Electron and proton transfer in NADH:ubiquinone oxidoreductase (Complex I) from Escherichia coli

Cells of every living organism on our planet − bacterium, plant or animal − are organized in such a way that despite differences in structure and function they utilize the same metabolic energy represented by electrochemical proton gradient across a membrane. This gradient of protons is generated by the series of membrane bound multisubunit proteins, Complex I, II, III and IV, organized in so-called respiratory or electron transport chain. In the eukaryotic cell it locates in the inner mitochondrial membrane while in the bacterial cell it locates in the cytoplasmic membrane. The function of the respiratory chain is to accept electrons from NADH and ubiquinol and transfer them to oxygen resulting in the formation of water. The free energy released upon these redox reactions is converted by respiratory enzymes into an electrochemical proton gradient, which is used for synthesis of ATP as well as for many other energy dependent processes. This thesis is focused on studies of the first member of the respiratory chain − NADH:ubiquinone oxidoreductase or Complex I. This enzyme has a boot-shape structure with hydrophilic and hydrophobic domains, the former of which has all redox groups of the protein, the flavin and eight to nine iron-sulfur clusters. Complex I serves as a proton pump coupling transfer of two electrons from NADH to ubiquinone to the translocation of four protons across the membrane. So far the mechanism of energy transduction by Complex I is unknown. In the present study we applied a set of different methods to study the electron and proton transfer reactions in Complex I from Escherichia coli. The main achievement was the experiment that showed that the electron transfer through the hydrophilic domain of Complex I is unlikely to be coupled to proton transfer directly or to conformational changes in the protein. In this work for the first time properties of all redox centers of Complex I were characterized in the intact purified bacterial enzyme. We also probed the role of several conserved amino acid residues in the electron transfer of Complex I. Finally, we found that highly conserved amino acid residues in several membrane subunits form a common pattern with a very prominent feature – the presence of a few lysines within the membrane. Based on the experimental data, we suggested a tentative principle which may govern the redox-coupled proton pumping in Complex I.

Theoretical Studies on Coupled Electron and Proton Transfer in Cytochrome c Oxidase

The complexity of life is based on an effective energy transduction machinery, which has evolved during the last 3.5 billion years. In aerobic life, the utilization of the high oxidizing potential of molecular oxygen powers this machinery. Oxygen is safely reduced by a membrane bound enzyme, cytochrome c oxidase (CcO), to produce an electrochemical proton gradient over the mitochondrial or bacterial membrane. This gradient is used for energy-requiring reactions such as synthesis of ATP by F0F1-ATPase and active transport. In this thesis, the molecular mechanism by which CcO couples the oxygen reduction chemistry to proton-pumping has been studied by theoretical computer simulations. By building both classical and quantum mechanical model systems based on the X-ray structure of CcO from Bos taurus, the dynamics and energetics of the system were studied in different intermediate states of the enzyme. As a result of this work, a mechanism was suggested by which CcO can prevent protons from leaking backwards in proton-pumping. The use and activation of two proton conducting channels were also enlightened together with a mechanism by which CcO sorts the chemical protons from pumped protons. The latter problem is referred to as the gating mechanism of CcO, and has remained a challenge in the bioenergetics field for more than three decades. Furthermore, a new method for deriving charge parameters for classical simulations of complex metalloenzymes was developed.

Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.

Proton translocation coupled to electron transfer reactions in terminal oxidases

Terminal oxidases are the final proteins of the respiratory chain in eukaryotes and some bacteria. They catalyze most of the biological oxygen consumption on Earth done by aerobic organisms. During the catalytic reaction terminal oxidases reduce dioxygen to water and use the energy released in this process to maintain the electrochemical proton gradient by functioning as a redox-driven proton pump. This membrane gradient of protons is extremely important for cells as it is used for many cellular processes, such as transportation of substrates and ATP synthesis. Even though the structures of several terminal oxidases are known, they are not sufficient in themselves to explain the molecular mechanism of proton pumping. In this work we have applied a complex approach using a variety of different techniques to address the properties and the mechanism of proton translocation by the terminal oxidases. The combination of direct measurements of pH changes during catalytic turnover, time-resolved potentiometric electrometry and optical spectroscopy, made it possible to obtain valuable information about various aspects of oxidase functioning. We compared oxygen binding properties of terminal oxidases from the distinct heme-copper (CcO) and cytochrome bd families and found that cytochrome bd has a high affinity for oxygen, which is 3 orders of magnitude higher than that of CcO. Interestingly, the difference between CcO and cytochrome bd is not only in higher affinity of the latter to oxygen, but also in the way that each of these enzymes traps oxygen during catalysis. CcO traps oxygen kinetically - the molecule of bound dioxygen is rapidly reduced before it can dissociate. Alternatively, cytochrome bd employs an alternative mechanism of oxygen trapping - part of the redox energy is invested into tight oxygen binding, and the price paid for this is the lack of proton pumping. A single cycle of oxygen reduction to water is characterized by translocation of four protons across the membrane. Our results make it possible to assign the pumping steps to discrete transitions of the catalytic cycle and indicate that during in vivo turnover of the oxidase these four protons are transferred, one at a time, during the P→F, F→OH, Oh→Eh, and Eh→R transitions. At the same time, each individual proton translocation step in the catalytic cycle is not just a single reaction catalyzed by CcO, but rather a complicated sequence of interdependent electron and proton transfers. We assume that each single proton translocation cycle of CcO is assured by internal proton transfer from the conserved Glu-278 to an as yet unidentified pump site above the hemes. Delivery of a proton to the pump site serves as a driving reaction that forces the proton translocation cycle to continue.

Irradiation of silicon particle detectors with MeV-protons

Silicon particle detectors are used in several applications and will clearly require better hardness against particle radiation in the future large scale experiments than can be provided today. To achieve this goal, more irradiation studies with defect generating bombarding particles are needed. Protons can be considered as important bombarding species, although neutrons and electrons are perhaps the most widely used particles in such irradiation studies. Protons provide unique possibilities, as their defect production rates are clearly higher than those of neutrons and electrons, and, their damage creation in silicon is most similar to the that of pions. This thesis explores the development and testing of an irradiation facility that provides the cooling of the detector and on-line electrical characterisation, such as current-voltage (IV) and capacitance-voltage (CV) measurements. This irradiation facility, which employs a 5-MV tandem accelerator, appears to function well, but some disadvantageous limitations are related to MeV-proton irradiation of silicon particle detectors. Typically, detectors are in non-operational mode during irradiation (i.e., without the applied bias voltage). However, in real experiments the detectors are biased; the ionising proton generates electron-hole pairs, and a rise in rate of proton flux may cause the detector to breakdown. This limits the proton flux for the irradiation of biased detectors. In this work, it is shown that, if detectors are irradiated and kept operational, the electric field decreases the introduction rate of negative space-charges and current-related damage. The effects of various particles with different energies are scaled to each others by the non-ionising energy loss (NIEL) hypothesis. The type of defects induced by irradiation depends on the energy used, and this thesis also discusses the minimum proton energy required at which the NIEL-scaling is valid.

Search for WW and WZ Resonances Decaying to Electron, Missing ET, and Two Jets in pp̅ Collisions at √s=1.96 TeV.

Using data from 2.9  fb-1 of integrated luminosity collected with the CDF II detector at the Tevatron, we search for resonances decaying into a pair of on-shell gauge bosons, WW or WZ, where one W decays into an electron and a neutrino, and the other boson decays into two jets. We observed no statistically significant excess above the expected standard model background, and we set cross section limits at 95% confidence level on G* (Randall-Sundrum graviton), Z′, and W′ bosons. By comparing these limits to theoretical cross sections, mass exclusion regions for the three particles are derived. The mass exclusion regions for Z′ and W′ are further evaluated as a function of their gauge coupling strength.

Search for WW and WZ Resonances Decaying to Electron, Missing ET, and Two Jets in pp̅ Collisions at √s=1.96 TeV.

Using data from 2.9/fb of integrated luminosity collected with the CDF II detector at the Tevatron, we search for resonances decaying into a pair of on-shell gauge bosons, WW or WZ, where one W decays into an electron and a neutrino, and the other boson decays into two jets. We observed no statistically significant excess above the expected standard model background, and we set cross section limits at 95% confidence level on G*(Randall-Sundrum graviton), Z', and W' bosons. By comparing these limits to theoretical cross sections, mass exclusion regions for the three particles are derived. The mass exclusion regions for Z' and W' are further evaluated as a function of their gauge coupling strength.

Measurement of the tt̅ production cross section in pp̅ collisions at √s=1.96 TeV using soft electron b-tagging

We present a measurement of the top quark pair production cross section in ppbar collisions at sqrt(s)=1.96 TeV using a data sample corresponding to 1.7/fb of integrated luminosity collected with the Collider Detector at Fermilab. We reconstruct ttbar events in the lepton+jets channel. The dominant background is the production of W bosons in association with multiple jets. To suppress this background, we identify electrons from the semileptonic decay of heavy-flavor jets. We measure a production cross section of 7.8 +/- 2.4 (stat) +/- 1.6 (syst) +/- 0.5 (lumi) pb. This is the first measurement of the top pair production cross section with soft electron tags in Run II of the Tevatron.