Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing

Developing a detailed understanding of the structure and energetics of protein folding transition states is a key step in describing the folding process. The phi-value analysis approach allows the energetic contribution of side-chains to be mapped out by comparing wild-type with individual mutants where conservative changes are introduced. Studies where multiple substitutions are made at individual sites are much rarer but are potentially very useful for understanding the contribution of each element of a side-chain to transition state formation, and for distinguishing the relative importance of specific packing versus hydrophobic interactions. We have made a series of conservative mutations at multiple buried sites in the N-terminal domain of L9 in order to assess the relative importance of specific side-chain packing versus less specific hydrophobic stabilization of the transition state. A total of 28 variants were prepared using both naturally occurring and non-naturally occurring amino acids at six sites. Analysis of the mutants by NMR and CD showed no perturbation of the structure. There is no correlation between changes in hydrophobicity and changes in stability. In contrast, there is excellent linear correlation between the hydrophobicity of a side-chain and the log of the folding rate, ln(k(f)). The correlation between ln(k(f)) and the change in hydrophobicity holds even for substitutions that change the shape and/or size of a side-chain significantly. For most sites, the correlation with the logarithm of the unfolding rate, ln(k(u)), is much worse. Mutants with more hydrophobic amino acid substitutions fold faster, and those with less hydrophobic amino acid substitutions fold slower. The results show that hydrophobic interactions amongst core residues are an important driving force for forming the transition state, and are more important than specific tight packing interactions. Finally, a number of substitutions lead to negative phi-values and the origin of these effects are described.     

Selenium and Psoriasis

Psoriasis is a chronic, immune-mediated skin disease characterized by production of reactive oxygen species due to the activation of tumor necrosis factor alpha (TNF-??), which is thought to be an important factor in inducing and maintaining psoriatic lesions. As an external factor, ultraviolet B (UVB) radiation stimulates TNF-?? production and secretion by human keratinocytes in vitro and can also reach the upper dermis and suppress endothelial cells in vitro. The selenium level in psoriatic patients has been found to be lower than expected, but studies on its role in the pathogenesis of the disease are scarce. Selenium can influence immune response by changing the expression of cytokines and their receptors or by making immune cells more resistant to oxidative stress. It was reported that selenium supplementation had inhibitory effects on TNF-?? levels in patients with psoriasis, but the details are not completely elucidated. Selenium compounds are also known to prevent the in vitro release of UVB-induced proinflammatory cytokines by inhibition of mRNA in human keratinocytes. In the present review, the protective role of selenium in oxidative stress, lesions, and immune system regulation in patients with psoriasis is summarized.     

Molecular phylogeny of relict-endemic <Emphasis Type="Italic">Liquidambar orientalis</Emphasis> Mill based on sequence diversity of the chloroplast-encoded <Emphasis Type="Italic">mat</Emphasis>K gene

The genetic diversity and evolutionary divergence in Liquidambar species and Liquidambar orientalis varieties were compared with respect to the matK gene. A total of 66 genotypes from 18 different populations were sampled in southwestern Turkey. The matK region, which is about 1,512 bp in length, was sequenced and studied. L. orientalis, L. styraciflua, and L. formosana had similar magnitude of nucleotide diversity, while L. styraciflua and L. acalycina possessed higher evolutionary divergence. The highest evolutionary divergence was found between L. styraciflua and eastern Asian Liquidambar species (0.0102). However, the evolutionary divergence between L. orientalis and other species was of a similar magnitude. The maximum-parsimony phylogenetic tree showed that L. styraciflua and L. orientalis formed a closer clade while East Asian species were in a separate clade. This suggests that the North Atlantic Land Bridge through southern Greenland may have facilitated continuous distribution of Liquidambar species from southeastern Europe to eastern North America in early Tertiary period. The maximum-parsimony tree with only 18 Oriental sweetgum populations indicated that there were two main clusters: one with mainly L. orientalis var. integriloba and the other with var. orientalis and undetermined populations. High nucleotide diversity (0.0028) and divergence (0.00072) were found in L. orientalis var. integriloba populations and Muğla-1 geographical region. This region could be considered as the major refugium and genetic diversity center for the species. The low genetic diversity and divergence at intraspecies level suggest that L. orientalis populations in Turkey share an ancestral polymorphism from which two varieties may have evolved.     

Chloramine T induced oxidative stress and the response of antioxidant system in <Emphasis Type="Italic">Phanerochaete chrysosporium</Emphasis>

In this study, the effect of chloramine T (Chl-T) on the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), glutathione reductase (GR) and glutathione S-transferase (GST); the levels of reduced (GSH) and oxidised glutathione (GSSG) and their ratios; and also membrane lipid peroxidation (LPO) levels in Phanerochaete chrysosporium were investigated in a dose- (0.25–1 mmol/L) and time-dependent (1.5–9 h) manner. The highest SOD activity was observed in 0.5 mmol/L Chl-T at 6th hour as 1.48-fold of its control. The observed highest level in CAT activities was 4.6-fold of control in 0.5 and 0.75 mmol/L at the 6th hour. The GSH levels that were over the control showed decreasing tendency from the beginning of incubation, except 0.25 mmol/L. In contrast with GSH level variations, GSSG levels reached 10.0-fold of its control by showing increasing tendency with the increases in concentration and time. While the GSH/GSSG ratios were over the control at 0.25 mmol/L during all incubation, they fell under the control values at the earlier hours of incubation with the increasing concentrations of Chl-T. Glutathione-related enzymes GSH-Px, GR and GST were also induced with Chl-T treatment, and the highest activities were 3.29-, 7.5- and 6.56-fold of their controls, respectively. On the other hand, the increases in LPO levels with increasing concentration and time up to 5.27-fold of its control showed that the inductions observed in antioxidant system could not prevent the Chl-T-based oxidative stress.     

Attributes of trees used by nesting and foraging woodpeckers (Aves: Picidae) in an area with old pollarded Oaks (Quercus spp.) in the Taurus Mountains,Turkey

We used three woodpecker species as umbrella species for old deciduous forests, and analysed their preferences in an area with old pollarded oaks in the Taurus Mountains, Turkey. Using plot inventories, we physically characterised trees utilised for nesting and foraging amongst woodpeckers in general and the Middle Spotted Woodpecker (Leiopicus medius) in particular. Trees more frequently visited by foraging woodpeckers differed from randomly chosen trees by being taller, having a larger circumference, greater bark furrow depth and shorter distance to neighbouring trees. Nesting trees were taller, had a higher proportion of dead wood but a lower surface area of natural cavities. Our results suggest that the woodpeckers in the study area rely upon woodlands containing mature trees, thus have the potential to function as suitable umbrella species’ to highlight the conservation value of oak forest habitats in southern Turkey.     

Double promoter expression systems for recombinant protein production by industrial microorganisms

Applied Microbiology and Biotechnology - Using double promoter expression systems is a promising approach to increase heterologous protein production. In this review, current double promoter...