Probing protein-cofactor interactions in the terminal oxidases by second derivative spectroscopy: study of bacterial enzymes with cofactor substitutions and heme A model compounds.

Second derivative absorption spectra are reported for the aa3-cytochrome c oxidase from bovine cardiac mitochondria, the aa3-600 ubiquinol oxidase from Bacillus subtilis, the ba3-cytochrome c oxidase from Thermus thermophilis, and the aco-cytochrome c oxidase from Bacillus YN-2000. Together these enzymes provide a range of cofactor combinations that allow us to unequivocally identify the origin of the 450-nm absorption band of the terminal oxidases as the 6-coordinate low-spin heme, cytochrome a. The spectrum of the aco-cytochrome c oxidase further establishes that the split Soret band of cytochrome a, with features at 443 and 450 nm, is common to all forms of the enzyme containing ferrocytochrome a and does not depend on ligand occupancy at the other heme cofactor as previously suggested. To test the universality of this Soret band splitting for 6-coordinate low-spin heme A systems, we have reconstituted purified heme A with the apo forms of the heme binding proteins, hemopexin, histidine-proline-rich glycoprotein and the H64V/V68H double mutant of human myoglobin. All 3 proteins bound the heme A as a (bis)histidine complex, as judged by optical and resonance Raman spectroscopy. In the ferroheme A forms, none of these proteins displayed evidence of Soret band splitting. Heme A-(bis)imidazole in aqueous detergent solution likewise failed to display Soret band splitting. When the cyanide-inhibited mixed-valence form of the bovine enzyme was partially denatured by chemical or thermal means, the split Soret transition of cytochrome a collapsed into a single band at 443 nm.(ABSTRACT TRUNCATED AT 250 WORDS)     

Oxygen and proton pathways in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump, which couples the reduction of oxygen to water to the translocation of protons across the membrane. The recently solved x-ray structures of cytochrome c oxidase permit molecular dynamics simulations of the underlying transport processes. To eventually establish the proton pump mechanism, we investigate the transport of the substrates, oxygen and protons, through the enzyme. Molecular dynamics simulations of oxygen diffusion through the protein reveal a well-defined pathway to the oxygen-binding site starting at a hydrophobic cavity near the membrane-exposed surface of subunit I, close to the interface to subunit III. A large number of water sites are predicted within the protein, which could play an essential role for the transfer of protons in cytochrome c oxidase. The water molecules form two channels along which protons can enter from the cytoplasmic (matrix) side of the protein and reach the binuclear center. A possible pumping mechanism is proposed that involves a shuttling motion of a glutamic acid side chain, which could then transfer a proton to a propionate group of heme α₃. Proteins 30:100–107, 1998. © 1998 Wiley-Liss, Inc.     

酮古龙酸菌细胞色素c的表达、成熟及活性分析

目的:从酮古龙酸菌Y25中扩增细胞色素c基因,在大肠杆菌中表达、成熟并进行生物活性分析。方法:从酮古龙酸菌Y25基因组中PCR扩增细胞色素c基因,构建pET22b表达载体;从大肠杆菌BL21(DE3)中扩增细胞色素c成熟基因簇ccmABCDEFGH,连接到带有山梨糖脱氢酶组成型启动子的pBBR1MCS2-P200载体中;将构建的2个质粒共转化大肠杆菌BL21(DE3),经IPTG诱导表达后进行血红素染色检测;通过氧化还原光谱法对Ni柱亲和纯化的重组蛋白进行活性分析。结果:扩增得到1404 bp的细胞色素c基因及6481 bp的ccmABCDEFGH基因簇;重组菌株经IPTG诱导表达后行SDS-PAGE分析,可见相对分子质量为50×103的表达条带;血红素染色显示重组蛋白结合有血红素;经氧化还原光谱扫描,显示亲和层析纯化得到的目的蛋白有细胞色素c特征吸收峰。结论:从酮古龙酸菌Y25中扩增得到了细胞色素c基因,在大肠杆菌中进行了表达和成熟,表达蛋白具有细胞色素c生物活性。     

酮古龙酸菌细胞色素c基因的克隆及表达

目的:从酮古龙酸菌SCB329中分离细胞色素c(Cytc)相关基因,在大肠杆菌中进行表达并验证。方法:根据酮古龙酸菌SCB329基因组序列设计引物,通过PCR从SCB329基因组中扩增cytc基因,酶切后连接pET22b表达载体,转化至大肠杆菌DH5α后提取质粒,经PCR、质粒双酶切及测序鉴定后,转入大肠杆菌BL21(DE3),并对表达条件进行考察;用Chelating Sepharose珠粒对可溶性的Cytc-His融合蛋白进行纯化;经光谱扫描和血红素染色等方法对表达蛋白定性分析。结果:PCR扩增的cytc基因长513 bp;重组菌在IPTG浓度为0.025 mmol/L的条件下,于28℃诱导10 h后,SDS-PAGE分析可见表达条带,相对分子质量约为18×103;Ni柱亲和层析纯化得到目的蛋白,纯化蛋白经光谱扫描呈现Cytc特征峰,血红素染色呈现阳性结果。结论:从酮古龙酸菌SCB329中分离得到一种cytc基因,并表达纯化了融合蛋白Cytc-His,纯化蛋白呈现Cytc特性,为研究酮古龙酸菌中产酸关键酶的电子传递机制奠定了基础。     

Can ferricyanide oxidize carbon monoxide-liganded cytochromea 3?

Evidence for the oxidation of CO-liganded cytochromea₃ by ferricyanide has been published recently. These observations conflict with the long-held belief that ferricyanide is thermodynamically incapable of oxidizing the CO complex. The present paper examines the facts on which the earlier idea was based. It is concluded that the earlier evidence did not establish that ferricyanide was incompetent as an oxidant for CO-liganded cytochormea₃.     

醌血红素蛋白的电子传递

醌蛋白是以吡咯喹啉醌（PQQ）及其结构类似物为辅酶的一类氧化还原酶。醌血红素蛋白是以PQQ和一个或多个血红素作为辅助因子的醌蛋白,包括醌血红素蛋白醇脱氢酶和醌血红素蛋白胺脱氢酶。简要综述了醌血红素蛋白的结构特点,在分子内从PQQ到血红素的电子传递,以及醌血红素蛋白与蛋白之间的分子间的电子传递。     

The Controlling Action of Actithiazic Acid on the Biosynthesis of Biotin-vitamers by Various Microorganisms

By the addition of actithiazic acid, or acidomycin (ACM), to culture media, the accumulation of desthiobiotin by various microorganisms was enhanced from two-fold to about seventyfold, while that of biotin was markedly reduced. Especially, Bacillus sphaericus accumulated 350 μg per ml of biotin-vitamers assayed with Saccharomyces cerevisiae. ACM was not incorporated into the desthiobiotin molecule by resting cells of B. sphaericus. The amount of biotin-vitamers assayed with S. cerevisiae which was synthesized from pimelic acid by the resting cells grown with ACM was twice as great as that synthesized by the cells grown without ACM. From these results, the mechanism of the controlling action of ACM on biotin biosynthesis was discussed.     

Complex structure of cytochrome c–cytochrome c oxidase reveals a novel protein–protein interaction mode

Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O₂ to generate H₂O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c–CcO complex at 2.0‐Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter‐molecular span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein–protein interaction at the docking interface represent the first known example of a new class of protein–protein interaction, which we term “soft and specific”. This interaction is likely to contribute to the rapid association/dissociation of the Cyt.c–CcO complex, which facilitates the sequential supply of four electrons for the O₂ reduction reaction.     

Tuning of Hemes b Equilibrium Redox Potential Is Not Required for Cross-Membrane Electron Transfer

In biological energy conversion, cross-membrane electron transfer often involves an assembly of two hemes b. The hemes display a large difference in redox midpoint potentials (ΔE_{m_}b), which in several proteins is assumed to facilitate cross-membrane electron transfer and overcome a barrier of membrane potential. Here we challenge this assumption reporting on heme b ligand mutants of cytochrome bc₁ in which, for the first time in transmembrane cytochrome, one natural histidine has been replaced by lysine without loss of the native low spin type of heme iron. With these mutants we show that ΔE_{m_}b can be markedly increased, and the redox potential of one of the hemes can stay above the level of quinone pool, or ΔE_{m_}b can be markedly decreased to the point that two hemes are almost isopotential, yet the enzyme retains catalytically competent electron transfer between quinone binding sites and remains functional in vivo. This reveals that cytochrome bc₁ can accommodate large changes in ΔE_{m_}b without hampering catalysis, as long as these changes do not impose overly endergonic steps on downhill electron transfer from substrate to product. We propose that hemes b in this cytochrome and in other membranous cytochromes b act as electronic connectors for the catalytic sites with no fine tuning in ΔE_{m_}b required for efficient cross-membrane electron transfer. We link this concept with a natural flexibility in occurrence of several thermodynamic configurations of the direction of electron flow and the direction of the gradient of potential in relation to the vector of the electric membrane potential.     

Light-induced conformational change at low temperature in the coordination of heme c-556 in the reaction center of Rhodopseudomonas viridis

Isolated reaction centers of Rhodopseudomonas viridis with the two high-potential hemes reduced were illuminated at 5 K. Difference spectra show a bleaching of the heme c-556 alpha bands and a red shift of the Soret band. These effects are reversed by warming to around 80 K. They are not induced by near infra-red light absorbed by the chlorine pigments of the reaction centers and they are not associated with electron transfer from P to Q_A. It is concluded that, following direct excitation, heme c-556 becomes five-coordinated. We find no evidence of a significant photooxidation of heme c-559 under the same conditions.     

Investigating the Mechanism of Electron Transfer to the Binuclear Center in Cu-Heme Oxidases

Novel experimental evidence is presented further supporting the hypothesis that, starting with resting oxidized cytochrome c oxidase, the internal electron transfer to the oxygen binding site is kinetically controlled. The reduction of the enzyme was followed spectroscopically and in the presence of NO or CO, used as trapping ligands for reduced cytochrome a₃; ruthenium hexamine was used as a spectroscopically silent electron donor. Consistent with the high combination rate constant for reduced cytochrome a₃, NO proved to be a very efficient trapping ligand, while CO did not. The results are discussed in view of two alternative (thermodynamic and kinetic) hypotheses of control of electron transfer to the binuclear (cyt.a₃-Cu_B) center. Fulfilling the prediction of the kinetic control hypothesis: i) the reduction of cytochrome a₃ and ligation are synchronous and proceed at the intrinsic rate of cytochrome a₃ reduction, ii) the measured rate of formation of the nitrosyl derivative is independent of the concentration of both the reductant and NO.     

黄素氧还蛋白参与的固氮链电子传递

棕色固氮菌中电子载体Fld直接向固氮酶铁蛋白传递电子。Fld_(ox)至Fld_R是双电子二步还原反应,极谱半波电位分别为-210、-550 mV。Fld_(ox)至Fld_(SR)的中点电位为-280 mV,Fld_(SR)至Fld_R为-500mV。铁蛋白中点电位为-256mV,加MgATP后为-390 mV。Fld_R与铁蛋白ox组成的电池电动势为244mV,电子传递可自发进行,反应的J△G~o为-23KJ/摩尔,铁蛋白被Fld_R还原的K_a=1.3×120~4,加入MgATP后△G~o为-10.6KJ/摩尔,K_a=72。因此,未加入MgATP时电子传递反应更易进行。     

A ba3 oxygen reductase from the thermohalophilic bacterium Rhodothermus marinus

The aerobic respiratory chain of the thermohalophilic bacterium Rhodothermus marinus has been extensively studied. In this study the isolation and characterization of a third oxygen reductase expressed in this organism are described. This newly isolated enzyme is a typical member of the type B family of haem-copper oxygen reductases, showing 43% amino acid sequence identity and 63% similarity with the ba3 oxygen reductase from Thermus thermophilus. It constitutes two subunits with apparent molecular masses of 42 and 38 kDa. It contains a low-spin B-type haem and a high-spin A-type haem. A stoichiometry of 1B: 1A haem per protein was obtained by spectral integration of UV-visible spectra. Metal analysis showed the presence of two iron and three copper ions, which is in agreement with the existence of a CuA centre. Taking advantage of having two spectroscopically distinct haems, the redox behaviour of the ba3 oxygen reductase was analysed and discussed in the framework of a model with interacting centres. Both haems, B and A, present two transitions, have unusually low reduction potentials of -65 mV and an interaction potential of -52.5 mV.