Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

Biological electron transfer in copper proteins

Nature has used a variety of protein systems to mediate electron transfer. In this thesis I examine aspects of the control of biological electron transfer by two copper proteins that act as natural electron carriers.

In the first study, I have made a mutation to one of the ligand residues in the azurin blue copper center, methionine 121 changed to a glutamic acid. Studies of intramolecular electron transfer rates from that mutated center to covalently attached ruthenium complexes indicate that the weak axial methionine ligand is important not only for tuning the reduction potential of the blue copper site but also for maintaining the low reorganization energy that is important for fast electron transfer at long distances.

In the second study, I begin to examine the reorganization energy of the purple copper center in the CuA domain of subunit II of cytochrome c oxidase. In this copper center, the unpaired electron is delocalized over the entire binuclear site. Because long-range electron transfer into and out of this center occurs over long distances with very small driving forces, the reorganization energy of the CuA center has been predicted to be extremely low. I describe a strategy for measuring this reorganization energy starting with the construction of a series of mutations introducing surface histidines. These histidines can then be labeled with a series of ruthenium compounds that differ primarily in their reduction potentials. The electron transfer rates to these ruthenium compounds can then be used to determine the reorganization energy of the CuA site.

A simple method for counting bacteria with active electron transport system in water and sediment samples [Translation from: Kiel. Meeresforsch. 31(2) 83-86, 1975]

Description of a simple method for counting bacteria with active electron transport systems in water and sediment samples. Sodium succinate, NADH and NADPH served as electron donors. It is possible to see several sites of electron transport in the larger cells. Especially impressive are the plankton-algae, protozoa, and small metazoa. This is a partial translation of the ”method” section only.

The photorefractive sensitivity and the effective electron transport length in two-centre holographic recording

In this paper the photorefractive sensitivity defined for single-centre holographic recording is modified to adapt two-centre holographic recording. Based on the time analytic solution of Kukhtarev equations for doubly doped crystals, the analytical expression of photorefractive sensitivity is given. For comparison with single-centre holographic recording and summing the electron competition effects between the deeper and shallower traps, an effective electron transport length is proposed, which varies with the intensity ratios of recording light to sensitive light. According to analyses in this paper, the lower photorefractive sensitivity in two-centre holographic recording is mainly due to the lower concentration of unionized dopants in the shallower centre and the lower effective electron transport length.

Disfunção mitocondrial e cardíaca em camundongos induzida por dieta rica em ácidos graxos poliinsaturados

Indivíduos obesos apresentam maior risco de morbidade e mortalidade atribuída às doenças cardiovasculares. A composição da dieta é um fator que prediz o fenótipo cardíaco em resposta a obesidade e, o tipo de ácido graxo pode afetar de forma diferencial a estrutura e a função do miocárdio. Estudos têm mostrado que a disfunção mitocondrial exerce um papel chave na patogênese da insuficiência e hipertrofia cardíaca, e as alterações mitocondriais observadas em falhas cardíacas apontam para defeitos em sítios específicos da cadeia transportadora de elétrons. Desta forma, o objetivo deste estudo foi avaliar a função contrátil ventricular em camundongos, alimentados com dieta hiperlipídica, rica em ácidos graxos poliinsaturados, buscando elucidações através da bioenergética mitocondrial. Após desmame, camundongos machos C57Bl/6 passaram a receber dieta manipulada contendo 7% (C) ou 19% (HF) de óleo de soja, até os 135 dias de idade. A ingestão alimentar e a massa corporal foram monitoradas e foi realizado teste de tolerância à glicose. No final do período experimental, os animais foram anestesiados e submetidos à avaliação da composição corporal por Absortimetria de Raios X de Dupla Energia (DXA), e em seguida, sacrificados por exsanguinação. No plasma foram determinados o perfil lipídico e a insulina. O coração, o tecido adiposo intra-abdominal e o subcutâneo foram coletados, pesados, processados para análise histomorfológica. Fibras cardíacas do ventrículo esquerdo foram utilizadas para análise da respiração mitocondrial através de oxígrafo. O coração também foi utilizado para a técnica de perfusão de coração isolado de Langendorff, e para análise da expressão de proteínas relacionadas à bioenergética de cardiomiócitos, através de Western Blotting. O índice de HOMA e de adiposidade foram calculados. O grupo HF apresentou maior adiposidade, sem alteração na ingestão alimentar. Foi observada intolerância a glicose, hiperinsulinemia e resistência à insulina, além de alterações desfavoráveis no perfil lipídico. Foi observado alteração na morfologia cardíaca e quadro de cardiomiopatia hipertrófica, refletindo em alteração hemodinâmica, determinando maior contratilidade, maior pressão ventricular e função diastólica prejudicada. Em relação à atividade mitocondrial dos cardiomiócitos foi observada menor oxidação de carboidratos (-47%) e de ácidos graxos (-60%). Porém, sem alteração na expressão de proteínas relacionadas à bioenergética de cardiomiócitos, CPT1, UCP2, GLUT1, GLUT4, AMPK e pAMPK. A partir desses resultados, concluímos que o tipo e a quantidade de ácidos graxos predizem o fenótipo cardíaco na obesidade, promovendo alteração na capacidade oxidativa mitocondrial, na morfologia e na hemodinâmica cardíaca

Temperature dependent electron transport in amorphous oxide semiconductor thin film transistors

A temperature-dependent mobility model in amorphous oxide semiconductor (AOS) thin film transistors (TFTs) extracted from measurements of source-drain terminal currents at different gate voltages and temperatures is presented. At low gate voltages, trap-limited conduction prevails for a broad range of temperatures, whereas variable range hopping becomes dominant at lower temperatures. At high gate voltages and for all temperatures, percolation conduction comes into the picture. In all cases, the temperature-dependent mobility model obeys a universal power law as a function of gate voltage. © 2011 IEEE.

Surface acoustic waves in liquid helium for enhanced single-electron transport applications

High frequency Rayleigh and Sezawa modes propagating in the ZnO/GaAs system capable of operating immersed in liquid helium have been engineered. In the case of the Rayleigh mode, the strong attenuation produced by the liquid is counteracted by the strengthening of the mode induced by the ZnO. However, in the case of the Sezawa modes, the attenuation is strongly reduced taking advantage of the depth profile of their acoustic Poynting vectors, that extend deeper into the layered system, reducing the energy radiated into the fluid. Thus, both tailored modes will be suitable for acoustically-driven single-electron and single-photon devices in ZnO-coated GaAs-based systems with the best thermal stability provided by the liquid helium bath. © 2012 IEEE.

Rashba electron transport in one-dimensional quantum waveguides

The properties of Rashba wave function in the planar one-dimensional waveguide are studied, and the following results are obtained. Due to the Rashba effect, the plane waves of electron with the energy E divide into two kinds of waves with the wave vectors k(1)=k(0)+k(delta) and k(2)=k(0)-k(delta), where k(delta) is proportional to the Rashba coefficient, and their spin orientations are +pi/2 (spin up) and -pi/2 (spin down) with respect to the circuit, respectively. If there is gate or ferromagnetic contact in the circuit, the Rashba wave function becomes standing wave form exp(+/- ik(delta)l)sin[k(0)(l-L)], where L is the position coordinate of the gate or contact. Unlike the electron without considering the spin, the phase of the Rashba plane or standing wave function depends on the direction angle theta of the circuit. The travel velocity of the Rashba waves with the wave vector k(1) or k(2) are the same hk(0)/m*. The boundary conditions of the Rashba wave functions at the intersection of circuits are given from the continuity of wave functions and the conservation of current density. Using the boundary conditions of Rashba wave functions we study the transmission and reflection probabilities of Rashba electron moving in several structures, and find the interference effects of the two Rashba waves with different wave vectors caused by ferromagnetic contact or the gate. Lastly we derive the general theory of multiple branches structure. The theory can be used to design various spin polarized devices.