Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.

The Regulation of Photosynthetic Electron Transport during Nutrient Deprivation in Chlamydomonas reinhardtii1

The light-saturated rate of photosynthetic O2 evolution in Chlamydomonas reinhardtii declined by approximately 75% on a per-cell basis after 4 d of P starvation or 1 d of S starvation. Quantitation of the partial reactions of photosynthetic electron transport demonstrated that the light-saturated rate of photosystem (PS) I activity was unaffected by P or S limitation, whereas light-saturated PSII activity was reduced by more than 50%. This decline in PSII activity correlated with a decline in both the maximal quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers (PSII centers capable of performing a charge separation but unable to reduce the plastoquinone pool). In addition to a decline in the light-saturated rate of O2 evolution, there was reduced efficiency of excitation energy transfer to the reaction centers of PSII (because of dissipation of absorbed light energy as heat and because of a transition to state 2). These findings establish a common suite of alterations in photosynthetic electron transport that results in decreased linear electron flow when C. reinhardtii is limited for either P or S. It was interesting that the decline in the maximum quantum efficiency of PSII and the accumulation of the secondary quinone electron acceptor of PSII nonreducing centers were regulated specifically during S-limited growth by the SacI gene product, which was previously shown to be critical for the acclimation of C. reinhardtii to S limitation (J.P. Davies, F.H. Yildiz, and A.R. Grossman [1996] EMBO J 15: 2150–2159).

The synaptic activity of HsDmc1, a human recombination protein specific to meiosis

Human Dmc1 protein, a meiosis-specific homolog of Escherichia coli RecA protein, has previously been shown to promote DNA homologous pairing and strand-exchange reactions that are qualitatively similar to those of RecA protein and Rad51. Human and yeast Rad51 proteins each form a nucleoprotein filament that is very similar to the filament formed by RecA protein. However, recent studies failed to find a similar filament made by Dmc1 but showed instead that this protein forms octameric rings and stacks of rings. These observations stimulated further efforts to elucidate the mechanism by which Dmc1 promotes the recognition of homology. Dmc1, purified to a state in which nuclease and helicase activities were undetectable, promoted homologous pairing and strand exchange as measured by fluorescence resonance energy transfer (FRET). Observations on the intermediates and products, which can be distinguished by FRET assays, provided direct evidence of a three-stranded synaptic intermediate. The effects of helix stability and mismatched base pairs on the recognition of homology revealed further that human Dmc1, like human Rad51, requires the preferential breathing of A⋅T base pairs for recognition of homology. We conclude that Dmc1, like human Rad51 and E. coli RecA protein, promotes homologous pairing and strand exchange by a “synaptic pathway” involving a three-stranded nucleoprotein intermediate, rather than by a “helicase pathway” involving the separation and reannealing of DNA strands.

Excited-state dynamics in photosystem II: Insights from the x-ray crystal structure

The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.

Mechanism of oligonucleotide release from cationic liposomes.

We propose a mechanism for oligonucleotide (ODN) release from cationic lipid complexes in cells that accounts for various observations on cationic lipid-nucleic acid-cell interactions. Fluorescent confocal microscopy of cells treated with rhodamine-labeled cationic liposome/ fluorescein-labeled ODN (F-ODN) complexes show the F-ODN separates from the lipid after internalization and enters the nucleus leaving the fluorescent lipid in cytoplasmic structures. ODN displacement from the complex was studied by fluorescent resonance energy transfer. Anionic liposome compositions (e.g., phosphatidylserine) that mimic the cytoplasmic facing monolayer of the cell membrane released ODN from the complex at about a 1:1 (-/+) charge ratio. Release was independent of ionic strength and pH. Physical separation of the F-ODN from monovalent and multivalent cationic lipids was confirmed by gel electrophoresis. Fluid but not solid phase anionic liposomes are required, whereas the physical state of the cationic lipids does not effect the release. Water soluble molecules with a high negative linear charge density, dextran sulfate, or heparin also release ODN. However, ATP, spermidine, spermine, tRNA, DNA, polyglutamic acid, polylysine, bovine serum albumin, or histone did not release ODN, even at 100-fold charge excess (-/+). Based upon these results, we propose that the complex, after internalization by endocytosis, induces flip-flop of anionic lipids from the cytoplasmic facing monolayer. Anionic lipids laterally diffuse into the complex and form a charged neutralized ion-pair with the cationic lipids. This leads to displacement of the ODN from the cationic lipid and its release into the cytoplasm.

Microspectroscopic imaging tracks the intracellular processing of a signal transduction protein: fluorescent-labeled protein kinase C beta I.

We have devised a microspectroscopic strategy for assessing the intracellular (re)distribution and the integrity of the primary structure of proteins involved in signal transduction. The purified proteins are fluorescent-labeled in vitro and reintroduced into the living cell. The localization and molecular state of fluorescent-labeled protein kinase C beta I isozyme were assessed by a combination of quantitative confocal laser scanning microscopy, fluorescence lifetime imaging microscopy, and novel determinations of fluorescence resonance energy transfer based on photobleaching digital imaging microscopy. The intensity and fluorescence resonance energy transfer efficiency images demonstrate the rapid nuclear translocation and ensuing fragmentation of protein kinase C beta I in BALB/c3T3 fibroblasts upon phorbol ester stimulation, and suggest distinct, compartmentalized roles for the regulatory and catalytic fragments.

Radiation target analysis of RNA.

Ribozymes are polynucleotide molecules with intrinsic catalytic activity, capable of cleaving nucleic acid substrates. Large RNA molecules were synthesized containing a hammerhead ribozyme moiety of 52 nucleotides linked to an inactive leader sequence, for total lengths of either 262 or 1226 nucleotides. Frozen RNAs were irradiated with high energy electrons. Surviving ribozyme activity was determined using the ability of the irradiated ribozymes to cleave a labeled substrate. The amount of intact RNA remaining was determined from the same irradiated samples by scanning the RNA band following denaturing gel electrophoresis. Radiation target analyses of these data revealed a structural target size of 80 kDa and a ribozyme activity target size of 15 kDa for the smaller ribozyme, and 319 kDa and 16 kDa, respectively, for the larger ribozyme. The disparity in target size for activity versus structure indicates that, in contrast to proteins, there is no spread of radiation damage far from the primary site of ionization in RNA molecules. The smaller target size for activity indicates that only primary ionizations occurring in the specific active region are effective. This is similar to the case for oligosaccharides. We concluded that the presence of the ribose sugar in the polymer chain restricts radiation damage to a small region and prevents major energy transfer throughout the molecule. Radiation target analysis should be a useful technique for evaluating local RNA:RNA and RNA:protein interactions in vitro.

Ultraviolet-B photodestruction of a light-harvesting complex.

Cyanobacteria are important contributors to global photosynthesis in both marine and terrestrial environments. Quantitative data are presented on UV-B-induced damage to the major cyanobacterial photosynthetic light harvesting complex, the phycobilisome, and to each of its constituent phycobiliproteins. The photodestruction quantum yield, phi295 nm, for the phycobiliproteins is high (approximately 10(-3), as compared with approximately 10(-7) for visible light). Energy transfer on a picosecond time scale does not compete with photodestruction. Photodamage to phycobilisomes in vitro and in living cells is amplified by causing dissociation and loss of function of the complex. In photosynthetic organisms, UV-B damage to light-harvesting complexes may significantly exceed that to DNA.

Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye.

Isolated guanine quadruplex structures have been described at high resolution both in solution and in the solid state. The existence of this unusual DNA structure in vivo and its biological significance remain to be determined. We describe the binding of 3,3'-diethyloxadicarbocyanine to dimeric hairpin guanine quadruplexes. This interaction results in a set of unique spectrophotometric signatures, none of which arises from binding to single strands or Watson-Crick duplexes. These unique signatures include a new absorbance peak (lambda max = 534 nm), an induced circular dichroism (lambda = 534-626 nm), a quenching of the dye fluorescence upon excitation with visible light, and strong energy transfer from DNA. This last effect provides the basis for detecting hairpin quadruplex structures in the presence of excess amounts of nonquadruplex DNA structures, such as single strands and Watson-Crick duplexes. The mechanism of quadruplex recognition by this dye is discussed, along with the possibility of using this dye as a probe for hairpin quadruplex structures in vitro and in vivo.

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.

Ion heating in transitions to CERC in the stellarator TJ-II

In TJ-II stellarator plasmas, in the electron cyclotron heating regime, an increase in the ion temperature is observed, synchronized with that of the electron temperature, during the transition to the core electron-root confinement (CERC) regime. This rise in ion temperature should be attributed to the joint action of the electron–ion energy transfer (which changes slightly during the CERC formation) and an enhancement of the ion confinement. This improvement must be related to the increase in the positive electric field in the core region. In this paper, we confirm this hypothesis by estimating the ion collisional transport in TJ-II under the physical conditions established before and after the transition to CERC. We calculate a large number of ion orbits in the guiding-centre approximation considering the collisions with a background plasma composed of electrons and ions. The ion temperature profile and the thermal flux are calculated in a self-consistent way, so that the change in the ion heat transport can be assessed.

Reações fotoinduzidas em alguns complexos de rênio e desenvolvimento de dispositivos moleculares

Neste trabalho foi realizado o estudo do comportamento fotoquímico e fotofísico de complexos mononucleares de rênio do tipo fac-[Re(CO)3(N N)(L)]+(N N = 1,10-fenantrolina, phen, dipirido[3,2-a:2,3-c]fenazina, dppz, L= trans-1,2bis(4-piridil)etileno, trans-bpe, trans-4-estirilpiridina. trans-stpy) e dos complexos binucleares [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+, [(CO)3(phen)Re(trans-bpe)Fe(CN5]2- e [(phen)(CO)3Re(trans-bpe)Os(terpy)(bpy)]3+. O enfoque principal deste trabalho é a investigação das propriedades fotoquímicas dos complexos fac-[ Re(CO)3(phen)(trans-bpe)]+, fac-[Re(CO)3(phen)(trans-stpy)]+ fac-[Re(CO)3(dppz)(trans-bpe)+ e [(CO)3(phen)Re(trans-bpe)Re(phen)(CO)3]2+. Observou-se que os compostos em solução de acetonitrila, sob irradiação a 313, 334 ou 365 nm, apresentam variação espectral com definição de pontos isosbésticos, resultante do processo de fotoisomerização trans→cis do ligante coordenado trans-piridil etileno. Os rendimentos quânticos, Φ, da reação de fotoisomerização foram calculados com base no decaimento espectral das bandas de absorção das transições eletrônicas. Os valores médios determinados para a fotoisomeriação dos complexos em solução de CH3CN variam de 0,15 - 0,39 sob excitação a 313 nm e de 0,12 - 0,33 sob excitação a 365 nm. As reações de fotoisomerização foram monitoradas também por medidas de emissão e por RMN de 1H. Observou-se um aumento da intensidade de luminescência com o tempo de irradiação dos complexos, consistente com o estado emissivo 3MLCT dπ[(Re)→π*(α-diimina). Após irradiação, as reações de fotoisomerização dos complexos foram monitoradas por RMN de 1H. Os sinais de prótons do isômero trans tiveram um decréscimo gradual, enquanto que a intensidade dos sinais referentes aos prótons da espécie cis aumentaram. Os rendimentos quânticos para o processo de fotoisomerização dos complexos foram calculados através da integração das áreas dos sinais de prótons. Os valores obtidos foram maiores, pelo menos o dobro, que aqueles valores obtidos via espectroscopia UV-Vis. O comportamento fotoquímico dos complexos incorporados em polimetacrilato de metila, PMMA, foi também investigado. A fotólise cios complexos em filmes de PMMA conduz à variação espectral, de absorção e emissão, similar àquela observada em solução de acetonitrila, atribuícla ao processo de fotoisomerização trans → cis do ligante coordenado. Este estudo mostra que a fotoisomerização do ligante coordenado trans-piridil etileno pode ser promovida também em meio rígido. Essa característica. típica de um dispositivo molecular, pode ser convenientemente explorada no desenvolvimento de fotossensores. As medidas de TRIR mostram que o estado excitado de menor energia para o fac-[Re(CO)3(phen)(trans-bpe)+ é o 3ππ*. Para o fac-[Re(CO)3(phen)(cis-bpe)]+ a ordem dos estados excitados aparecem invertidas com o 3MLCT <3ππ*, evidenciado pela emissão do complexo cis à temperatura ambiente. Nas espécies binucleares, [(phen) Re(CO)3(trans-bpe)Os(terpy)(bpy)]3+ e [(CO)3(phen)Re(trans-bpe)Fe(CN)5]2-, a fotoisomerização trans → cis do ligante coordenado trans-bpe, característica da subunidade fac-[Re(CO)3(phen)(trans-bpe)]+, é inibida pela competição de transferência de energia intramolecular. Em meio rígido, em PMMA ou em EPA a 77 K, os máximos de emissão dos complexos fac-[Re(CO)3(phen)(cis-bpe)]+, fac-[Re(CO)3(phen)(cis-stpy)r e [(CO)3(phen)Re(cis-bpe)Re(phen)(CO)3]2+ sofrem um deslocamento hipsocrômico com o aumento da rigidez do meio. As mudanças nas propriedades emissivas, em termos de energia e tempo de vida do estado excitado, são discutidas baseadas no efeito rigidocrômico luminescente. O trabalho mostra uma forma interessante de fotos sensibilizar um substrato orgâmco usando o fato de que a coordenação estende a absorção do ligante a uma região de comprimento de onda maior e promove a fotoisomerização assistida por complexos metálicos em energias menores.

Fracturas pélvicas em doentes politraumatizados : um estudo caso

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

CENP-C reshapes and stabilizes CENP-A nucleosomes at the centromere

Inheritance of each chromosome depends upon its centromere. A histone H3 variant, centromere protein A (CENP-A), is essential for epigenetically marking centromere location. We find that CENP-A is quantitatively retained at the centromere upon which it is initially assembled. CENP-C binds to CENP-A nucleosomes and is a prime candidate to stabilize centromeric chromatin. Using purified components, we find that CENP-C reshapes the octameric histone core of CENP-A nucleosomes, rigidifies both surface and internal nucleosome structure, and modulates terminal DNA to match the loose wrap that is found on native CENP-A nucleosomes at functional human centromeres. Thus, CENP-C affects nucleosome shape and dynamics in a manner analogous to allosteric regulation of enzymes. CENP-C depletion leads to rapid removal of CENP-A from centromeres, indicating their collaboration in maintaining centromere identity.

Reiki como terapia não convencional: conhecimentos dos enfermeiros

Enquadramento: O interesse pelas Terapias Não Convencionais (TNC) teve um grande desenvolvimento no início deste século. O Reiki é uma terapia realizada através da colocação das mãos em pontos específicos do corpo e que utiliza a transferência de energia para proporcionar um bem-estar natural. A Enfermagem em especial a de Reabilitação, também apresenta dentro das suas intervenções específicas, uma vertente essencial baseada no toque à pessoa a quem presta cuidados, sendo por isso importante possuir conhecimentos sobre estas técnicas. Objetivos: Avaliar os conhecimentos dos enfermeiros acerca do Reiki e identificar fatores determinantes nesse conhecimento. Métodos: Trata-se de um estudo transversal, descritivo e correlacional, realizado numa amostra de 49 enfermeiros a exercer funções em instituições da região centro do país, baseado num questionário de conhecimentos elaborado pelas investigadoras. Resultados: Constatamos que os conhecimentos globais dos enfermeiros sobre o Reiki eram para 59,1% razoáveis, para 38,6% altos e apenas 2,3% apresentava baixos conhecimentos. Pudemos verificar diferenças estatisticamente significativas entre o “Conhecimento Total”, e as variáveis “ter iniciação em Reiki” e “ter recebido tratamento com Reiki” para o grupo de enfermeiros dos Cuidados Diferenciados (CD). Encontraram-se diferenças estatisticamente significativas, também, entre a dimensão “Conceito e História” e grupos etários, habilitações literárias, categoria profissional e tempo de serviço para os enfermeiros a exercer nos CD. Conclusão: Os conhecimentos dos enfermeiros sobre o Reiki são bastante significativos, sendo estes claramente superiores no grupo que exerce funções em CD. Por outro lado encontrámos fatores que interferem na determinação desses conhecimentos e que por isso importa controlar. Palavras-chave: Reiki; Enfermagem; Conhecimentos.