Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A

Bovine pancreatic ribonuclease (RNase A) forms two three-dimensional (3D) domain swapped dimers. Crystallographic investigations have revealed that these dimers display completely different quaternary structures: one dimer (N-dimer), which presents the swapping of the N-terminal helix, is characterized by a compact structure, whereas the other (C-dimer), which is stabilized by the exchange of the C-terminal end, shows a rather loose assembly of the two subunits. The dynamic properties of monomeric RNase A and of the N-dimer have been extensively characterized. Here, we report a molecular dynamics investigation carried out on the C-dimer. This computational experiment indicates that the quaternary structure of the C-dimer undergoes large fluctuations. These motions do not perturb the proper folding of the two subunits, which retain the dynamic properties of RNase A and the N-dimer. Indeed, the individual subunits of the C-dimer display the breathing motion of the beta-sheet structure, which is important for the enzymatic activity of pancreatic-like ribonucleases. In contrast to what has been observed for the N-dimer, the breathing motion of the two subunits of the C-dimer is not coupled. This finding suggests that the intersubunit communications in a 3D domain swapped dimer strongly rely on the extent of the interchain interface. Furthermore, the observation that the C-dimer is endowed with a high intrinsic flexibility holds interesting implications for the specific properties of 3D domain swapped dimers. Indeed, a survey of the quaternary structures of the other 3D domain swapped dimers shows that large variations are often observed when the structural determinations are conducted in different experimental conditions. The 3D domain swapping phenomenon coupled with the high flexibility of the quaternary structure may be relevant for protein-protein recognition, and in particular for the pathological aggregations.     

ON WEIGHTING AND CONGRUENCE

Abstract — A priori differential weighting of molecular characters is a common methodological practice in molecular phylogenetics and evolution. This has been a largely subjective exercise with few criteria for deciding which characters to down-weight and how much to do so. A priori differential weighting is conducted to remove heterogeneity from the data sets and to improve the congruence among the informative, and usually more conservative characters. Herein, we test whether congruence is improved with a priori differential weighting by using the incongruence length difference test on a linked genetic data set consisting of 14 mammalian taxa and the 13 protein coding genes of the mitochondrial genome. Weighting by omitting the third codon position did not improve congruence with respect to the equally weighted data, while weighting transversions did improve the congruence between the 13 protein coding genes. Nonetheless, the most parsimonious tree found from transversion weighting did not differ from one using all of the data equally weighted.     

The building stones of Roman Sagalassos (SW Turkey): Facies analysis and provenance

Summary Different types of builing stones have been macro-scopically and petrographically characterized at the ancient city of Sagalassos (SW Turkey). The natural building stones include limestone, conglomerate, breccia, marble, travertine, granite and sand-to siltstone of different qualities. The provenance of most of the building stones may be related to local lithological units, both in the immediate area of the city and on its territory. Also, some stone types were clearly imported from considerable distance. Throughout the history of the city, local beige and pink good quality limestone remained the most important building stone. Both the high quality white limestone from the territory of the city and the marbles imported from a distance of 250 km, represent only a small fraction of the total amount of building stones used. While the use of the white limestone can be considered to form a clear but limited trend from the Trajanic period (98–117 AD) onwards, the import of the marbles must be considered as a rare event. The selection of building stone went hand in hand with the appreciation for structural strength and suitability for carving complex architectural decoration, together with the desire to obtain a polychrome architecture.     

Phenotypic and Molecular Typing of Salmonella Strains Reveals Different Contamination Sources in Two Commercial Pig Slaughterhouses

This study aimed to define the origin of Salmonella contamination on swine carcasses and the distribution of Salmonella serotypes in two commercial slaughterhouses during normal activity. Salmonellae were isolated from carcasses, from colons and mesenteric lymph nodes of individual pigs, and from the slaughterhouse environment. All strains were serotyped; Salmonella enterica serotype Typhimurium and Salmonella enterica serotype Derby isolates were additionally typed beyond the serotype level by pulsed-field gel electrophoresis (PFGE) and antibiotic resistance profiling (ARP); and a subset of 31 serotype Typhimurium strains were additionally phage typed. PFGE and ARP had the same discriminative possibility. Phage typing in combination with PFGE could give extra information for some strains. In one slaughterhouse, 21% of the carcasses were contaminated, reflecting a correlation with the delivery of infected pigs. Carcass contamination did not result only from infection of the corresponding pig; only 25% of the positive carcasses were contaminated with the same serotype or genotype found in the corresponding feces or mesenteric lymph nodes. In the other slaughterhouse, 70% of the carcasses were contaminated, and only in 4% was the same genotype or serotype detected as in the feces of the corresponding pigs. The other positive carcasses in both slaughterhouses were contaminated by genotypes present in the feces or lymph nodes of pigs slaughtered earlier that day or from dispersed sources in the environment. In slaughterhouses, complex contamination cycles may be present, resulting in the isolation of many different genotypes circulating in the environment due to the supply of positive animals and in the contamination of carcasses, probably through aerosols.     

The genetic status of the violet copper Lycaena helle– a relict of the cold past in times of global warming

Rising temperatures and agricultural changes (intensification and succession on fallow land) during the last few decades have caused a strong decline of moist and cool sites on nutrient-poor grasslands and species depending on these habitats. We tested the effects of habitat deterioration on a local and regional scale in such a species, the highly endangered butterfly Lycaena helle , which was more widely distributed over central Europe during the postglacial period, but has recently become restricted to some remnants. We analysed five polymorphic microsatellite loci in 220 individuals sampled at ten different localities. The study sites in Germany, Luxembourg and Belgium are geographically split into three mountain regions: the Ardennes, the Eifel and the Westerwald; the latter is separated from the other two by the river Rhine. A comparatively high genetic diversity was detected in all local populations and genetic differentiation was found among the Ardennes, the Eifel and the Westerwald (F_CT: 0.084). The genetic differentiation among all populations (F_ST: 0.137) underlines natural and anthropogenic habitat fragmentation. While ongoing gene flow seems to exist among the Eifel populations indicating the only intact metapopulation, a high genetic differentiation in the Ardennes and the Westerwald indicates a disruption of population connectivity. Our genetic data obtained on different spatial scales show the genetic consequence of long-term isolation and should trigger necessary conservation measures at the metapopulation level.