Denatured proteins and early folding intermediates simulated in a reduced conformational space

Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.     

Genetic Analysis and Species Specific Amplification of the Artemisinin Resistance-Associated Kelch Propeller Domain in P. falciparum and P. vivax

Plasmodium falciparum resistance to artemisinin has emerged in the Greater Mekong Subregion and now poses a threat to malaria control and prevention. Recent work has identified mutations in the kelch propeller domain of the P. falciparum K13 gene to be associated artemisinin resistance as defined by delayed parasite clearance and ex vivo ring stage survival assays. Species specific primers for the two most prevalent human malaria species, P. falciparum and P. vivax, were designed and tested on multiple parasite isolates including human, rodent, and non- humans primate Plasmodium species. The new protocol described here using the species specific primers only amplified their respective species, P. falciparum and P. vivax, and did not cross react with any of the other human malaria Plasmodium species. We provide an improved species specific PCR and sequencing protocol that could be effectively used in areas where both P. falciparum and P. vivax are circulating. To design this improved protocol, the kelch gene was analyzed and compared among different species of Plasmodium. The kelch propeller domain was found to be highly conserved across the mammalian Plasmodium species.     

Interaction between invasive and potentially invasive shrub species does not influence relationships between their ecological success and distance from propagule sources

Although interactions between alien and native plant species are well studied, data on interactions between two co-existing alien species with respect to their invasibility are scarce. The aims of this study were (1) to evaluate three factors shaping abundance of the alien shrub species Cornus alternifolia: abundance of another alien (invasive) shrub species (Prunus serotina), type of tree stand (coniferous vs. broadleaved) and distance to propagule sources and (2) to assess the potential dispersal distance of the species studied. Densities of both species were assessed within 194 experimental plots (located in experimental plantations of trees) in Rogów Arboretum (Central Poland). P. serotina occurred on 79 and C. alternifolia on 33 of the 194 plots. The furthest distance of C. alternifolia from the propagule source was 338 m. C. alternifolia reached higher densities in coniferous than broadleaved tree stands. Density of C. alternifolia depended on tree stand type and distance from the propagule source, but did not depend on density of P. serotina. Density of C. alternifolia decreased with increasing distance from the propagule source; however, this relationship was modified by the type of tree stand: densities were lower in broadleaved than in coniferous stands. The presence of the invasive species seems to neither facilitate nor limit the dispersal distance of C. alternifolia, as these two species differ in shade tolerance. The study also provided the first information about C. alternifolia potential invasiveness, because earlier this species was noticed only as casually escaping from cultivation in Slovakia.