Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation

<p>Abstract</p> <p>Background</p> <p>Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the <it>trans </it>conformation. In spite of their infrequent occurrence, <it>cis </it>peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes.</p> <p>Results</p> <p>We perform a systematic analysis of regions in protein sequences that contain a proline <it>cis </it>peptide bond in order to discover non-random associations between the primary sequence and the nature of proline <it>cis/trans </it>isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of <it>cis </it>proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of <it>cis </it>prolyl bonds.</p> <p>Conclusion</p> <p><it>Cis </it>patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures.</p

Induction of EpRE-mediated gene expression by a series of mediterranean botanicals and their constituents

Ethnopharmacological relevance: A variety of Mediterranean plant species, traditionally used for the prevention and treatment of several health conditions, contain ingredients with potential biological activity of which many remain unexplored. Among the beneficial health effects of bioactive phytochemicals is the activation of cellular defense mechanisms involving the activation of EpRE (electrophile responsive element) - mediated changes in gene expression. Aim of the study: The present study aimed to identify botanicals and their active constituents able to activate the EpRE mediated gene expression within a series of Mediterranean plant species known for their hepatoprotective and/or cardioprotective properties. Materials and methods: Methanolic extracts of 18 botanicals were prepared and tested for their ability to induce gene expression in EpRE-LUX reporter cells. Subsequently, LC-MS (Liquid Chromatography Mass Spectrometry) analysis combined with MAGMa (MS Annotation based on in silico Generated Metabolites) software for automated compound annotation was used to facilitate tentative identification of the active constituents within two of the active extracts. Selected annotated compounds were tested in the EpRE-LUX reporter gene assay followed by definite identification of the most active ones. Results: It appeared that 9 of the 18 extracts were able to activate EpRE-mediated gene expression. Many active ingredients of the methanolic extracts from Juglans regia and Rhamnus frangula were revealed. Among them, chrysophanol and aloe-emodin were confirmed to be active EpRE inducing ingredients and were definitely identified in the Rhamnus Frangula extract. Conclusions: The protective effect of half of the tested botanical varieties via the activation of EpRE-mediated gene expression was confirmed. The study also provided an example of how in vitro bioassays can be combined with LC-MS and the automated chemical annotation software MAGMa, to identify biologically active constituents in complex botanical extracts.</p

Carbonization of Human Fingernails: Toward the Sustainable Production of Multifunctional Nitrogen and Sulfur Codoped Carbon Nanodots with Highly Luminescent Probing and Cell Proliferative/Migration Properties

A simple yet effective method is employed to prepare multifunctional fluorescent carbon nanodots (CNDs) from human fingernails. The results demonstrate that the CNDs have excellent optical properties and a quantum yield of 81%, which is attributed to the intrinsic composition of the precursor material itself. The CNDs are used to develop an ultrasensitive fluorescent probe for the detection of hexavalent chromium (limit of detection: 0.3 nM) via a combined inner-filter and static mechanism. Moreover, the toxicity of the CNDs over four epithelial cell lines is assessed. A negligible toxicity is induced on the three of the cell lines, whereas an increase in HEK-293 cell viability is demonstrated, granting cell proliferation properties to the as-synthesized CNDs. According to cell cycle analysis, cell proliferation is achieved by enhancing the transition of cells from the S phase to the G2/M one. Interestingly, CNDs are found to significantly promote cell migration, maybe because of their free-radical scavenging ability, making the CNDs suitable for wound healing applications. In addition, relevant experiments have revealed the blood compatibility of the CNDs. Finally, the CNDs were found suitable for cell imaging applications, and all of the aforementioned merits make it possible for them to be used for extraordinary, more advanced biological applications

Development of a Multi-Enzymatic Approach for the Modification of Biopolymers with Ferulic Acid

A series of polymers, including chitosan (CS), carboxymethylcellulose (CMC) and a chitosan&ndash;gelatin (CS&ndash;GEL) hybrid polymer, were functionalized with ferulic acid (FA) derived from the enzymatic treatment of arabinoxylan through the synergistic action of two enzymes, namely, xylanase and feruloyl esterase. Subsequently, the ferulic acid served as the substrate for laccase from Agaricus bisporus (AbL) in order to enzymatically functionalize the above-mentioned polymers. The successful grafting of the oxidized ferulic acid products onto the different polymers was confirmed through ultraviolet&ndash;visible (UV&ndash;Vis) spectroscopy, attenuated total reflectance (ATR) spectroscopy, scanning electron microscopy (SEM) and nuclear magnetic resonance (NMR) spectroscopy. Additionally, an enhancement of the antioxidant properties of the functionalized polymers was observed according to the DDPH and ABTS protocols. Finally, the modified polymers exhibited strong antimicrobial activity against bacterial populations of Escherichia coli BL21DE3 strain, suggesting their potential application in pharmaceutical, cosmeceutical and food industries

Synthesis and antiproliferative activity of two diastereomeric lignan amides serving as dimeric caffeic acid-l-DOPA hybrids

Two new diastereomeric lignan amides (4 and 5) serving as dimeric caffeic acid-l-DOPA hybrids were synthesized. The synthesis involved the FeCl3-mediated phenol oxidative coupling of methyl caffeate to afford trans-diester 1a as a mixture of enantiomers, protection of the catechol units, regioselective saponification, coupling with a suitably protected l-DOPA derivative, separation of the two diastereomers thus obtained by flash column chromatography and finally global chemoselective deprotection of the catechol units. The effect of hybrids 4 and 5 and related compounds on the proliferation of two breast cancer cell lines with different metastatic potential and estrogen receptor status (MDA-MB-231 and MCF-7) and of one epithelial lung cancer cell line, namely A-549, was evaluated for concentrations ranging from 1 to 256 μM and periods of treatment of 24, 48 and 72 h. Both hybrids showed interesting and almost equipotent antiproliferative activities (IC50 64-70 μM) for the MDA-MB-231 cell line after 24-48 h of treatment, but they were more selective and much more potent (IC50 4-16 μM) for the MCF-7 cells after 48 h of treatment. The highest activity for both hybrids and both breast cancer lines was observed after 72 h of treatment (IC50 1-2 μM), probably as the result of slow hydrolysis of their methyl ester functions