine triphosphate (ATP). We have previously demonstrated that two contiguous cysteine residues in helix 3 of COX subunit I (COX I) have evolved under positive Darwinian selection. This motif, absent in approximately 99.9 % of databased COX I proteins from eukaryotes, Archaea, and Bacteria, lies directly at the docking point of COX I helix 3 and cytochrome C. Modeling of bovine COX I suggests the possibility that a vicinal disulfide bridge at this position could cause premature helix termination. The helix 3-4 loop makes crucial contacts with the active site of COX, and we postulate that the C-C motif might cause a conformational change that decouples (or partly decouples) electron transport from proton pumping. Such decoupling would permit bladderworts to optimize power output (which equals energy times rate) during times of need, albeit with a 20 % reduction in overall energy efficiency of the respiratory chain. A new model for the evolution of bladderwort carnivory is proposed that includes respiration as an additional tradeoff parameter.

Single-electron photoreduction of the PM intermediate of cytochrome c oxidase

The P(M)-->F transition of the catalytic cycle of cytochrome c oxidase from bovine heart was investigated using single-electron photoreduction and monitoring the subsequent events using spectroscopic and electometric techniques. The P(M) state of the oxidase was generated by exposing the oxidized enzyme to CO plus O2. Photoreduction results in rapid electron transfer from heme a to oxoferryl heme a3 with a time constant of about 0.3 ms, as indicated by transients at 605 nm and 580 nm. This rate is approximately 5-fold more rapid than the rate of electron transfer from heme a to heme a3 in the F-->O transition, but is significantly slower than formation of the F state from the P(R) intermediate in the reaction of the fully reduced enzyme with O2 to form state F (70-90 micros). The approximately 0.3 ms P(M)-->F transition is coincident with a rapid photonic phase of transmembrane voltage generation, but a significant part of the voltage associated with the P(M)-->F transition is generated much later, with a time constant of 1.3 ms. In addition, the P(M)-->F transition of the R. sphaeroides oxidase was also measured and also was shown to have two phases of electrogenic proton transfer, with tau values of 0.18 and 0.85 ms.

The menaquinol-oxidizing cytochrome bc complex from Thermus thermophilus: Protein domains and subunits

A recently resolved respiratory complex III, isolated from the extreme thermophile Thermus thermophilus, is discussed in terms of cofactor and subunit composition, and with respect to the origin of its protein modules. The four polypeptides, encoded by a single operon, share general homologies to canonical complexes both of the bc and b6f type, but exhibit some unexpected features as well. Evidence for high thermostability of the isolated protein and for its quinol substrate specificity is derived from EPR and kinetic measurements. A functional integration of this complex into an aerobic electron transfer scheme, connecting known dehydrogenase activities to the terminal oxidase branches of Thermus is outlined, as well as the specific principles of redox protein interactions prevailing at high temperature. Findings from this enzyme are linked to present knowledge on other menaquinol oxidizing bc complexes.

Design principles of proton-pumping haem-copper oxidases

Transmembrane electrochemical proton gradients are used to store free energy in biological systems, and to drive the synthesis of biomolecules and transmembrane transport. These gradients are maintained by membrane-bound proton transporters that employ free energy provided by, for example, electron transfer or light. In recent years, the structures of several membrane proteins involved in proton translocation have been determined, and indicate that both protein-bound water molecules and protonatable amino acid residues play central roles in transmembrane proton conduction. From these structures, in combination with functional studies, have emerged general principles of proton transfer across membranes and control mechanisms for such reactions, in particular with regard to the electron-transfer-driven proton pump cytochrome c oxidase.

Photoreactions of cytochrome C oxidase

The photoreduction of oxidized bovine heart cytochrome c oxidase (CcO) by visible and UV radiation was investigated in the absence and presence of external reagents. In the former case, the quantum yields for direct photoreduction of heme A (heme a + heme a(3)) were 2.6 +/- 0.5 x 10(-3), 4 +/- 1 x 10(-4), and 4 +/- 2 x 10(-6) with pulsed laser irradiation at 266, 355 and 532 nm, respectively. Within experimental uncertainty, the quantum yields did not depend on pulse energy, implying that the mechanism is monophotonic. Irradiation with 355 nm light resulted in spectral changes similar to those produced independently by reduction with dithionite, whereby the low-spin heme a and Cu(A) are reduced first. Extended illumination at 355 and 532 nm yielded substantial amounts of reduced heme a(3). Heme decomposition was noted with 266 nm light. In the presence of formate and cyanide ions, which bind at the binuclear heme a(3)/copper center in CcO, irradiation at 355 nm caused selective reduction of only the low-spin heme a and Cu(A). The addition of ferrioxalate ion dramatically increased the efficiency of cytochrome c oxidase photoreduction. The quantum efficiency for heme A reduction was found to be near unity, significantly greater than for other known methods of photoreduction. The active reductant is most likely ferrous iron, and its reduction of the enzyme is thermodynamically driven by the reformation of ferrioxalate in the presence of excess oxalate ion. Other metalloenzymes with redox potentials similar to those of cytochrome c oxidase should be amenable to indirect photoreduction by this method.

Characterization and redox properties of cytochrome c552 from Thermus thermophilus adsorbed on different self-assembled thiol monolayers, used to model the chemical environment of the redox partner

The structure of cytochrome c552 (Cyt-c552) from Thermus thermophilus shows many differences to other c-type cytochromes. The rich lysine domain close to the heme does not exist in this cytochrome, allowing us to postulate that the interaction with its redox partner must be different to the cytochrome c/cytochrome c oxidase interaction. We report a study of Cyt-c552 adsorbed on self-assembled monolayers (SAMs) of functionalized alkanethiols used to mimic the chemical properties of its redox partner (ba3-oxydase). Hydrophilic (-COOH), polar (-OH), hydrophobic (-CH3), and mixed (-OH/-CH3) SAMs grafted on roughened silver electrodes were characterized by X-ray photoelectron spectroscopy. Surface enhanced resonance Raman spectroscopy (SERRS) was employed to determine the structure and the redox properties (E degrees and number of transferred electron) of the heme of Cyt-c552 adsorbed on roughened silver electrodes coated by the different SAMs. The surface that most closely models the environment of the ba3-oxidase is a mixed SAM formed by 50% polar [Ag-(CH2)5-CH2OH] and 50% hydrophobic [Ag-(CH2)5-CH3] alkanethiols. Only the native form B1(6cLS) of Cyt-c552 is detected by SERRS when the protein is adsorbed on such a surface that promotes a protein orientation favorable for the electron transfer (number of transferred electron = 1). We shall discuss the differences and similarities of the electron-transfer mechanism of Cyt-c552 compared to cyt-c.

Sequence analysis of the cbb3 oxidases and an atomic model for the Rhodobacter sphaeroides enzyme

The cbb3-type oxidases are members of the heme-copper oxidase superfamily, distant by sequence comparisons, but sharing common functional characteristics. To understand the minimal common properties of the superfamily, and to learn about cbb3-type oxidases specifically, we have analyzed a wide set of heme-copper oxidase sequences and built a homology model of the catalytic subunit of the cbb3 oxidase from Rhodobacter sphaeroides. We conclude that with regard to the active site surroundings, the cbb3 oxidases greatly resemble the structurally known oxidases, while major differences are found in three segments: the additional N-terminal stretch of ca. 60 amino acids, the segment following helix 3 to the end of helix 5, and the C-terminus from helix 11 onward. The conserved core contains the active site tyrosine and also an analogue of the K-channel of proton transfer, but centered on a well-conserved histidine in the lower part of helix 7. Modeling the variant parts of the enzyme suggests that two periplasmic loops (between helices 3 and 4 and between helices 11 and 12) could interact with each other as a part of the active site structure and might have an important role in proton pumping. An analogue of the D-channel is not found, but an alternative channel might form around helix 9. A preliminary packing model of the trimeric enzyme is also presented.

Proton pumping mechanism of bovine heart cytochrome c oxidase

X-ray structures of bovine heart cytochrome c oxidase at 1.8/1.9 A resolution in the oxidized/reduced states exhibit a redox coupled conformational change of an aspartate located near the intermembrane surface of the enzyme. The alteration of the microenvironment of the carboxyl group of this aspartate residue indicates the occurrence of deprotonation upon reduction of the enzyme. The residue is connected with the matrix surface of the enzyme by a hydrogen-bond network that includes heme a via its propionate and formyl groups. These X-ray structures provide evidence that proton pumping occurs through the hydrogen bond network and is driven by the low spin heme. The function of the aspartate is confirmed by mutation of the aspartate to asparagine. Although the amino acid residues of the hydrogen bond network and the structures of the low spin heme peripheral groups are not completely conserved amongst members of the heme-copper terminal oxidase superfamily, the existence of low spin heme and the hydrogen bond network suggests that the low spin heme provides the driving element of the proton-pumping process.

Reduction of dioxygen by enzymes containing copper

The reduction of dioxygen is a key step in many important biological processes including respiration and ligand oxidation. Enzymes containing either iron or copper or, indeed, both elements are often involved in this process, yet the catalytic mechanisms employed are not fully understood at the current time despite intensive biochemical, spectroscopic and structural studies. The aim of this article is to highlight the current structural knowledge regarding the process of dioxygen reduction using examples of copper-containing enzymes.

Transmembrane proton translocation by cytochrome c oxidase

Respiratory heme-copper oxidases are integral membrane proteins that catalyze the reduction of molecular oxygen to water using electrons donated by either quinol (quinol oxidases) or cytochrome c (cytochrome c oxidases, CcOs). Even though the X-ray crystal structures of several heme-copper oxidases and results from functional studies have provided significant insights into the mechanisms of O2 -reduction and, electron and proton transfer, the design of the proton-pumping machinery is not known. Here, we summarize the current knowledge on the identity of the structural elements involved in proton transfer in CcO. Furthermore, we discuss the order and timing of electron-transfer reactions in CcO during O2 reduction and how these reactions might be energetically coupled to proton pumping across the membrane.

Filling the catalytic site of cytochrome c oxidase with electrons. Reduced CuB facilitates internal electron transfer to heme a3

In the reductive phase of its catalytic cycle, cytochrome c oxidase receives electrons from external electron donors. Two electrons have to be transferred into the catalytic center, composed of heme a(3) and Cu(B), before reaction with oxygen takes place. In addition, this phase of catalysis appears to be involved in proton translocation. Here, we report for the first time the kinetics of electron transfer to both heme a(3) and Cu(B) during the transition from the oxidized to the fully reduced state. The state of reduction of both heme a(3) and Cu(B) was monitored by a combination of EPR spectroscopy, the rapid freeze procedure, and the stopped-flow method. The kinetics of cytochrome c oxidase reduction by hexaamineruthenium under anaerobic conditions revealed that the rate-limiting step is the initial electron transfer to the catalytic site that proceeds with apparently identical rates to both heme a(3) and Cu(B). After Cu(B) is reduced, electron transfer to oxidized heme a(3) is enhanced relative to the rate of entry of the first electron.

Nitric oxide and the respiratory enzyme

Available information on the molecular mechanisms by which nitric oxide (NO) controls the activity of the respiratory enzyme (cytochrome-c-oxidase) is reviewed. We report that, depending on absolute electron flux, NO at physiological concentrations reversibly inhibits cytochrome-c-oxidase by two alternative reaction pathways, yielding either a nitrosyl- or a nitrite-heme a3 derivative. We address a number of hypotheses, envisaging physiological and/or pathological effects of the reactions between NO and cytochrome-c-oxidase.

Electron transfer among the CuA-, heme b- and a3-centers of Thermus thermophilus cytochrome ba3

The 1-methyl-nicotinamide radical (MNA(*)), produced by pulse radiolysis has previously been shown to reduce the Cu(A)-site of cytochromes aa(3), a process followed by intramolecular electron transfer (ET) to the heme a but not to the heme a(3) [Farver, O., Grell, E., Ludwig, B., Michel, H. and Pecht, I. (2006) Rates and equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase. Biophys. J. 90, 2131-2137]. Investigating this process in the cytochrome ba(3) of Thermus thermophilus (Tt), we now show that MNA(*) also reduces Cu(A) with a subsequent ET to the heme b and then to heme a(3), with first-order rate constants 11200 s(-1), and 770 s(-1), respectively. The results provide clear evidence for ET among the three spectroscopically distinguishable centers and indicate that the binuclear a(3)-Cu(B) center can be reduced in molecules containing a single reduction equivalent.