A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability

Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc₁ complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc₁ complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c₁ was found to greatly enhance the interaction between cyt. b and cyt. c₁, and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc₁ complex in an extreme thermal environment.     

Structure–Function of the Cytochrome b6f Complex†

The structure and function of the cytochrome b₆ f complex is considered in the context of recent crystal structures of the complex as an eight subunit, 220 kDa symmetric dimeric complex obtained from the thermophilic cyanobacterium, Mastigocladus laminosus, and the green alga, Chlamydomonas reinhardtii. A major problem confronted in crystallization of the cyanobacterial complex, proteolysis of three of the subunits, is discussed along with initial efforts to identify the protease. The evolution of these cytochrome complexes is illustrated by conservation of the hydrophobic heme‐binding transmembrane domain of the cyt b polypeptide between b₆ f and bc₁ complexes, and the rubredoxin‐like membrane proximal domain of the Rieske [2Fe‐2S] protein. Pathways of coupled electron and proton transfer are discussed in the framework of a modified Q cycle, in which the heme c_n, not found in the bc₁ complex, but electronically tightly coupled to the heme b_n of the b₆ f complex, is included. Crystal structures of the cyanobacterial complex with the quinone analogue inhibitors, NQNO or tridecyl‐stigmatellin, show the latter to be ligands of heme c_n, implicating heme c_n as an n‐side plastoquinone reductase. Existing questions include (a) the details of the shuttle of: (i) the [2Fe‐2S] protein between the membrane‐bound PQH₂ electron/H⁺ donor and the cytochrome f acceptor to complete the p‐side electron transfer circuit; (ii) PQ/PQH₂ between n‐ and p‐sides of the complex across the intermonomer quinone exchange cavity, through the narrow portal connecting the cavity with the p‐side [2Fe‐2S] niche; (b) the role of the n‐side of the b₆ f complex and heme c_n in regulation of the relative rates of noncyclic and cyclic electron transfer. The likely presence of cyclic electron transport in the b₆ f complex, and of heme c_n in the firmicute bc complex suggests the concept that hemes b_n‐c_n define a branch point in bc complexes that can support electron transport pathways that differ in detail from the Q cycle supported by the bc₁ complex.     

Construction of a Triangle‐Shaped Trimer and a Tetrahedron Using an α‐Helix‐Inserted Circular Permutant of Cytochrome c555

Highly‐ordered protein structures have gained interest for future uses for biomaterials. Herein, we constructed a building block protein (BBP) by the circular permutation of the hyperthermostable Aquifex aeolicus cytochrome (cyt) c₅₅₅, and assembled BBP into a triangle‐shaped trimer and a tetrahedron. The angle of the intermolecular interactions of BBP was controlled by cleaving the domain‐swapping hinge loop of cyt c₅₅₅ and connecting the original N‐ and C‐terminal α‐helices with an α‐helical linker. We obtained BBP oligomers up to ≈40 mers, with a relatively large amount of trimers. According to the X‐ray crystallographic analysis of the BBP trimer, the N‐terminal region of one BBP molecule interacted intermolecularly with the C‐terminal region of another BBP molecule, resulting in a triangle‐shaped structure with an edge length of 68 Å. Additionally, four trimers assembled into a unique tetrahedron in the crystal. These results demonstrate that the circular permutation connecting the original N‐ and C‐terminal α‐helices with an α‐helical linker may be useful for constructing organized protein structures.     

Synthesis and Prediction of the Ubiquinol‐cytochrome c Reductase Inhibitory Activity of 3,4‐Dihydroisoquinolines and 2‐Azaspiro[4.5]decanes (Spiropyrrolines)

Isoquinolines rank as the second largest group among the plant alkaloids. Natural isoquinolines and synthetic isoquinoline derivatives exhibit numerous biological activities. In this study, the approaches to synthesis of new 3,4‐dihydroisoquinoline and 2‐azaspiro[4.5]decane (spiropyrroline) derivatives annelated by C(3)─C(4) bonds with a cyclohexyl or cyclopentyl moiety have been developed. In accord with the results of biological activity prediction by the pass software, molecular docking was carried out on the ubiquinol‐cytochrome c reductase (bc₁ complex) model. Compounds 6e and 12a , d were found out as potential Q₀ site inhibitors of the bovine bc₁ complex.     

Characterization of the Cytochrome c Membrane‐Binding Site Using Cardiolipin‐Containing Bicelles with NMR

Cytochrome (cyt) c transports electrons from Complex III to Complex IV in mitochondria. Cyt c is ordinarily anchored to the mitochondrial membrane through interaction with cardiolipin (CL), however its release into the cytosol initiates apoptosis. The cyt c interaction site with CL‐containing bicelles was characterized by NMR spectroscopy. Chemical shift perturbations in cyt c signals upon interaction with bicelles revealed that a relatively wide region, which includes the A‐site, the CXXCH motif, and the N‐ and C‐terminal helices, and contains multiple Lys residues, interacts cooperatively with CL. The specific cyt c–CL interaction increased with increasing CL molecules in the bicelles. The location of the cyt c interaction site for CL was similar to those for Complex III and Complex IV, thus indicating that cyt c recognizes lipids and partner proteins in a similar way. In addition to elucidating the cyt c membrane‐binding site, these results provide insight into the dynamic aspect of cyt c interactions in mitochondria.     

Determination of Cytochrome C with Cellulose – DNA Modified Carbon Paste Electrodes

A sensor for cytochrome c (cyt c) was developed using a carbon paste electrode (CPE) modified with cellulose‐DNA. Cyt c was adsorbed on the cellulose‐DNA modified CPE through the electrostatic interaction between them. Owing to this process, a pair of well‐defined peaks appeared at +48 mV/85 mV (E_pc/E_pa vs. Ag/AgCl). This property of the cellulose‐DNA modified CPE was utilized for the analysis of cyt c in a biological sample. The optimum experimental conditions for analysis were investigated and a calibration plot was obtained between 1.0×10^?4 M and 1.0×10^?6 M (±5% at n=5) at the optimized condition. The detection limit for cyt c at the optimized experimental condition was 5.0×10^?7 M (S/N=3) for 30 min of deposition time with differential pulse voltammetry (DPV). The real sample analysis was carried out with the standard addition method to evaluate the developed method. The content of cyt c in total proteins of 80.0 mg/mL in rat mitocondria fractions was determined to be 0.12 (±0.02) mg/mL.     

Cytochrome c‐Capped Fluorescent Gold Nanoclusters: Imaging of Live Cells and Delivery of Cytochrome c

Cytochrome c‐capped fluorescent gold nanoclusters (Au‐NCs) are used for imaging of live lung and breast cells. Delivery of cytochrome c inside the cells is confirmed by covalently attaching a fluorophore (Alexa Fluor 594) to cytochrome c‐capped Au‐NCs and observing fluorescence from Alexa 594 inside the cell. Mass spectrometry studies suggest that in bulk water, addition of glutathione (GSH) to cytochrome c‐capped Au‐NCs results in the formation of glutathione‐capped Au‐NCs and free apo‐cytochrome c. Thus glutathione displaces cytochrome c as a capping agent. Using confocal microscopy, the emission spectra and decay of Au‐NCs are measured in live cells. From the position of the emission maximum it is shown that the Au‐NCs exist as Au₈ in bulk water and as Au₁₃ inside the cells. Fluorescence resonance energy transfer from cytochrome c–Au‐NC (donor) to Mitotracker Orange (acceptor) indicates that the Au‐NCs localise in the mitochondria of live cells.     

Microscale Crystals of Cytochrome c and Calixarene on Electrodes: Interprotein Electron Transfer between Defined Sites

The assembly of redox proteins on electrodes is an important step in biosensor development. Recently, p‐sulfonato‐calix[4]arene was shown to act as “molecular glue” for the assembly and crystallization of cytochrome c (cyt c). Electrochemical data are presented for microscale cyt c–calixarene crystals grown on self‐assembled monolayers (SAM)‐modified Au electrodes. The crystals were characterized by cyclic voltammetry and exceptionally high concentrations of electroactive cyt c were obtained. The peak currents were found to increase linearly with the square root of the scan rate, thus allowing an evaluation of the rate constant for electron self‐exchange. This study revealed high electroactivity accompanied by fast interprotein electron transfer in crystals, which may have implications for the construction of novel bioelectronic devices.     

Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors

Here we report the discovery of tetracyclic benzothiazepines (BTZs) as highly potent and selective antimalarials along with the identification of the Plasmodium falciparum cytochrome bc₁ complex as the primary functional target of this novel compound class. Investigation of the structure activity relationship within this previously unexplored chemical scaffold has yielded inhibitors with low nanomolar activity. A combined approach employing genetically modified parasites, biochemical profiling, and resistance selection validated inhibition of cytochrome bc₁ activity, an essential component of the parasite respiratory chain and target of the widely used antimalarial drug atovaquone, as the mode of action of this novel compound class. Resistance to atovaquone is eroding the efficacy of this widely used antimalarial drug. Intriguingly, BTZ-based inhibitors retain activity against atovaquone resistant parasites, suggesting this chemical class may provide an alternative to atovaquone in combination therapy.     

Mimicking Tyrosine Phosphorylation in Human Cytochrome c by the Evolved tRNA Synthetase Technique

Phosphorylation of tyrosine 48 of cytochrome c is related to a wide range of human diseases due to the pleiotropic role of the heme‐protein in cell life and death. However, the structural conformation and physicochemical properties of phosphorylated cytochrome c are difficult to study as its yield from cell extracts is very low and its kinase remains unknown. Herein, we report a high‐yielding synthesis of a close mimic of phosphorylated cytochrome c, developed by optimization of the synthesis of the non‐canonical amino acid p‐carboxymethyl‐L ‐phenylalanine (pCMF) and its efficient site‐specific incorporation at position 48. It is noteworthy that the Y48pCMF mutation significantly destabilizes the Fe?Met bond in the ferric form of cytochrome c, thereby lowering the pK_a value for the alkaline transition of the heme‐protein. This finding reveals the differential ability of the phosphomimic protein to drive certain events. This modified cytochrome c might be an important tool to investigate the role of the natural protein following phosphorylation.     

Striking Improvement in Peroxidase Activity of Cytochrome c by Modulating Hydrophobicity of Surface‐Functionalized Gold Nanoparticles within Cationic Reverse Micelles

This work demonstrates a remarkable enhancement in the peroxidase activity of mitochondrial membrane protein cytochrome c (cyt c) by perturbing its tertiary structure in the presence of surface‐functionalised gold nanoparticles (GNPs) within cetyltrimethylammonium bromide (CTAB) reverse micelles. The loss in the tertiary structure of cyt c exposes its heme moiety (which is buried inside in the native globular form), which provides greater substrate (pyrogallol and H₂O₂) accessibility to the reactive heme residue. The surfactant shell of the CTAB reverse micelle in the presence of co‐surfactant (n‐hexanol) exerted higher crowding effects on the interfacially bound cyt c than similar anionic systems. The congested interface led to protein unfolding, which resulted in a 56‐fold higher peroxidase activity of cyt c than that in water. Further perturbation in the protein’s structure was achieved by doping amphiphile‐capped GNPs with varying hydrophobicities in the water pool of the reverse micelles. The hydrophobic moiety on the surface of the GNPs was directed towards the interfacial region, which induced major steric strain at the interface. Consequently, interaction of the protein with the hydrophobic domain of the amphiphile further disrupted its tertiary structure, which led to better opening up of the heme residue and, thereby, superior activity of the cyt c. The cyt c activity in the reverse micelles proportionately enhanced with an increase in the hydrophobicity of the GNP‐capping amphiphiles. A rigid cholesterol moiety as the hydrophobic end group of the GNP strikingly improved the cyt c activity by up to 200‐fold relative to that found in aqueous buffer. Fluorescence studies with both a tryptophan residue (Trp59) of the native protein and the sodium salt of fluorescein delineated the crucial role of the hydrophobicity of the GNP‐capping amphiphiles in improving the peroxidase activity of cyt c by unfolding its tertiary structure within the reverse micelles.     

DNA Interactions of the Functionalized (Mixed Polypyridine)ruthenium(II) Complex Bis(2,2′‐bipyridine‐κN1,κN1′)(methyl dipyrido[3,2‐a : 2′,3′‐c]phenazine‐11‐carboxylate‐κN4,κN5)ruthenium(2+) ([Ru(bpy)2(dppz‐11‐CO2Me)]2+)

A novel polypyridine ligand, dipyrido[3,2‐a:2′,3′‐c]phenazine‐11‐carboxylic acid methyl ester (=dppz‐11‐CO₂Me), and its ruthenium(II) complex, [Ru(bpy)₂(dppz‐11‐CO₂Me)]²⁺ ( 1 ), were synthesized and characterized. The binding properties of this complex to calf‐thymus DNA (CT‐DNA) were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that the complex binds to DNA in an intercalative mode and serves as a molecular ‘light switch’ for DNA. When irradiated at 365 nm, the complex 1 promoted the photocleavage of plasmid pBR‐322 DNA.     

Syntheses,Crystal Structures,and Fluorescence Properties of Two Transition Metal‐Organic Coordination Polymers Based on 4,4′‐Dimethyl‐2,2′‐bipyridine

Two transition metal‐organic coordination polymers, [Mn₂(1,3‐bdc)₂(Me₂bpy)₂] · Me₂bpy ( 1 ) and [Co(4,4′‐oba)(Me₂bpy)] ( 2 ) were hydrothermally synthesized and structurally characterized by elemental analysis, IR spectroscopy, TG, and single‐crystal X‐ray diffraction [1,3‐H₂bdc = benzene‐1,3‐dicarboxylic acid, H₂oba = 4,4′‐oxybis(benzoic acid) Me₂bpy = 4,4′‐dimethyl‐2,2′‐bipyridine]. Compound 1 crystallizes in the orthorhombic system, space group P2₁2₁2₁, with a = 23.371(5), b = 14.419(3), and c = 14.251(3) Å. Compound 2 crystallizes in the monoclinic system, space group P2₁/c, with a = 7.4863(15), b = 18.272(4), c = 16.953(5) Å, and β = 107.44(3)°. The crystal structure of complex 1 is a wave‐like layer with central Mn²⁺ atoms bridged by 1,3‐bdc ligands, whereas the structure of compound 2 presents a ladder chain of hexacoordinate Co²⁺ atoms, in which the metal atoms are bridged by 4,4′‐oba ligands and decorated by Me₂bpy ligands. The two compounds are further extended into 3D supramolecular structures through π–π stacking interactions. Additionally, the compounds show intense fluorescence in solid state at room temperature.     

α‐Tris(2,4‐pentanedionato‐κ2O,O′)chromium(III) at 290 and 110 K: a new δ phase at 110 K

The crystal structure of the title compound, [Cr(C₅H₇O₂)₃], has been determined at 290 and 110 K to provide information on thermal vibrations and disorder. The α polymorph at room temperature has been reported [Morosin (1965). Acta Cryst. 19 , 131–137]. The reinvestigation of this structure, presented here, indicates the presence of weak uninterpretable supercell reflections together with disorder streaks. The discussed structure can thus be considered as an average structure. After cooling to 110 K, a new δ polymorph was found, which is a superstructure of the α polymorph. The space group remains P2₁/c and the phase transition can therefore be considered as klassengleich. The unit‐cell volume increases by a factor of six, resulting in six independent molecules in the asymmetric unit.     

Chromium‐based clinopyroxene‐type germanates NaCrGe2O6 and LiCrGe2O6 at 298 K

The structure analyses of sodium chromium digermanate, NaCrGe₂O₆, (I), and lithium chromium digermanate, LiCrGe₂O₆, (II), provide important structural information for the clinopyroxene family, and form part of our ongoing studies on the phase transitions and magnetic properties of clinopyroxenes. (I) shows C2/c symmetry at 298 K, contains one Na, one Cr (both site symmetry 2 on special position 4e), one Ge and three O‐atom positions (on general positions 8f) and displays the well known clinopyroxene topology. The basic units of the structure of (I) are infinite zigzag chains of edge‐sharing Cr³⁺O₆ octahedra (M1 site), infinite chains of corner‐sharing GeO₄ tetrahedra, connected to the M1 chains by common corners, and Na sites occupying interstitial space. (II) was found to have P2₁/c symmetry at 298 K. The structure contains one Na, one Cr, two distinct Ge and six O‐atom positions, all on general positions 4e. The general topology of the structure of (II) is similar to that of (I); however, the loss of the twofold symmetry makes it possible for two distinct tetrahedral chains, having different conformation states, to exist. While sodium is (6+2)‐fold coordinated, lithium displays a pure sixfold coordination. Structural details are given and chemical comparison is made between silicate and germanate chromium‐based clinopyroxenes.     

4‐Ethynyl‐1,2‐methylenedioxybenzene at 150 K

The title compound, C₉H₆O₂, contains two moderate C—H?O hydrogen bonds. That involving the terminal alkyne gives rise to chains along the b axis. The other hydrogen bond occurs over a centre of symmetry, leading to dimers. The combination of the two interactions gives rise to rings, each comprising six mol­ecules, which are part of infinite sheets in the bc plane.     

Photobiochemical Production of Carbon Monoxide by Thermus thermophilus ba3‐Cytochrome c Oxidase

We report the photobiochemical production of carbon monoxide by a terminal ba₃‐cytochrome c oxidase from T. thermophilus HB8. FTIR and time‐resolved step‐scan FTIR spectroscopies were combined to probe this process and also monitor the concomitant binding of the produced gas to other intact ba₃ molecules forming the ba₃–CO complex. The activation of this mechanism by ba₃‐oxidase under visible excitation raises the question as to whether such a mechanism is physiologically relevant to the extreme environment in which it operates.     

Functionalization of gold electrode surface with heterobifunctional poly(ethylene oxide)s having both mercapto and aldehyde groups

We synthesized heterobifunctional poly(ethylene oxide) (PEO) (α‐formyl‐ω‐mercapto‐PEO; CHO‐PEO₄₀₀‐SH, average molecular weight of PEO part being 400), which had both an aldehyde group as a binding site with amino group of protein and a mercapto group for gold electrode surface. The CHO‐PEO₄₀₀‐SH was adsorbed on a gold electrode surface and cytochrome c (cyt.c) was fixed on this modified electrode. The redox response of covalently immobilized cyt.c was observed on the cyclic voltammetry measurement, showing that CHO‐PEO₄₀₀‐SH can be used as a linker to fix cyt.c on an electrode. Another type of heterobifunctional PEO (α‐formyl‐ω‐(2‐pyridyldithio)‐PEO; CHO‐PEO₃₀₀‐SS‐Py), which had an aldehyde group and a 2‐pyridinethiol (2‐Py) through disulfide bond, was synthesized to form co‐adsorbed monolayer of PEO chain and 2‐Py on an electrode surface. It was expected, due to the spacer with shorter PEO chain and lower surface density, that better redox response of the fixed cyt.c was obtained. However, the redox response of fixed cyt.c was not detected on the CHO‐PEO₃₀₀‐SS‐Py modified gold electrode. Instead, this heterobifunctional PEO was found to function as a good promoter for cyt.c dissolved in phosphate buffer solution. Copyright © 2003 John Wiley & Sons, Ltd.     

Synthesis,biochemical evaluation and computational simulations of new cytochrome bc1 complex inhibitors based on N-(4-aryloxyphenyl) phthalimides

A series of N-(4-aryloxyphenyl)phthalimides were synthesized and identified as new inhibitors of the cytochrome bc1 complex. Furthermore, results obtained from computational simulations indicated that 3e' should bind to the Q_o site of the bc1 complex.     

Di‐9‐anthryl disulfide at 193 K

The title compound, C₂₈H₁₈S₂, crystallizes in the monoclinic space group P2₁/n and the structure shows pseudosymmetry close to the space group C2/c. At 193 K the compound has a long S—S bond of 2.1089 (12) Å and the S atom to anthracene bond distances are 1.776 (3) and 1.770 (2) Å. The C—S—S—C torsion angle is 76.06 (13)°.