Spectral analysis of cytochrome c: effect of heme conformation, axial ligand, peripheral substituents and local electric fields,

We present in this work low-temperature visible absorption spectra for recombinant Thermus thermophilus cytochrome c 552 . The Q-band presents a remarkable splitting at low temperature. We performed quantum chemical calculations to evaluate quantitatively the effect of heme conformation, axial ligand, peripheral substituents and local electric fields on the electronic spectra. In an attempt to find correlation between protein structure and spectral splitting, we carried out the same calculations on three other cytochrome c's: horse heart, tuna heart, and yeast. The quantum chemical calculations were performed at the INDO level with extensive configuration interaction. The electric field at the heme pocket was included in the calculations through a set of point charges fitting the actual electric field. The results obtained show clearly that all mentioned effects contribute to the observed spectral splitting in a complex nonadditive way

Confinamento e localização nas propriedades ópticas de heteroestruturas semicondutoras

Orientador: Maria Jose Santos Pompeu BrasilTese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb WataghinResumo: O objetivo deste trabalho, é a determinação de efeitos de interface nas propriedades ópticas de heteroestruturas semicondutoras. Sendo esta um área que tem tido intenso desenvolvimento nos últimos 20 anos, cabe perguntar que novas contribuições podem ser feitas. Uma particularidade deste campo de trabalho, está em que modelos simples conseguem explicar as tendências gerais observadas na prática, de modo que novos resultados experimentais vêm sempre acompanhados de interpretações qualitativas. Quando se pretende ir além destas generalizações semi-quantitativas observa-se que a dinâmica dos processos de emissão óptica em heteroestruturas semicondutoras dominada por rugosidade de interfaces é sumamente complexa. Deparamo-nos assim com a necessidade de estabelecer um modelo geral que descreva de forma precisa os fenômenos observados. Neste trabalho, estabelecemos as bases para um modelo quantitativo de interpretação de espectros de emissão óptica de heteroestruturas semicondutoras. Mediante a análise detalhada de experiências de magnetoluminescência e fotoluminescência resolvida no tempo sobre um conjunto de amostras com diferentes níveis de rugosidade de interface, determinamos os ingredientes físicos básicos na descrição dos processos dinâmicos excitônicos associados à emissão óptica. O alto grau de especialização da maioria das áreas de pesquisa atualmente, faz com que seja difícil fazer acessível um texto deste tipo a quem não pertence a essa área. Optamos então por dar uma introdução bastante geral, com idéias físicas simples com o objetivo principal de familiarizar o leitor com os termos utilizados, e discutir em detalhe e com rigor os resultados obtidos só nos Capítulos específicosAbstract: In this work we study the effects of interface roughness in the optical properties of semiconductor heterostructures. Although simple models can explain general trends observed in practice, quantitative information about the dynamic of the optical emission processes can only be obtained with more general and complex models. We develop a quantitative model in order to interpret optical emission spectra of semiconductor heterostructures. Comparing results of magnetoluminescence and time resolved photoluminescence on a set of samples with different degree of interface roughness we determine the basic physical ingredients necessary to describe dynamic processes of excitons in optical emissionDoutoradoFísicaDoutor em Ciência

Dissecting metal ion–dependent folding and catalysis of a single DNAzyme

Protein metalloenzymes use various modes for functions where metal–dependent global conformational change is required in some cases, but not in others. In contrast, most ribozymes appear to require a global folding that almost always precedes enzyme reactions. Herein we studied metal–dependent folding and cleavage activity of the 8–17 DNAzyme using single molecule fluorescence resonance energy transfer (FRET). Addition of Zn(2+) and Mg(2+) resulted in a folding step followed by cleavage reaction, suggesting that the DNAzyme may require metal–dependent global folding for activation. In the presence of Pb(2+), however, cleavage reaction occurred without a precedent folding step, suggesting that the DNAzyme may be prearranged to accept Pb(2+) for the activity. This feature may contribute to the remarkably fast Pb(2+)–dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use

Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy

Single-stranded DNA (ssDNA) is an essential intermediate in various DNA metabolic processes and interacts with a large number of proteins. Due to its flexibility, the conformations of ssDNA in solution can only be described using statistical approaches, such as flexibly jointed or worm-like chain models. However, there is limited data available to assess such models quantitatively, especially for describing the flexibility of short ssDNA and RNA. To address this issue, we performed FRET studies of a series of oligodeoxythymidylates, (dT)(N), over a wide range of salt concentrations and chain lengths (10 ≤ N ≤ 70 nucleotides), which provide systematic constraints for testing theoretical models. Unlike in mechanical studies where available ssDNA conformations are averaged out during the time it takes to perform measurements, fluorescence lifetimes may act here as an internal clock that influences fluorescence signals depending on how fast the ssDNA conformations fluctuate. A reasonably good agreement could be obtained between our data and the worm-like chain model provided that limited relaxations of the ssDNA conformations occur within the fluorescence lifetime of the donor. The persistence length thus estimated ranges from 1.5 nm in 2 M NaCl to 3 nm in 25 mM NaCl