The mechanism for proton pumping in cytochrome c oxidase from an electrostatic and quantum chemical perspective

AbstractThe mechanism for proton pumping in cytochrome c oxidase in the respiratory chain, has for decades been one of the main unsolved problems in biochemistry. However, even though several different suggested mechanisms exist, many of the steps in these mechanisms are quite similar and constitute a general consensus framework for discussing proton pumping. When these steps are analyzed, at least three critical gating situations are found, and these points are where the suggested mechanisms in general differ. The requirements for gating are reviewed and analyzed in detail, and a mechanism is suggested, where solutions for all the gating situations are formulated. This mechanism is based on an electrostatic analysis of a kinetic experiment fior the O to E transition. The key component of the mechanism is a positively charged transition state. An electron on heme a opens the gate for proton transfer from the N-side to a pump loading site (PLS). When the negative charge of the electron is compensated by a chemical proton, the positive transition state prevents backflow from the PLS to the N-side at the most critical stage of the pumping process. The mechanism has now been tested by large model DFT calculations, and these calculations give strong support for the suggested mechanism. This article is part of a Special Issue entitled: Respiratory Oxidases

Different types of biological proton transfer reactions studied by quantum chemical methods

AbstractDifferent types of proton transfer occurring in biological systems are described with examples mainly from ribonucleotide reductase (RNR) and cytochrome c oxidase (CcO). Focus is put on situations where electron and proton transfer are rather strongly coupled. In the long range radical transfer in RNR, it is shown that the presence of hydrogen atom transfer (HAT) is the most logical explanation for the experimental observations. In another example from RNR, it is shown that a transition state for concerted motion of both proton and electron can be found even if the donors are separated by a quite long distance. In CcO, the essential proton transfer for the OO bond cleavage, and the most recent modelings of proton translocation are described, indicating a few remaining major problems

Energy diagrams and mechanism for proton pumping in cytochrome c oxidase

AbstractThe powerful technique of energy diagrams has been used to analyze the mechanism for proton pumping in cytochrome c oxidase. Energy levels and barriers are derived starting out from recent kinetic experiments for the O to E transition, and are then refined using general criteria and a few additional experimental facts. Both allowed and non-allowed pathways are obtained in this way. A useful requirement is that the forward and backward rate should approach each other for the full membrane gradient. A key finding is that an electron on heme a (or the binuclear center) must have a significant lowering effect on the barrier for proton uptake, in order to prevent backflow from the pump-site to the N-side. While there is no structural gating in the present mechanism, there is thus an electronic gating provided by the electron on heme a. A quantitative analysis of the energy levels in the diagrams, leads to Prop-A of heme a3 as the most likely position for the pump-site, and the Glu278 region as the place for the transition state for proton uptake. Variations of key redox potentials and pKa values during the pumping process are derived for comparison to experiments

Mutations in the D-channel of cytochrome c oxidase causes leakage of the proton pump

AbstractIt has experimentally been found that certain mutations close to the entry point of the proton transfer channel in cytochrome c oxidase stop proton translocation but not the oxygen reduction chemistry. This effect is termed uncoupling. Since the mutations are 20Å away from the catalytic center, this is very surprising. A new explanation for this phenomenon is suggested here, involving a local effect at the entry point of the proton channel, rather than the long range effects suggested earlier

On the bond distance in methane

The equilibrium bond distance in methane was optimized using coupled-pair functional and contracted CI wave functions, and a Gaussian basis that includes g-type functions on carbon and d-type functions on hydrogen. The resulting bond distance, when corrected for core-valence correlation effects, agrees with the experimental value of 2.052 a(0) to within the experimental uncertainty of 0.002 a(0). The main source of error in the best previous studies, which showed discrepancies with experiment of 0.007 a(0) is shown to be basis set incompleteness. In particular, it is important that the basis set be close to saturation, at least for the lower angular quantum numbers

The dissociation energy of N2

The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined

Plasma chemical purification of flue gases using pulsed electron beams

The article presents the study of the pulsed electron beam propagation in oxygen and nitrogen. The researches were performed using the TEA-500 pulsed electron accelerator and drift tube. Parameters of the TEA-500 pulsed electron accelerator are as follows: the electron energy (varies) is 200-450 keV, the beam current is 10 kA, the half-amplitude current pulse duration is 60 ns, the pulse repetition rate is up to 10 Hz (in the pulse burst). The accelerator is equipped with the necessary means of diagnostics of the beam parameters: particle energy, current and current density, the total energy transferred by the beam. The drift tube includes a chamber consisting of two sections of reverse current shunts located along the entire length of the drift tube. The following precursors used N2 and O2. The specified types of gases were chosen as they are among the main components of the flue gases, whose treatment has been widely reported recently

Low molecular weight heparin (dalteparin) as adjuvant treatment to thrombolysis in acute myocardial infarction—a pilot study: Biochemical Markers in Acute Coronary Syndromes (BIOMACS II)

AbstractOBJECTIVESThis randomized, double blind, placebo-controlled pilot trial evaluated the effect of dalteparin as an adjuvant to thrombolysis in patients with acute myocardial infarction regarding early reperfusion, recurrent ischemia and patency at 24 h.BACKGROUNDLow-molecular-weight heparin, given subcutaneously twice daily without monitoring, might be an attractive alternative to conventional intravenous heparin in the treatment of acute myocardial infarction.METHODSIn 101 patients dalteparin/placebo 100 IU/kg was given just before streptokinase and a second injection 120 IU/kg after 12 h. Monitoring with continuous vector-ECG was done to obtain signs of early reperfusion and later ischemic episodes. Blood samples for myoglobin were obtained at start and after 90 min to evaluate signs of reperfusion. Coronary angiography was performed after 20–28 h to evaluate TIMI-flow in the infarct-related artery.RESULTSDalteparin added to streptokinase tended to provide a higher rate of TIMI grade 3 flow in infarct-related artery compared to placebo, 68% versus 51% (p = 0.10). Dalteparin had no effects on noninvasive signs of early reperfusion. In patients with signs of early reperfusion, there seemed to be a higher rate of TIMI grade 3 flow, 74% versus 46% (myoglobin) (p = 0.04) and 73% versus 52% (vector-ECG) (p = 0.11). Ischemic episodes 6–24 h. after start of treatment were fewer in the dalteparin group, 16% versus 38% (p = 0.04).CONCLUSIONSWhen dalteparin was added as an adjuvant to streptokinase and aspirin, there were tendencies for less ECG monitoring evidence of recurrent ischemia and better patency at 24 h, warranting further study

Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein

Although metallocofactors are ubiquitous in enzyme catalysis, how metal binding specificity arises remains poorly understood, especially in the case of metals with similar primary ligand preferences such as manganese and iron. The biochemical selection of manganese over iron presents a particularly intricate problem because manganese is generally present in cells at a lower concentration than iron, while also having a lower predicted complex stability according to the Irving–Williams series (MnII ZnII). Here we show that a heterodinuclear Mn/Fe cofactor with the same primary protein ligands in both metal sites self-assembles from MnII and FeII in vitro, thus diverging from the Irving–Williams series without requiring auxiliary factors such as metallochaperones. Crystallographic, spectroscopic, and computational data demonstrate that one of the two metal sites preferentially binds FeII over MnII as expected, whereas the other site is nonspecific, binding equal amounts of both metals in the absence of oxygen. Oxygen exposure results in further accumulation of the Mn/Fe cofactor, indicating that cofactor assembly is at least a two-step process governed by both the intrinsic metal specificity of the protein scaffold and additional effects exerted during oxygen binding or activation. We further show that the mixed-metal cofactor catalyzes a two-electron oxidation of the protein scaffold, yielding a tyrosine–valine ether cross-link. Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate