Ab initio 3-D structure prediction of an artificially designed three-alpha-helix bundle via all-atom molecular dynamics simulations

The rate at which knowledge about genomic sequences and their protein products is produced is increasing much faster than the rate of 3-dimensional protein structure determination by experimental methods, such as X-ray diffraction and nuclear magnetic resonance. One of the major challenges in structural bioinformatics is the conversion of genomic sequences into useful information, such as characterization of protein structure and function. Using molecular dynamics (MD) simulations, we predicted the 3-dimensional structure of an artificially designed three- alpha -helix bundle, called A3, from a fully extended initial conformation, based on its amino acid sequence. The MD protocol enabled us to obtain the secondary, in 1.0 ns, as well as the supersecondary and tertiary structures, in 4.0-10.0 ns, of A3, much faster than previously described for a similar protein system. The structure obtained at the end of the 10.0-ns MD simulation was topologically a three-alpha-helix bundle.     

Melatonin Promotes Oligodendroglial Maturation of Injured White Matter in Neonatal Rats

Objective

To investigate the effects of melatonin treatment in a rat model of white matter damage (WMD) in the developing brain. Additionally, we aim to delineate the cellular mechanisms of melatonin effect on the oligodendroglial cell lineage.

Methods

A unilateral ligation of the uterine artery in pregnant rat at the embryonic day 17 induces fetal hypoxia and subsequent growth restriction (GR) in neonatal pups. GR and control pups received a daily intra-peritoneal injection of melatonin from birth to post-natal day (P) 3.

Results

Melatonin administration was associated with a dramatic decrease in microglial activation and astroglial reaction compared to untreated GR pups. At P14, melatonin prevented white matter myelination defects with an increased number of mature oligodendrocytes (APC-immunoreactive) in treated GR pups. Conversely, melatonin was not found to be associated with an increased density of total oligodendrocytes (Olig2-immunoreactive), suggesting that melatonin is able to promote oligodendrocyte maturation but not proliferation. These effects appear to be melatonin-receptor dependent and were reproduced in vitro.

Interpretation

These data suggest that melatonin has a strong protective effect on developing damaged white matter through decreased microglial activation and oligodendroglial maturation leading to a normalization of the myelination process. Consequently, melatonin should be a considered as an effective neuroprotective candidate not only in perinatal brain damage but also in inflammatory and demyelinating diseases observed in adults.     

Novel markers for tying-up in horses by proteomics analysis of equine muscle biopsies

The aim of the study was to identify new biomarkers for acute tying-up in horses. Skeletal muscle biopsies were taken from 3 horses suffering from acute tying-up and 3 healthy horses. We performed 2D gel electrophoresis and mass spectrometry for identification of proteins that are differentially expressed in tying-up. 2D gel electrophoresis of skeletal muscle sequential extracts yielded more than 350 protein spots on each gel, of which 14 were differentially expressed more than two-fold (p < 0.05). In-gel digestion followed by peptide mass fingerprinting enabled identification of three significantly increased proteins: alpha actin, tropomyosin alpha chain and creatine kinase M chain (CKM). CKM was represented by multiple spots probably due to posttranslational modification, one of which appeared to be unique for tying-up. Since changes in the rates of synthesis and degradation of proteins are likely to lead to pathological conditions, identification of differentially expressed proteins in acute tying-up might result in the finding of more specific diagnostic markers and in new hypotheses for the common mechanisms that result in this condition. Our findings point to a specific isoform of CKM as a novel biomarker for tying-up suggesting that altered energy distribution within muscle cells is part of the disease etiology.     

Potential protein markers for nutritional health effects on colorectal cancer in the mouse as revealed by proteomics analysis

It is suggested that colorectal cancer might be prevented by changes in diet, and vegetable consumption has been demonstrated to have a protective effect. Until now, little is known about the effects of vegetable consumption at the proteome level. Therefore, the effect of increased vegetable intake on the protein expression in the colonic mucosa of healthy mice was studied. Aim was to identify the proteins that are differentially expressed by increased vegetable consumption and to discriminate their possible role in the protection against colorectal cancer. Mice were fed four different vegetable diets, which was followed by analysis of total cellular protein from colonic mucosal cells by a combination of 2-DE and MS. We found 30 proteins that were differentially expressed in one or more diets as compared to the control diet. Six could be identified by MALDI-TOF MS: myosin regulatory light chain 2, carbonic anhydrase I, high-mobility group protein 1, pancreatitis-associated protein 3, glyceraldehyde-3-phosphate dehydrogenase and ATP synthase oligomycin sensitivity conferral protein. Alterations in the levels of these proteins agree with a role in the protection against colon cancer. We conclude that these proteins are suitable markers for the health effect of food on cancer. The observed altered protein levels therefore provide support for the protective effects of vegetables against colorectal cancer.     

Radical trapping properties of imidazolyl nitrones

The ability of ten imidazolyl nitrones to directly scavenge free radicals (R(*)) generated in polar ((*)OH, O(*)(2)(-), SO(*)(3)(-) cysteinyl, (*)CH(3)) or in apolar (CH(3)-(*)CH-CH(3)) media has been studied. When oxygen or sulfur-centered radicals are generated in polar media, EPR spectra are not or weakly observed with simple spectral features. Strong line intensities and more complicated spectra are observed with the isopropyl radical generated in an apolar medium. Intermediate results are obtained with (*)CH(3) generated in a polar medium. EPR demonstrates the ability of these nitrones to trap radicals to the nitrone C(alpha) atom (alpha radical adduct) and to the imidazol C(5) atom (5-radical adduct). Beside the nucleophilic addition of the radical to the C(alpha) atom, the EPR studies suggest a two-step mechanism for the overall reaction of R(*) attacking the imidazol core. The two steps seem to occur very fast with the (*)OH radical obtained in a polar medium and slower with the isopropyl radical prepared in benzene. In conclusion, imidazolyl nitrones present a high capacity to trap and stabilize carbon-centered radicals.     

Determination of exemestane, a new aromatase inhibitor, in plasma by high-performance liquid chromatography with ultraviolet detection

A sensitive and selective high-performance liquid chromatographic method for the determination of 6-methylen-androsta-1,4-diene-3,17-dione (exemestane) and its 17-dihydro metabolite in human plasma has been developed. The analytes and internal standard (Norgestrel) were extracted from plasma samples with a methylene chloride—iso—octane mixture; the organic phase was dried and the residue was reconstituted with an acetonitrile—water mixture, then analyzed by reversed-phase liquid chromatography. Quantification was achieved by ultraviolet detection of the eluate. The linearity, precision and accuracy of the method were evaluated. No interference from the constituents of human blank plasma was observed. The lower limit of quantification was 10 ng/ml plasma. The suitability of the method for in vivo samples was checked by analysis of plasma samples drawn from healthy male volunteers who had received a 200-mg single oral dose of the test compound.     

Shoot development in grapevine (Vitis vinifera) is affected by the modular branching pattern of the stem and intra- and inter-shoot trophic competition

BACKGROUND AND AIMS: Shoot architecture variability in grapevine (Vitis vinifera) was analysed using a generic modelling approach based on thermal time developed for annual herbaceous species. The analysis of shoot architecture was based on various levels of shoot organization, including pre-existing and newly formed parts of the stem, and on the modular structure of the stem, which consists of a repeated succession of three phytomers (P0-P1-P2). METHODS: Four experiments were carried out using the cultivar 'Grenache N': two on potted vines (one of which was carried out in a glasshouse) and two on mature vines in a vineyard. These experiments resulted in a broad diversity of environmental conditions, but none of the plants experienced soil water deficit. KEY RESULTS: Development of the main axis was highly dependent on air temperature, being linearly related to thermal time for all stages of leaf development from budbreak to veraison. The stable progression of developmental stages along the main stem resulted in a thermal-time based programme of leaf development. Leaf expansion rate varied with trophic competition (shoot and cluster loads) and environmental conditions (solar radiation, VPD), accounting for differences in final leaf area. Branching pattern was highly variable. Classification of the branches according to ternary modular structure increased the accuracy of the quantitative analysis of branch development. The rate and duration of leaf production were higher for branches derived from P0 phytomers than for branches derived from P1 or P2 phytomers. Rates of leaf production, expressed as a -function of thermal time, were not stable and depended on trophic competition and environmental conditions such as solar radiation or VPD. CONCLUSIONS: The application to grapevine of a generic model developed in annual plants made it possible to identify constants in main stem development and to determine the hierarchical structure of branches with respect to the modular structure of the stem in response to intra- and inter-shoot trophic competition.