Photoproducts of bacteriorhodopsin mutants: a molecular dynamics study

Molecular dynamics simulations of wild-type bacteriorhodopsin (bR) and of its D85N, D85T, D212N, and Y57F mutants have been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent relaxation process were completed. The photoproducts can be classified into four distinct classes: 1) 13-cis retinal, with the retinal N-H+ bond oriented toward Asp-96; 2) 13-cis retinal, with the N-H+ oriented toward Asp-85 and hydrogen-bonded to a water molecule; 3) 13,14-di-cis retinal; 4) all-trans retinal. Simulations of wild-type bR and of its Y57F mutant resulted mainly in class 1 and class 2 products; simulations of D85N, D85T, and D212N mutants resulted almost entirely in class 1 products. The results support the suggestion that only class 2 products initiate a functional pump cycle. The formation of class 1 products for the D85N, D85T, and D212N mutants can explain the reversal of proton pumping under illumination by blue and yellow light

The β Subunit of the Na+/K+-ATPase Follows the Conformational State of the Holoenzyme

The Na+/K+-ATPase is a ubiquitous plasma membrane ion pump that utilizes ATP hydrolysis to regulate the intracellular concentration of Na+ and K+. It is comprised of at least two subunits, a large catalytic α subunit that mediates ATP hydrolysis and ion transport, and an ancillary β subunit that is required for proper trafficking of the holoenzyme. Although processes mediated by the α subunit have been extensively studied, little is known about the participation of the β subunit in conformational changes of the enzyme. To elucidate the role of the β subunit during ion transport, extracellular amino acids proximal to the transmembrane region of the sheep β1 subunit were individually replaced for cysteines. This enabled sulfhydryl-specific labeling with the environmentally sensitive fluorescent dye tetramethylrhodamine-6-maleimide (TMRM) upon expression in Xenopus oocytes. Investigation by voltage-clamp fluorometry identified three reporter positions on the β1 subunit that responded with fluorescence changes to alterations in ionic conditions and/or membrane potential. These experiments for the first time show real-time detection of conformational rearrangements of the Na+/K+-ATPase through a fluorophore-labeled β subunit. Simultaneous recording of presteady-state or stationary currents together with fluorescence signals enabled correlation of the observed environmental changes of the β subunit to certain reaction steps of the Na+/K+-ATPase, which involve changes in the occupancy of the two principle conformational states, E1P and E2P. From these experiments, evidence is provided that the β1-S62C mutant can be directly used to monitor the conformational state of the enzyme, while the F64C mutant reveals a relaxation process that is triggered by sodium transport but evolves on a much slower time scale. Finally, shifts in voltage dependence and kinetics observed for mutant K65C show that this charged lysine residue, which is conserved in β1 isoforms, directly influences the effective potential that determines voltage dependence of extracellular cation binding and release

Relatedness within and between Agta residential groups

Theoretical models relating to the evolution of human behaviour usually make assumptions about the kinship structure of social groups. Since humans were hunter–gatherers for most of our evolutionary history, data on the composition of contemporary hunter–gatherer groups has long been used to inform these models. Although several papers have taken a broad view of hunter–gatherer social organisation, it is also useful to explore data from single populations in more depth. Here, we describe patterns of relatedness among the Palanan Agta, hunter–gatherers from the northern Philippines. Across 271 adults, mean relatedness to adults across the population is r = 0.01 and to adult campmates is r = 0.074, estimates that are similar to those seen in other hunter–gatherers. We also report the distribution of kin across camps, relatedness and age differences between spouses, and the degree of shared reproductive interest between camp mates, a measure that incorporates affinal kinship. For both this this measure (s) and standard relatedness (r), we see no major age or sex differences in the relatedness of adults to their campmates, conditions that may reduce the potential for conflicts of interest within social groups