The two -state model of receptor activation: The agonist and the efficacy

The Two State model describes how drugs activate receptors by inducing or supporting a conformational change in the receptor from “off” to “on”. The beta 2 adrenergic receptor system is the model system which was used to formalize the concept of two states, and the mechanism of hormone agonist stimulation of this receptor is similar to ligand activation of other seven transmembrane receptors. Hormone binding to beta 2 adrenergic receptors stimulates the intracellular production of cyclic adenosine monophosphate (cAMP), which is mediated through the stimulatory guanyl nucleotide binding protein (Gs) interacting with the membrane bound enzyme adenylylcyclase (AC). ^ The effects of cAMP include protein phosphorylation, metabolic regulation and transcriptional regulation. The beta 2 adrenergic receptor system is the most well known of its family of G protein coupled receptors. Ligands have been scrutinized extensively in search of more effective therapeutic agents at this receptor as well as for insight into the biochemical mechanism of receptor activation. Hormone binding to receptor is thought to induce a conformational change in the receptor that increases its affinity for inactive Gs, catalyzes the release of GDP and subsequent binding of GTP and activation of Gs. ^ However, some beta 2 ligands are more efficient at this transformation than others, and the underlying mechanism for this drug specificity is not fully understood. The central problem in pharmacology is the characterization of drugs in their effect on physiological systems, and consequently, the search for a rational scale of drug effectiveness has been the effort of many investigators, which continues to the present time as models are proposed, tested and modified. ^ The major results of this thesis show that for many b2 -adrenergic ligands, the Two State model is quite adequate to explain their activity, but dobutamine (+/−3,4-dihydroxy-N-[3-(4-hydroxyphenyl)-1-methylpropyl]- b -phenethylamine) fails to conform to the predictions of the Two State model. It is a weak partial agonist, but it forms a large amount of high affinity complexes, and these complexes are formed at low concentrations much better than at higher concentrations. Finally, dobutamine causes the beta 2 adrenergic receptor to form high affinity complexes at a much faster rate than can be accounted for by its low efficiency activating AC. Because the Two State model fails to predict the activity of dobutamine in three different ways, it has been disproven in its strictest form. ^

Heavy metal contents in bottom sediments and Fe-Mn nodules and their states in bottom and interstitial waters from the Clarion-Clipperton province

Ultrafiltration with tagged atoms was used to study physicochemical states (dissolved, colloidal, suspended) of Mn, Co, Ni, Zn, and Ce in bottom and interstitial waters collected in two areas of the Pacific Ocean with Fe-Mn nodules of different size, shape, structure and origin in different abundances. Use of filters with pore diameter of 0.05 ?m allowed to identify colloidal forms of the metals in bottom sediments and interstitial waters. It was demonstrated experimentally that differences in physicochemical situation in the studied areas could result in formation of nodules by different mechanisms, producing characteristic differences that were observed.

Ocean acidification not likely to affect the survival and fitness of two yemperate benthic foraminiferal species: results from culture experiments

Specimens of Bolivina argentea and Bulimina marginata, two widely distributed temperate benthic foraminiferal species, were cultured at constant temperature and controlled pCO2 (ambient, 1000 ppmv, and 2000 ppmv) for six weeks to assess the effect of elevated atmospheric CO2 concentrations on survival and fitness using Adenosine Triphosphate (ATP) analyses and on shell microfabric using high-resolution SEM and image analysis. To characterize the carbonate chemistry of the incubation seawater, total alkalinity and dissolved inorganic carbon were measured approximately every two weeks. Survival and fitness were not directly affected by elevated pCO2 and the concomitant decrease in seawater pH and calcite saturation states (Omega c), even when seawater was undersaturated with respect to calcite. These results differ from some previous observations that ocean acidification can cause a variety of effects on benthic foraminifera, including test dissolution, decreased growth, and mottling (loss of symbiont color in symbiont-bearing species), suggesting that the benthic foraminiferal response to ocean acidification may be species specific. If so, this implies that ocean acidification may lead to ecological winners and losers even within the same taxonomic group.

Two-layer particle filter for multiple target detection and tracking

This paper deals with the detection and tracking of an unknown number of targets using a Bayesian hierarchical model with target labels. To approximate the posterior probability density function, we develop a two-layer particle filter. One deals with track initiation, and the other with track maintenance. In addition, the parallel partition method is proposed to sample the states of the surviving targets.

X-Ray Diffraction, Calorimetric and Dielectric Relaxation Study of the Amorphous and Smectic States of a Main Chain Liquid Crystalline Polymer

Los polímeros cristales líquidos (LCP) son sistemas complejos que forman mesofases que presentan orden orientacional y polímeros amorfos. Con frecuencia, el estado amorfo isotrópico no puede ser estudiado debido a la rápida formación de mesofases. En este trabajo se ha sintetizado y estudiado un nuevo LCP: poli(trietilenglicol metil p, p '-bibenzoato), PTEMeB. Este polímero presenta una formación de mesofase bastante lenta haciendo posible estudiar de forma independiente tanto los estados amorfo y de cristal líquidos. La estructura y las transiciones de fase del PTEMeB han sido investigados por calorimetría (DSC), con MAXS / WAXS con temperatura variable que emplean radiación de sincrotrón y con difracción de rayos X. Estos estudios han mostrado la existencia de dos transiciones vítreas, relacionadas con las fases amorfa y cristal líquido. Se ha realizado un estudio de relajación dieléctrica en amplios intervalos de temperatura y presión. Se ha encontrado que la transición vítrea dinámica de la fase amorfa es más lenta que la del cristal líquido. El estudio de la relajación ? nos ha permitido seguir la formación isoterma de la mesofase a presión atmosférica. Además, con el estudio el comportamiento dinámico a alta presión se ha encontrado que se produce la formación rápida de la mesofase inducida por cambios bruscos de presión. Liquid crystalline polymers (LCPs) are complex systems that include features of both orientationally ordered mesophases and amorphous polymers. Frequently, the isotropic amorphous state cannot be studied due to the rapid mesophase formation. Here, a new main chain LCP, poly(triethyleneglycol methyl p,p'-bibenzoate), PTEMeB, has been synthesized. It shows a rather slow mesophase formation making possible to study independently both the amorphous and the liquid crystalline states. The structure and phase transitions of PTEMeB have been investigated by calorimetry, variable-temperature MAXS/WAXS employing synchrotron radiation, and X-ray diffraction in oriented fibers. These experiments have pointed out the presence of two glass transitions, related to the amorphous or to the liquid crystal phases. Additionally, the mesophase seems to be a coexistence of orthogonal and tilted smectic phases. A dielectric relaxation study of PTEMeB over broad ranges of temperature and pressure has been performed. The dynamic glass transition turns out to be slower for the amorphous state than for the liquid crystal. Monitoring of the α relaxation has allowed us to follow the isothermal mesophase formation at atmospheric pressure. Additionally, the dynamical behavior at high pressures has pointed out the fast formation of the mesophase induced by sudden pressure changes.

Decomposition driven interface evolution for layers of binary mixtures: I. Model dirivation and base states

A dynamical model is proposed to describe the coupled decomposition and profile evolution of a free surfacefilm of a binary mixture. An example is a thin film of a polymer blend on a solid substrate undergoing simultaneous phase separation and dewetting. The model is based on model-H describing the coupled transport of the mass of one component (convective Cahn-Hilliard equation) and momentum (Navier-Stokes-Korteweg equations) supplemented by appropriate boundary conditions at the solid substrate and the free surface. General transport equations are derived using phenomenological nonequilibrium thermodynamics for a general nonisothermal setting taking into account Soret and Dufour effects and interfacial viscosity for the internal diffuse interface between the two components. Focusing on an isothermal setting the resulting model is compared to literature results and its base states corresponding to homogeneous or vertically stratified flat layers are analyzed.

Interband absorption of photons by extended states in intermediate band solar cells

This paper considers sub-bandgap photon absorption in an InAs/GaAs quantum dot matrix. Absorption coefficients are calculated for transitions from the extended states in the valence band to confined states in the conduction band. This completes a previous body of work in which transitions between bound states were calculated. The calculations are based on the empirical k·p Hamiltonian considering the quantum dots as parallelepipeds. The extended states may be only partially extended?in one or two dimensions?or extended in all three dimensions. It is found that extended-to-bound transitions are, in general, weaker than bound-to-bound transitions, and that the former are weaker when the initial state is extended in more coordinates. This study is of direct application to the research of intermediate band solar cells and other semiconductor devices based on light absorption in semiconductors nanostructured with quantum dots.

Virtual-bound, filamentary and layered states in a box-shaped quantum dot of square potential form the exact numerical solution of the effective mass Schrodinger equation

The effective mass Schrodinger equation of a QD of parallelepipedic shape with a square potential well is solved by diagonalizing the exact Hamiltonian matrix developed in a basis of separation-of-variables wavefunctions. The expected below bandgap bound states are found not to differ very much from the former approximate calculations. In addition, the presence of bound states within the conduction band is confirmed. Furthermore, filamentary states bounded in two dimensions and extended in one dimension and layered states with only one dimension bounded, all within the conduction band which are similar to those originated in quantum wires and quantum wells coexist with the ordinary continuum spectrum of plane waves. All these subtleties are absent in spherically shaped quantum dots, often used for modeling.

On a two species chemotaxis model with slow chemical diffucion.

In this paper we consider a system of three parabolic equations modeling the behavior of two biological species moving attracted by a chemical factor. The chemical substance verifies a parabolic equation with slow diffusion. The system contains second order terms in the first two equations modeling the chemotactic effects. We apply an iterative method to obtain the global existence of solutions using that the total mass of the biological species is conserved. The stability of the homogeneous steady states is studied by using an energy method. A final example is presented to illustrate the theoretical results.

Runup variability due to time dependence and stochasticity in the beach profiles: two extreme cases of the Spanish coast

Equations for extreme runup worked out from several experimental studies are compared. Infragraviatory oscillations dominate the swash in a dissipative state but not in intermediate - reflective states. Therefore two kinds of equation depending on either significant wave height, H-0, or the Iribarren number, xi(0), should be used. Through a sand bed physical model with a uniform sand bed slope, equations are proposed for both beach states, and results are compared with precedent field and physical model experiments. Once the equations are chosen, the time-longshore variability in a medium - long term time scale of the foreshore slope is evaluated in two extreme cases relating to the Spanish coast. The Salinas beach on the North coast (Bay of Biscay) displayed a permanent dissipative beach state with small variations in the beach foreshore slope both along the shore and in time, so foreshore slope deviations in a medium-long term period were irrelevant and extreme runup is predicted with the wave height worked out from the design return period. Peniscola beach on the East coast (Mediterranean sea) displayed an intermediate state. If only time variations are analysed, variations in determining extreme runup are irrelevant. In contrast, significant differences were found when the longshore variations were studied in this Mediterranean beach.

Magnetization reversal assisted by half antivortex states in nanostructured circular cobalt disks

The half antivortex, a fundamental topological structure which determines magnetization reversal of submicron magnetic devices with domain walls, has been suggested also to play a crucial role in spin torque induced vortex core reversal in circular disks. Here, we report on magnetization reversal in circular disks with nanoholes through consecutive metastable states with half antivortices. In-plane anisotropic magnetoresistance and broadband susceptibility measurements accompanied by micromagnetic simulations reveal that cobalt (Co) disks with two and three linearly arranged nanoholes directed at 45° and 135° with respect to the external magnetic field show reproducible step-like changes in the anisotropic magnetoresistance and magnetic permeability due to transitions between different intermediate states mediated by vortices and half antivortices confined to the dot nanoholes and edges, respectively. Our findings are relevant for the development of multi-hole based spintronic and magnetic memory devices.

The roles of the two proton input channels in cytochrome c oxidase from Rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transfer

The crystal structures of cytochrome c oxidase from both bovine and Paracoccus denitrificans reveal two putative proton input channels that connect the heme-copper center, where dioxygen is reduced, to the internal aqueous phase. In this work we have examined the role of these two channels, looking at the effects of site-directed mutations of residues observed in each of the channels of the cytochrome c oxidase from Rhodobacter sphaeroides. A photoelectric technique was used to monitor the time-resolved electrogenic proton transfer steps associated with the photo-induced reduction of the ferryl-oxo form of heme a3 (Fe4+ = O2−) to the oxidized form (Fe3+OH−). This redox step requires the delivery of a “chemical” H+ to protonate the reduced oxygen atom and is also coupled to proton pumping. It is found that mutations in the K channel (K362M and T359A) have virtually no effect on the ferryl-oxo-to-oxidized (F-to-Ox) transition, although steady-state turnover is severely limited. In contrast, electrogenic proton transfer at this step is strongly suppressed by mutations in the D channel. The results strongly suggest that the functional roles of the two channels are not the separate delivery of chemical or pumped protons, as proposed recently [Iwata, S., Ostermeier, C., Ludwig, B. & Michel, H. (1995) Nature (London) 376, 660–669]. The D channel is likely to be involved in the uptake of both “chemical” and “pumped” protons in the F-to-Ox transition, whereas the K channel is probably idle at this partial reaction and is likely to be used for loading the enzyme with protons at some earlier steps of the catalytic cycle. This conclusion agrees with different redox states of heme a3 in the K362M and E286Q mutants under aerobic steady-state turnover conditions.

Respiratory chain is required to maintain oxidized states of the DsbA-DsbB disulfide bond formation system in aerobically growing Escherichia coli cells

DsbA, the disulfide bond catalyst of Escherichia coli, is a periplasmic protein having a thioredoxin-like Cys-30-Xaa-Xaa-Cys-33 motif. The Cys-30–Cys-33 disulfide is donated to a pair of cysteines on the target proteins. Although DsbA, having high oxidizing potential, is prone to reduction, it is maintained essentially all oxidized in vivo. DsbB, an integral membrane protein having two pairs of essential cysteines, reoxidizes DsbA that has been reduced upon functioning. It is not known, however, what might provide the overall oxidizing power to the DsbA–DsbB disulfide bond formation system. We now report that E. coli mutants defective in the hemA gene or in the ubiA-menA genes markedly accumulate the reduced form of DsbA during growth under the conditions of protoheme deprivation as well as ubiquinone/menaquinone deprivation. Disulfide bond formation of β-lactamase was impaired under these conditions. Intracellular state of DsbB was found to be affected by deprivation of quinones, such that it accumulates first as a reduced form and then as a form of a disulfide-linked complex with DsbA. This is followed by reduction of the bulk of DsbA molecules. These results suggest that the respiratory electron transfer chain participates in the oxidation of DsbA, by acting primarily on DsbB. It is remarkable that a cellular catalyst of protein folding is connected to the respiratory chain.

Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting

Two variables define the topological state of closed double-stranded DNA: the knot type, K, and ΔLk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(ΔLk, K), is related to two conditional distributions: P(ΔLk|K), the distribution of ΔLk for a particular K, and P(K|ΔLk) and also to two simple distributions: P(ΔLk), the distribution of ΔLk irrespective of K, and P(K). We explored the relationships between these distributions. P(ΔLk, K), P(ΔLk), and P(K|ΔLk) were calculated from the simulated distributions of P(ΔLk|K) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(K|ΔLk), the distribution of knot types for a particular value of ΔLk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ΔLk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at |ΔLk| > 12, only one or two knot types dominate the P(K|ΔLk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed.