Tuning DNA “strings”: Modulating the rate of DNA replication with mechanical tension

Recent experiments have measured the rate of replication of DNA catalyzed by a single enzyme moving along a stretched template strand. The dependence on tension was interpreted as evidence that T7 and related DNA polymerases convert two (n = 2) or more single-stranded template bases to double helix geometry in the polymerization site during each catalytic cycle. However, we find structural data on the T7 enzyme–template complex indicate n = 1. We also present a model for the “tuning” of replication rate by mechanical tension. This model considers only local interactions in the neighborhood of the enzyme, unlike previous models that use stretching curves for the entire polymer chain. Our results, with n = 1, reconcile force-dependent replication rate studies with structural data on DNA polymerase complexes.

Indirect coupling of phosphate release to de novo tension generation during muscle contraction.

A key question in muscle contraction is how tension generation is coupled to the chemistry of the actomyosin ATPase. Biochemical and mechanochemical experiments link tension generation to a change in structure associated with phosphate release. Length-jump and temperature-jump experiments, on the other hand, implicate phase 2slow, a significantly faster, markedly strain-sensitive kinetic process in tension generation. We use a laser temperature jump to probe the kinetics and mechanism of tension generation in skinned rabbit psoas fibers--an appropriate method since both phosphate release and phase 2slow are readily perturbed by temperature. Kinetics characteristic of the structural change associated with phosphate release are observed only when phosphate is added to fibers. When present, it causes a reduction in fiber tension; otherwise, no force is generated when it is perturbed. We therefore exclude this step from tension generation. The kinetics of de novo tension generation by the temperature-jump equivalent of phase 2slow appear unaffected by phosphate binding. We therefore propose that phosphate release is indirectly coupled to de novo tension generation via a steady-state flux through an irreversible step. We conclude that tension generation occurs in the absence of chemical change as the result of an entropy-driven transition between strongly bound crossbridges in the actomyosin-ADP state. The mechanism resembles the operation of a clock, with phosphate release providing the energy to tension the spring, and the irreversible step functions as the escapement mechanism, which is followed in turn by tension generation as the movement of the hands.

Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension.

Hypoxia-inducible factor 1 (HIF-1) is found in mammalian cells cultured under reduced O2 tension and is necessary for transcriptional activation mediated by the erythropoietin gene enhancer in hypoxic cells. We show that both HIF-1 subunits are basic-helix-loop-helix proteins containing a PAS domain, defined by its presence in the Drosophila Per and Sim proteins and in the mammalian ARNT and AHR proteins. HIF-1 alpha is most closely related to Sim. HIF-1 beta is a series of ARNT gene products, which can thus heterodimerize with either HIF-1 alpha or AHR. HIF-1 alpha and HIF-1 beta (ARNT) RNA and protein levels were induced in cells exposed to 1% O2 and decayed rapidly upon return of the cells to 20% O2, consistent with the role of HIF-1 as a mediator of transcriptional responses to hypoxia.

Interfacial activation-based molecular bioimprinting of lipolytic enzymes.

Interfacial activation-based molecular (bio)-imprinting (IAMI) has been developed to rationally improve the performance of lipolytic enzymes in nonaqueous environments. The strategy combinedly exploits (i) the known dramatic enhancement of the protein conformational rigidity in a water-restricted milieu and (ii) the reported conformational changes associated with the activation of these enzymes at lipid-water interfaces, which basically involves an increased substrate accessibility to the active site and/or an induction of a more competent catalytic machinery. Six model enzymes have been assayed in several model reactions in nonaqueous media. The results, rationalized in light of the present biochemical and structural knowledge, show that the IAMI approach represents a straightforward, versatile method to generate manageable, activated (kinetically trapped) forms of lipolytic enzymes, providing under optimal conditions nonaqueous rate enhancements of up to two orders of magnitude. It is also shown that imprintability of lipolytic enzymes depends not only on the nature of the enzyme but also on the "quality" of the interface used as the template.

Efeito do cobre como adição interfacial no sistema tribológico pino X disco.

O presente trabalho de mestrado teve como meta realizar um estudo do comportamento do cobre particulado em ensaios tribológicos do tipo pino contra disco. O cobre é atualmente utilizado em até 15% em massa das pastilhas de freios automotivos e tal utilização é responsável pela emissão de até 70% do cobre particulado presente no ar. Devido ao caráter carcinogênico do cobre, se faz necessária sua substituição. Foram realizados ensaios tribológicos pino disco com adição de diferentes meios interfaciais. Foram utilizados pares tribológicos aço/aço, em ensaios a seco de pino contra disco com adição de meio interfacial nanoparticulado de óxido de ferro, grafite e de cobre metálico em diferentes granulometrias (400 m, 20 m e 50 nm). Após os ensaios, amostras das superfícies de pinos e discos para cada uma das adições de cobre, bem como para a condição sem adição de meio interfacial, foram caracterizadas utilizando técnicas de microscopia eletrônica de varredura, de forma a entender o comportamento das partículas de cobre e sua contribuição para o coeficiente de atrito. As adições de cobre obtiveram os maiores coeficientes de atrito, e entre elas os coeficientes de atrito foram mais altos durante todos os ensaios para a adição de 50 nm, seguido de 20 m e 400 m. A análise das superfícies tribológicas em MEV mostrou heterogeneidade das superfícies ensaiadas em relação à presença de debris oxidados e camadas compactas. Observou-se a presença de cobre apenas nas superfícies ensaiadas com adição dos cobres de 50 nm e 20 m. A presença de um filme óxido compacto e contínuo foi observada apenas nas superfícies tribológicas ensaiadas sem adição de meio interfacial e com adição de cobre a 400 m.

Regulation of Sticholysin II-Induced Pore Formation by Lipid Bilayer Composition, Phase State, and Interfacial Properties

Sticholysin II (StnII) is a pore-forming toxin that uses sphingomyelin (SM) as the recognition molecule in targeting membranes.After StnII monomers bind to SM, several toxin monomers act in concert to oligomerize into a functional pore. The regulation of StnII binding to SM, and the subsequent pore-formation process, is not fully understood. In this study, we examined how the biophysical properties of bilayers, originating from variations in the SM structure, from the presence of sterol species, or from the presence of increasingly polyunsaturated glycerophospholipids,affected StnII-induced pore formation. StnII-induced pore formation, as determined from calcein permeabilization, was fastest in the pure unsaturated SM bilayers. In 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/saturated SM bilayers (4:1 molar ratio), pore formation became slower as the chain length of the saturated SMs increased from 14 up to 24 carbons. In the POPC/palmitoyl-SM (16:0-SM) 4:1 bilayers, SM could not support pore formation by StnII if dimyristoyl-PC was included at 1:1 stoichiometry with 16:0-SM, suggesting that free clusters of SM were required for toxin binding and/or pore formation. Cholesterol and other sterols facilitated StnII-induced pore formation markedly, but the efficiency did not appear to correlate with the sterol structure. Benzyl alcohol was more efficient than sterols in enhancing the pore-formation process, suggesting that the effect on pore formation originated from alcohol-induced alteration of the hydrogen-bonding network in the SM-containing bilayers. Finally, we observed that pore formation by StnII was enhanced in the PC/16:0-SM 4:1 bilayers, in which the PC was increasingly unsaturated. We conclude that the physical state of bilayer lipids greatly affected pore formation by StnII. Phase boundaries were not required for pore formation, although SM in a gel state attenuated pore formation.

Exploring the interfacial neutral pH region of Pt(111) electrodes

The interfacial properties of Pt(111) single crystal electrodes have been investigated in the pH range 3 < pH < 5 in order to obtain information about the acidity of electrosorbed water. Proper experimental conditions are defined to avoid local pH changes while maintaining the absence of specifically adsorbed anions and preserving the cleanliness of the solution. For this purpose, buffer solutions resulting from mixtures of NaF and HClO4 are used. Total charge curves are obtained at different pHs from the integration of the voltammetric currents in combination with CO charge displacement experiments. Analysis of the composition of the interphase as a function of the pH provides information for the understanding of the notion of interfacial pH.

Towards the understanding of the interfacial pH scale at Pt(1 1 1) electrodes

The determination of the potentials of zero total and free charge, pztc and pzfc respectively, were made in a wide pH range by using the CO displacement method and the same calculation assumptions used previously for Pt(1 1 1) electrodes in contact with non-specifically adsorbing anions. Calculation of the pzfc involves, in occasions, long extrapolations that lead us to the introduction of the concept of potential of zero extrapolated charge (pzec). It was observed that the pztc changes with pH but the pzec is independent of this parameter. It was observed that the pztc > pzec at pH > 3.4 but the opposite is true for pH > 3.4. At the latter pH both pzec and pztc coincide. This defines two different pH regions and means that adsorbed hydrogen has to be corrected in the “acidic” solutions at the pztc while adsorbed OH is the species to be corrected in the “alkaline” range. The comparison of the overall picture suggests that neutral conditions at the interface are attained at significantly acidic solutions than those at the bulk.

Role of the interfacial water structure on electrocatalysis: Oxygen reduction on Pt(1 1 1) in methanesulfonic acid

Most of electrocatalytic reactions occur in an aqueous environment. Understanding the influence of water structure on reaction dynamics is fundamental in electrocatalysis. In this work, the role of liquid water structure on the oxygen reduction at Pt(1 1 1) electrode is analyzed in methanesulfonic (MTSA) and perchloric acids. This is because these different anions can exert a different influence on liquid water structure. Results reveal a lower ORR electrode activity in MTSA than in HClO4 solutions and they are discussed in light of anion's influence on water structural ordering. From them, the existence of an outer-sphere, rate determining, step in the ORR mechanism is suggested.

Jordan, a state of tension /

Bibliography: p. 401-424.

Oxygen consumption by the isolated rat liver : effects of hematocrit, temperature, perfusion rate and oxygen tension /

Reproduced by Armed Services Technical Information Agency, Arlington, Va.

Using an outflow meter to predict braking traction speed gradients as a function of surface tension. Technical report.

Mode of access: Internet.

Studies of interfacial effects between mercury and steel /

"Work performed under Contract No. AT-(40-1)-1310."

Axial tension and bending interaction curves for members loaded inelastically,

Mode of access: Internet.