Stopped-flow studies of cytochrome oxidase reconstituted into liposomes: proton pumping and control of activity

The transient kinetics of proton pumping and the electron transfer properties of cytochrome oxidase inserted into small unilamellar vesicles have been investigated by stopped-flow spectrophotometry. In the presence of valinomycin, proton pumping and cytochrome c oxidation by cytochrome oxidase are synchronous up to rate constants of approximately 9 sec-1. Moreover, the enzyme depleted of subunit III ("three-less oxidase") was also shown to pump protons, although with a significantly smaller stoichiometry. Thus, subunit III is not the only (or even the main) proton channel, although it may be involved in the regulation of activity. The kinetics of cytochrome c oxidation by COV in the absence and in the presence of ionophores have been investigated. Analysis of the time course of the process in the transient and steady state phases indicates that the onset of control by the electrochemical gradient follows the transfer of four electrons, i.e., one complete turnover of the oxidase. Two possible alternative interpretations for the control of the turnover phase are presented and discussed.     

Concerted changes in an allosteric macromolecule

This paper reports an analysis of the behaviour of allosteric macromolecules in the framework of the simple Monod-Wyman-Changeux model. The emphasis is on the analysis of the reciprocal influence of the various parameters which enter into the model, with particular reference to the relationship among a number of sites in the macromolecule and the Hill parameter n. This appears of interest for the behaviour of some of the extremely large respiratory proteins containing up to 100, or more, oxygen binding sites, where a very large value of n is often coupled with a relatively small value of the total interaction free energy.     

Limited seed retention during winter inhibits vegetation establishment in spring,affecting lateral marsh expansion capacity

Coastal systems worldwide deliver vital ecosystem services, such as biodiversity, carbon sequestration, and coastal protection. Effectivity of these ecosystem services increases when vegetation is present. Understanding the mechanisms behind vegetation establishment in bio‐geomorphic systems is necessary to understand their ability to recover after erosive events and potential adaptations to climate change. In this study, we examined how seed availability affects vegetation establishment in the salt marsh–intertidal flat transition zone: the area with capacity for lateral marsh expansion. This requires vegetation establishment; therefore, seed availability is essential. In a 6‐month field experiment, we simulated a before and after winter seed dispersal at two locations, the salt‐marsh vegetation edge and the intertidal flat, and studied seed retention, the seed bank, and the seed viability of three pioneer marsh species: Salicornia procumbens, Aster tripolium, and Spartina anglica. During winter storm conditions, all supplied seeds eroded away with the sediment surface layer. After winter, supplied seeds from all three species were retained, mostly at the surface while 9% was bioturbated downwards. In the natural seed bank, A. tripolium and S. anglica were practically absent while S. procumbens occurred more frequently. The viability of S. procumbens seeds was highest at the surface, between 80% and 90%. The viability quickly decreased with depth, although viable S. procumbens seeds occurred up to 15 cm depth. Only when seeds were supplied after winter, many S. procumbens and some S. anglica individuals did establish successfully in the transition zone. Viable seed availability formed a vegetation establishment threshold, even with a local seed source. Our results suggest that, although boundary conditions such as elevation, inundation, and weather conditions were appropriate for vegetation establishment in spring, the soil surface in winter can be so dynamic that it limits lateral marsh expansion. These insights can be used for designing effective nature‐based coastal protection.     

TreeViewJ: An application for viewing and analyzing phylogenetic trees

Background  

Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images.     

Enhanced protein glutathiolation and oxidative stress in cigarette smokers

There are many functional assays of oxidative damage to DNA, protein, and lipids but few reliable markers of chronic oxidative stress. The glutathiolation of proteins at key Cys residues is considered an important redox-sensitive, posttranslational signaling mechanism in the regulation of critical cellular functions. To determine whether protein bound glutathione (GSSP) is a sensitive indicator of oxidative stress, red blood cell and plasma concentrations were measured and compared between smokers and nonsmokers. In a community-based study conducted in Westchester County, New York, USA, blood samples were obtained from 354 cigarette smokers and 97 never smokers. The mean concentration of blood GSSP (micromol/L) was 32% higher in cigarette smokers and 43% higher when standardized by hemoglobin concentrations (p <.01). Plasma GSSP levels were also 20% higher in smokers than in nonsmokers (p <.001). The relationship was dose-dependent, with blood GSSP levels significantly correlated with cigarettes smoked per day, plasma cotinine, and plasma thiocyanate (r values ranged from .25 to .40). In smokers, there were no significant differences in GSSP and GSH levels by GSTM1 or GSTM3 genotype. Intraindividual variation in blood samples, as determined by taking serial samples over a 2-week period, was low (CV = 12.1%, n = 8). GSSP levels are stable over time but increase in response to the abundant free radicals in cigarette smoke. These findings support the use of GSSP as a sensitive biomarker of oxidative stress.     

Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin

In recent years, increased interest in the origin of protein thermal stability has gained attention both for its possible role in understanding the forces governing the folding of a protein and for the design of new highly stable engineered biocatalysts. To study the origin of thermostability, we have performed molecular dynamics simulations of two rubredoxins, from the mesophile Clostridium pasteurianum and from the hyperthermophile Pyrococcus furiosus. The simulations were carried out at two temperatures, 300 and 373 K, for each molecule. The length of the simulations was within the range of 6-7.2 ns. The rubredoxin from the hyperthermophilic organism was more flexible than its mesophilic counterpart at both temperatures; however, the overall flexibility of both molecules at their optimal growth temperature was the same, despite 59% sequence homology. The conformational space sampled by both molecules was larger at 300 K than at 373 K. The essential dynamics analysis showed that the principal overall motions of the two molecules are significantly different. On the contrary, each molecule showed similar directions of motion at both temperatures.