PredβTM: A Novel β-Transmembrane Region Prediction Algorithm

Predicting the transmembrane regions is an important aspect of understanding the structures and architecture of different β-barrel membrane proteins. Despite significant efforts, currently available β-transmembrane region predictors are still limited in terms of prediction accuracy, especially in precision. Here, we describe PredβTM, a transmembrane region prediction algorithm for β-barrel proteins. Using amino acid pair frequency information in known β-transmembrane protein sequences, we have trained a support vector machine classifier to predict β-transmembrane segments. Position-specific amino acid preference data is incorporated in the final prediction. The predictor does not incorporate evolutionary profile information explicitly, but is based on sequence patterns generated implicitly by encoding the protein segments using amino acid adjacency matrix. With a benchmark set of 35 β-transmembrane proteins, PredβTM shows a sensitivity and precision of 83.71% and 72.98%, respectively. The segment overlap score is 82.19%. In comparison with other state-of-art methods, PredβTM provides a higher precision and segment overlap without compromising with sensitivity. Further, we applied PredβTM to analyze the β-barrel membrane proteins without defined transmembrane regions and the uncharacterized protein sequences in eight bacterial genomes and predict possible β-transmembrane proteins. PredβTM can be freely accessed on the web at http://transpred.ki.si/.     

The influence of jasmonic acid on biophysical properties of potato leaf protoplasts and roots

Summary Jasmonic acid (JA) and its derivatives are a novel group of plant endogenous growth regulators. In our experiments some new data about the physiological effects of JA were obtained using electron paramagnetic resonance spectroscopy. Experiments were performed on potato plants (Solanum tuberosum L. cv. Vesna) grown in vitro. Different quantities of JA (0.1–10 M) were added to the growth medium. Root samples of plants grown on media supplemented with JA showed a more rapid spin probe N-oxyl-2,2,6,6-tetramethyl piperidine reduction than the control plants, which is a possible indicator of altered root permeability. Samples of leaf protoplasts were probed with methyl ester of 5-doxyl-haxadecanoic acid. We observed a membrane fluidity decrease in protoplasts isolated from plants grown on higher concentrations of JA (1 and 10 M).Abbreviations JA jasmonic acid - Me-JA methyl jasmonate - EPR electron paramagnetic resonance - RubisCO ribulose-1,5-biphosphate carboxylase/oxigenase - MeFASL(10,3) methyl ester of 5-doxyl-hexadecanoic acid - MES (2(N-morpholino)ethanesulfonic acid) - TEMPO N-oxyl-2,2,6,6-tetramethyl piperidine     

Dual-specificity phosphatases in the hypo-osmotic stress response of keratin-defective epithelial cell lines

Although mutations in intermediate filament proteins cause many human disorders, the detailed pathogenic mechanisms and the way these mutations affect cell metabolism are unclear. In this study, selected keratin mutations were analysed for their effect on the epidermal stress response. Expression profiles of two keratin-mutant cell lines from epidermolysis bullosa simplex patients (one severe and one mild) were compared to a control keratinocyte line before and after challenge with hypo-osmotic shock, a common physiological stress that transiently distorts cell shape. Fewer changes in gene expression were found in cells with the severely disruptive mutation (55 genes altered) than with the mild mutation (174 genes) or the wild type cells (261 genes) possibly due to stress response pre-activation in these cells. We identified 16 immediate-early genes contributing to a general cell response to hypo-osmotic shock, and 20 genes with an altered expression pattern in the mutant keratin lines only. A number of dual-specificity phosphatases (MKP-1, MKP-2, MKP-3, MKP-5 and hVH3) are differentially regulated in these cells, and their downstream targets p-ERK and p-p38 are significantly up-regulated in the mutant keratin lines. Our findings strengthen the case for the expression of mutant keratin proteins inducing physiological stress, and this intrinsic stress may affect the cell responses to secondary stresses in patients' skin.     

Epidermal stem cells: the cradle of epidermal determination, differentiation and wound healing

The field of epidermal stem cells has dramatically advanced in the last decade, leading to a better understanding of the molecular factors, signalling pathways and cellular events that identify and characterize stem cells, thus revealing their immense potential for therapeutic use. Furthermore, multipotent epidermal stem cells present the major advantage of easy accessibility with the discovery of their specific location within the bulge of the hair follicle. This review focuses on the most recent findings on epidermal stem cells, and their potential role in initial epidermal commitment, differentiation and wound healing processes in the skin.     

Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase

Using a combination of genomic and post-genomic approaches is rapidly altering the number of identified human influx carriers. A transmembrane protein bilitranslocase (TCDB 2.A.65) has long attracted attention because of its function as an organic anion carrier. It has also been identified as a potential membrane transporter for cellular uptake of several drugs and due to its implication in drug uptake, it is extremely important to advance the knowledge about its structure. However, at present, only the primary structure of bilitranslocase is known. In our work, transmembrane subunits of bilitranslocase were predicted by a previously developed chemometrics model and the stability of these polypeptide chains were studied by molecular dynamics (MD) simulation. Furthermore, sodium dodecyl sulfate (SDS) micelles were used as a model of cell membrane and herein we present a high-resolution 3D structure of an 18 amino acid residues long peptide corresponding to the third transmembrane part of bilitranslocase obtained by use of multidimensional NMR spectroscopy. It has been experimentally confirmed that one of the transmembrane segments of bilitranslocase has alpha helical structure with hydrophilic amino acid residues oriented towards one side, thus capable of forming a channel in the membrane.