Proton translocation by cytochrome c oxidase.

Cell respiration in mitochondria and some bacteria is catalysed by cytochrome c oxidase, which reduces O2 to water, coupled with translocation of four protons across the mitochondrial or bacterial membrane. The enzyme's catalytic cycle consists of a reductive phase, in which the oxidized enzyme receives electrons from cytochrome c, and an oxidative phase, in which the reduced enzyme is oxidized by O2. Previous studies indicated that proton translocation is coupled energetically only to the oxidative phase, but this has been challenged. Here, with the purified enzyme inlaid in liposomes, we report time-resolved measurements of membrane potential, which show that half of the electrical charges due to proton-pumping actually cross the membrane during reduction after a preceding oxidative phase. pH measurements confirm that proton translocation also occurs during reduction, but only when immediately preceded by an oxidative phase. We conclude that all the energy for proton translocation is conserved in the enzyme during its oxidation by O2. One half of it is utilized for proton-pumping during oxidation, but the other half is unlatched for this purpose only during re-reduction of the enzyme.     

Ferryl and hydroxy intermediates in the reaction of oxygen with reduced cytochrome c oxidase

Cytochrome c oxidase catalyses the 4-electron reduction of dioxygen to water and translocates protons vectorially across the inner mitochondrial membrane. Proposed reaction pathways for the catalytic cycle of the O2 reduction are difficult to verify without knowing the structures of the intermediates, but we now have such information for the catalytic intermediates in the first steps of the reaction of O2 with cytochrome c oxidase from resonance Raman spectroscopy, a technique that enables iron-ligand stretching modes to be identified. Here we report on two more key intermediates: a ferryl-oxo (Fe4 = O2-) and a ferric-hydroxy (Fe3+--OH-) intermediate at the level of 3- and 4-electron reduction, respectively. We identified these intermediates by their characteristic iron-oxygen stretching frequencies (786 cm-1 for Fe4+ = O2-, and 450 cm-1 for Fe3+ -- OH-) and oxygen and deuterium isotope shifts. The oxo atom in the ferryl intermediate is hydrogen-bonded and the iron-oxygen bond in the hydroxy intermediate is anomalously weak. With the identification of the primary, ferryl and hydroxy intermediates, the predominant structures at almost all stages of O2 reduction are now known and the catalytic pathway can be described with more certainty.     

Reduction of cytochrome c oxidase by a second electron leads to proton translocation

Cytochrome c oxidase, the terminal enzyme of cellular respiration in mitochondria and many bacteria, reduces O(2) to water. This four-electron reduction process is coupled to translocation (pumping) of four protons across the mitochondrial or bacterial membrane; however, proton pumping is poorly understood. Proton pumping was thought to be linked exclusively to the oxidative phase, that is, to the transfer of the third and fourth electron. Upon re-evaluation of these data, however, this proposal has been questioned, and a transport mechanism including proton pumping in the reductive phase--that is, during the transfer of the first two electrons--was suggested. Subsequently, additional studies reported that proton pumping during the reductive phase can occur, but only when it is immediately preceded by an oxidative phase. To help clarify the issue we have measured the generation of the electric potential across the membrane, starting from a defined one-electron reduced state. Here we show that a second electron transfer into the enzyme leads to charge translocation corresponding to pumping of one proton without necessity for a preceding turnover.     

A mechanistic principle for proton pumping by cytochrome c oxidase

In aerobic organisms, cellular respiration involves electron transfer to oxygen through a series of membrane-bound protein complexes. The process maintains a transmembrane electrochemical proton gradient that is used, for example, in the synthesis of ATP. In mitochondria and many bacteria, the last enzyme complex in the electron transfer chain is cytochrome c oxidase (CytcO), which catalyses the four-electron reduction of O2 to H2O using electrons delivered by a water-soluble donor, cytochrome c. The electron transfer through CytcO, accompanied by proton uptake to form H2O drives the physical movement (pumping) of four protons across the membrane per reduced O2. So far, the molecular mechanism of such proton pumping driven by electron transfer has not been determined in any biological system. Here we show that proton pumping in CytcO is mechanistically coupled to proton transfer to O2 at the catalytic site, rather than to internal electron transfer. This scenario suggests a principle by which redox-driven proton pumps might operate and puts considerable constraints on possible molecular mechanisms by which CytcO translocates protons.     

Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase

Electron transfer in cell respiration is coupled to proton translocation across mitochondrial and bacterial membranes, which is a primary event of biological energy transduction. The resulting electrochemical proton gradient is used to power energy-requiring reactions, such as ATP synthesis. Cytochrome c oxidase is a key component of the respiratory chain, which harnesses dioxygen as a sink for electrons and links O2 reduction to proton pumping. Electrons from cytochrome c are transferred sequentially to the O2 reduction site of cytochrome c oxidase via two other metal centres, Cu(A) and haem a, and this is coupled to vectorial proton transfer across the membrane by a hitherto unknown mechanism. On the basis of the kinetics of proton uptake and release on the two aqueous sides of the membrane, it was recently suggested that proton pumping by cytochrome c oxidase is not mechanistically coupled to internal electron transfer. Here we have monitored translocation of electrical charge equivalents as well as electron transfer within cytochrome c oxidase in real time. The results show that electron transfer from haem a to the O2 reduction site initiates the proton pump mechanism by being kinetically linked to an internal vectorial proton transfer. This reaction drives the proton pump and occurs before relaxation steps in which protons are taken up from the aqueous space on one side of the membrane and released on the other.     

Structure of cytochrome c nitrite reductase.

The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction of nitrite to ammonia as one of the key steps in the biological nitrogen cycle, where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification. Here we report on the crystal structure of this enzyme from the microorganism Sulfurospirillum deleyianum, which we solved by multiwavelength anomalous dispersion methods. We propose a reaction scheme for the transformation of nitrite based on structural and spectroscopic information. Cytochrome c nitrite reductase is a functional dimer, with 10 close-packed haem groups of type c and an unusual lysine-coordinated high-spin haem at the active site. By comparing the haem arrangement of this nitrite reductase with that of other multihaem cytochromes, we have been able to identify a family of proteins in which the orientation of haem groups is conserved whereas structure and function are not.     

Assignment of Soret MLCT band of reduced form of copper binuclear cluster in cytochrome c oxidase film

Low concentration of dithionite results in the reduction of Cu-Cn binuclear and heine a active sites of the cytochrome c oxidase thin solid film immersed in the acidic phosphate buffer, but Fe-Cu binuclear center keeps in the oxidation state. It manifests as a negative peak at 426 nm and a positive one at -408 nln in the difference spectra induced by dithionite. The former implies decrease of the oxidized form of heme a center, that is, Fea^3 →Fea^2 . And the latter results from the contribution of metal-ligand charge transfer (MLCT) transition in the reduced binuclear Cu-Cu cluster, rather than from that of heine a center. This stronger Soret MLCT band must be helpful to overcoming the difficulty in distinguishing the weaker copper sign from the stronger one of iron when studying copper-iron protein.     

Expression, purification and characterization of the soluble CuA domain of cytochrome c oxidase ofParacoccus versutus

The key subunit Ⅱ of cytochrome c oxidase (CcO) contains a soluble binuclear copper center (Cu_A) domain. The Cu_A domain of Paracoccus versutus was cloned, expressed, purified and characterized. The gene encoding the Cu_A domain in pET11d vector was expressed in E. coli BL21 (DE3). The results showed that the Cu_A domain was expressed mostly in inclusion bodies and the Cu_A domain protein synthesized in E. coli cells represents approximately 10 percent of the total cellular proteins. Dissolved in urea, dialyzed and recombined with Cu⁺/Cu²⁺ and purified by the Q-sepharose fast flow anion-exchange column and Sephadex G-75 gel filtration column, the soluble purple-colored protein, which shows a single band in electrophoresis, was obtained. The UV-visible absorption spectrum of Cu_A domain showed that there are intense band at 478 nm and a shoulder peak at 530 nm, and two weak bands at 360 and 806 nm respectively, which can be assigned to the charge transfer and the interactions of obitals of Cu—S and Cu——Cu in the mixed-valence binuclear metal center (Cu₂S₂R₂). The far-UV CD spectrum indicated that this domain is predominantly in β-sheet structure. The fluorescence spectra showed that its maximal excitation wavelength and maximal emission wavelength are at 280 and 345 nm, respectively.     

Coherent dynamics of a flux qubit coupled to a harmonic oscillator

In the emerging field of quantum computation and quantum information, superconducting devices are promising candidates for the implementation of solid-state quantum bits (qubits). Single-qubit operations, direct coupling between two qubits and the realization of a quantum gate have been reported. However, complex manipulation of entangled states-such as the coupling of a two-level system to a quantum harmonic oscillator, as demonstrated in ion/atom-trap experiments and cavity quantum electrodynamics-has yet to be achieved for superconducting devices. Here we demonstrate entanglement between a superconducting flux qubit (a two-level system) and a superconducting quantum interference device (SQUID). The latter provides the measurement system for detecting the quantum states; it is also an effective inductance that, in parallel with an external shunt capacitance, acts as a harmonic oscillator. We achieve generation and control of the entangled state by performing microwave spectroscopy and detecting the resultant Rabi oscillations of the coupled system.     

“大连相干光源”为化学反应中的分子“拍电影”

 自由电子激光被称为第4代先进光源，是帮助人类探索物质微观世界的最先进的研究工具，在能源、物理、化学、材料、生物等多个学科领域具有变革性的推动作用。基于可调极紫外相干光源的综合实验研究装置（简称"大连相干光源"）的成功研制，填补了中国在这一领域的空白，有望成为推动中国科技实现跨越式发展的"利器"。介绍了大连相干光源的研制背景和国内外的发展现状，阐述了装置成功研制的意义，并展望了未来的应用前景。     

Directional electron transfer in ruthenium-modified horse heart cytochrome c

Cytochrome c can be modified by [(NH3)5RuII/III-] specifically at the imidazole moiety of histidine 33, and we have recently discussed the thermodynamics and kinetics of electron transfer within this modified protein. X-ray crystal structures of the oxidized and reduced forms of tuna cytochrome c indicate that the separation between the haem group of cytochrome c and the ruthenium label is 12-16 A. Internal electron transfer from the [(NH3)5RuII-] centre to the Fe(III) haem centre occurs with a rate constant k congruent to 53 s-1 (25 degrees C) (delta H = 3.5 kcal mol-1, delta S = -39 EU), as measured by pulse radiolysis. The measured unimolecular rate constant, k congruent to 53 s-1, is on the same timescale as a number of conformational changes that occur within the cytochrome c molecule. These results raise the question of whether electron transfer or protein conformational change is the rate limiting step in this process. We describe here an experiment that probes this intramolecular electron transfer step further. It involves reversing the direction of electron transfer by changing the redox potential of the ruthenium label. Electron transfer in the new ruthenium-cytochrome c derivative described here is from haem(II) to the Ru(III) label, whereas in (NH3)5Ru-cytochrome c the electron transfer is from Ru(II) to haem(III). Intramolecular electron transfer from haem(II) to Ru(III) in the new ruthenium-cytochrome c described here proceeds much slower (greater than 10(5) times) than the electron transfer from Ru(II) to haem(III) in the (NH3)5Ru-cytochrome c. We therefore conclude that electron transfer in cytochrome c is directional, with the protein envelope presumably involved in this directionality.     

纳米火棉胶膜自组装细胞色素c的直接电化学研究

用纳米火棉胶膜将细胞色素c固定在玻碳电极表面,制备了细胞色素c-火棉胶膜修饰电极.吸附在火棉胶膜上的细胞色素c可以与电极发生直接电子传递.在pH=7.0的0.1mol/LPBS缓冲溶液中可得到一对准可逆的细胞色素c的血红素辅基Fe(Ⅲ)/Fe(Ⅱ)电对氧化还原峰,实验求得细胞色素c异相电子传递速率常数k0为65.4μm/s.进一步考察了扫速、溶液pH值等因素对细胞色素c电子传递的影响,并用电化学阻抗法研究了修饰电极的电化学行为.