The Mechanism by which Oxygen and Cytochrome \u3ci\u3ec\u3c/i\u3e Increase the Rate of Electron Transfer from Cytochrome a to Cytochrome a3 of Cytochrome \u3ci\u3ec\u3c/i\u3e Oxidase

When cytochrome c oxidase is isolated from mitochondria, the purified enzyme requires both cytochrome c and O2 to achieve its maximum rate of internal electron transfer from cytochrome a to cytochrome a3. When reductants other than cytochrome c are used, the rate of internal electron transfer is very slow. In this paper we offer an explanation for the slow reduction of cytochrome a3 when reductants other than cytochrome c are used and for the apparent allosteric effects of cytochrome c and O2. Our model is based on the conventional understanding of cytochrome oxidase mechanism (i.e. electron transfer from cytochrome a/Cu(A) to cytochrome a3/Cu(B)), but assumes a relatively rapid two-electron transfer between cytochrome a/Cu(A) and cytochrome a3/Cu(B) and a thermodynamic equilibrium in the \u27resting\u27 enzyme (the enzyme as isolated) which favors reduced cytochrome a and oxidized cytochrome a3. Using the kinetic constants that are known for this reaction, we find that the activating effects of O2 and cytochrome c on the rate of electron transfer from cytochrome a to cytochrome a3 conform to the predictions of the model and so provide no evidence of any allosteric effects or control of cytochrome c oxidase by O2 or cytochrome c

Coarse-grained model of entropic allostery

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins

A first--order irreversible thermodynamic approach to a simple energy converter

Several authors have shown that dissipative thermal cycle models based on Finite-Time Thermodynamics exhibit loop-shaped curves of power output versus efficiency, such as it occurs with actual dissipative thermal engines. Within the context of First-Order Irreversible Thermodynamics (FOIT), in this work we show that for an energy converter consisting of two coupled fluxes it is also possible to find loop-shaped curves of both power output and the so-called ecological function against efficiency. In a previous work Stucki [J.W. Stucki, Eur. J. Biochem. vol. 109, 269 (1980)] used a FOIT-approach to describe the modes of thermodynamic performance of oxidative phosphorylation involved in ATP-synthesis within mithochondrias. In that work the author did not use the mentioned loop-shaped curves and he proposed that oxidative phosphorylation operates in a steady state simultaneously at minimum entropy production and maximum efficiency, by means of a conductance matching condition between extreme states of zero and infinite conductances respectively. In the present work we show that all Stucki's results about the oxidative phosphorylation energetics can be obtained without the so-called conductance matching condition. On the other hand, we also show that the minimum entropy production state implies both null power output and efficiency and therefore this state is not fulfilled by the oxidative phosphorylation performance. Our results suggest that actual efficiency values of oxidative phosphorylation performance are better described by a mode of operation consisting in the simultaneous maximization of the so-called ecological function and the efficiency.Comment: 20 pages, 7 figures, submitted to Phys. Rev.

Optical and structural characterization of Ge clusters embedded in ZrO2

The change of optical and structural properties of Ge nanoclusters in ZrO2 matrix have been investigated by spectroscopic ellipsometry versus annealing temperatures. Radio-frequency top-down magnetron sputtering approach was used to produce the samples of different types, i.e. single-layers of pure Ge, pure ZrO2 and Ge-rich-ZrO2 as well as multi-layers stacked of 40 periods of 5-nm-Ge-rich-ZrO2 layers alternated by 5-nm-ZrO2 ones. Germanium nanoclusters in ZrO2 host were formed by rapid-thermal annealing at 600-800 ∘C during 30 s in nitrogen atmosphere. Reference optical properties for pure ZrO2 and pure Ge have been extracted using single-layer samples. As-deposited multi-layer structures can be perfectly modeled using the effective medium theory. However, annealed multi-layers demonstrated a significant diffusion of elements that was confirmed by medium energy ion scattering measurements. This fact prevents fitting of such annealed structure either by homogeneous or by periodic multi-layer model

Cosmic-ray strangelets in the Earth's atmosphere

If strange quark matter is stable in small lumps, we expect to find such lumps, called ``strangelets'', on Earth due to a steady flux in cosmic rays. Following recent astrophysical models, we predict the strangelet flux at the top of the atmosphere, and trace the strangelets' behavior in atmospheric chemistry and circulation. We show that several strangelet species may have large abundances in the atmosphere; that they should respond favorably to laboratory-scale preconcentration techniques; and that they present promising targets for mass spectroscopy experiments.Comment: 28 pages, 4 figures, revtex

Ground-state properties of tubelike flexible polymers

In this work we investigate structural properties of native states of a simple model for short flexible homopolymers, where the steric influence of monomeric side chains is effectively introduced by a thickness constraint. This geometric constraint is implemented through the concept of the global radius of curvature and affects the conformational topology of ground-state structures. A systematic analysis allows for a thickness-dependent classification of the dominant ground-state topologies. It turns out that helical structures, strands, rings, and coils are natural, intrinsic geometries of such tubelike objects

Maintenance of respiratory control in mitochondria after rate zonal centrifugation

The respiratory control of rat liver mitochondria is lost when they are subjected to rate zonal centrifugation in a sucrose gradient (8.0% to 46.6%, w/w) at values for ω 2 t necessary for resolution. High sucrose concentration and high ω 2 t are both responsible. Respiratory control can be maintained in iso-osmotic Ficoll + 8.3% sucrose media, and after zonal centrifugation in such media at values of ω 2 t sufficient for resolution.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44800/1/10863_2005_Article_BF01539061.pd