Search results for "sequence"
showing 10 items of 4987 documents
Identification of Three-Way DNA Junction Ligands through Screening of Chemical Libraries and Validation by Complementary in Vitro Assays
2019
International audience; The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, the chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy t…
Detection and localisation of disulphide bonds in a synthetic peptide reproducing the sequence 1-30 of Par j 1.0101 by electrospray ionisation mass s…
2001
The structural characterisation of a synthetic peptide reproducing the sequence 1–30 of Par j 1.0101, a major allergenic protein present in the pollen of Parietaria judaica, by combined use of chemical and enzymatic cleavage, reversed-phase high-performance liquid chromatography (RP-HPLC) and electrospray ionisation mass spectrometry (ESI-MS), is described. Direct ESI-MS of the synthetic peptide after reaction with methyl iodide showed that the product is a mixture of two peptides: one form in which two out of the four cysteine residues present in the sequence are oxidised and a minor amount of another form in which all the cysteines are fully reduced. It was ascertained, using the combined…
Characterization of heat-labile toxin-subunit B from Escherichia coli by liquid chromatography-electrospray ionization-mass spectrometry and matrix-a…
2012
The possibilities of characterizing the heat-labile enterotoxin (LT) of enterotoxigenic Escherichia coli (ETEC) by liquid chromatography electrospray mass spectrometry (LC/ESI-MS) and matrix-assisted laser desorption with time-of-flight mass spectrometry (MALDI-TOF-MS) were investigated. The B subunit from recombinant E. coli (expression in Pichia pastoris) can be detected by LC/ESI-MS expressed in P. pastoris and the charge envelope signals can be observed; LC/ESI-MS and MALDI-TOF-MS analysis allowed the acquisition of labile toxin subunit B (LTB) molecular weight and preliminary structural characterization of LTB toxin. MALDI-TOF analysis after reduction and alkylation of the protein evid…
Triterpene Saponins from Cyclamen trocopteranthum
2010
Two new triterpene saponins ( 1- 2) together with three known saponins, deglucocyclamin I ( 3), cyclamin ( 4), and mirabilin ( 5), were isolated from the tubers of Cyclamen trocopteranthum. They were elucidated as 3 beta- O-{4- O-[3-hydroxyl-3-methylglutaryl]- beta-D-xylopyranosyl-(1 --> 2)- beta-D-glucopyranosyl-(1 --> 4)-[ beta-D-glucopyranosyl-(1 --> 2)]- alpha-L-arabinopyranosyl}-16 alpha-hydroxy-13 beta,28-epoxy-oleanan-30-al ( 1) and 3 beta- O-{4- O-[3-hydroxyl-3-methylglutaryl]- beta-D-xylopyranosyl-(1 --> 2)-[ beta-D-glucopyranosyl-(1 --> 6)]- beta-D-glucopyranosyl-(1 --> 4)-[ beta-D-glucopyranosyl-(1 --> 2)]- alpha-L-arabinopyranosyl}-16 alpha-hydroxy-20,30-lactone-olean-12-ene ( 2…
Structural analysis of the O-specific polysaccharide isolated from Plesiomonas shigelloides O51 lipopolysaccharide.
2009
Plesiomonasshigelloides strain CNCTC 110/92 (O51) was identified as a new example of plesiomonads synthesising lipopolysaccharides (LPSs) that show preference for a non-aqueous surrounding during phenol/water extraction. Chemical analyses combined with (1)H and (13)C NMR spectroscopy, MALDI-TOF and ESI mass spectrometry showed that the repeating units of the O-specific polysaccharides isolated from phenol and water phase LPSs of P. shigelloides O51 have the same structure: -->4)-beta-D-GlcpNAc3NRA-(1-->4)-alpha-L-FucpAm3OAc-(1-->3)-alpha-D-QuipNAc-(1-->, containing the rare sugar constituent 2,3-diamino-2,3-dideoxyglucuronic acid (GlcpNAc3NRA), and substituents such as D-3-hydroxybutyric ac…
Proteomic analysis of the acid-soluble nacre matrix of the bivalve Unio pictorum: detection of novel carbonic anhydrase and putative protease inhibit…
2010
10 pages; International audience; The matrix extracted from mollusc shell nacre is a mixture of proteins and glycoproteins that is thought to play a major role in controlling biomineral synthesis and in increasing its mechanical properties. We investigated the nacreous shell of the freshwater mussel Unio pictorum, to which we applied a proteomics approach adapted to mollusc shell proteins. On one hand, the acid-soluble nacre matrix was fractionated by SDS-PAGE and the five main protein bands (P95, P50, P29, P16, and P12) were digested with trypsin and analyzed by nanoLC-MS/MS followed by de novo sequencing. On the other hand, the acid-soluble nacre matrix was analyzed in a similar manner, w…
Chemoenzymatic Synthesis of Functional Sialyl LewisX Mimetics with a Heteroaromatic Core
2014
Functional mimetics of the sialyl Lewis(X) tetrasaccharide were prepared by the enzymatic sialylation of a 1,3-diglycosylated indole and a glycosyl azide, which was subsequently transformed into a 1,4-diglycosylated 1,2,3-triazole, by using the trans-sialidase of Trypanosoma cruzi. These compounds inhibited the binding of E-, L-, and P-selectin-coated nanoparticles to polyacrylamide-bound sialyl-Lewis(X) -containing neighboring sulfated tyrosine residues (sTyr/sLe(X) -PAA) at low or sub-millimolar concentrations. Except for E-selectin, the mimetics showed higher activities than the natural tetrasaccharide.
Levansucrases from Pseudomonas syringae pv. tomato and P. chlororaphis subsp. aurantiaca: Substrate specificity, polymerizing properties and usage of…
2011
Levansucrases of Pseudomonas syringae pv. tomato DC3000 (Lsc3) and Pseudomonas chlororaphis subsp. aurantiaca (also Pseudomonas aurantiaca) (LscA) have 73% identity of protein sequences, similar substrate specificity and kinetic properties. Both enzymes produce levan and fructooligosaccharides (FOS) of varied length from sucrose, raffinose and sugar beet molasses. A novel high-throughput chip-based nanoelectrospray mass spectrometric method was applied to screen alternative fructosyl acceptors for levansucrases. Lsc3 and LscA could both transfructosylate D-xylose, D-fucose, L- and D-arabinose, D-ribose, D-sorbitol, xylitol, xylobiose, D-mannitol, D-galacturonic acid and methyl-α-D-glucopyra…
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN
2013
BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the…
Alignment-Free Sequence Comparison over Hadoop for Computational Biology
2015
Sequence comparison i.e., The assessment of how similar two biological sequences are to each other, is a fundamental and routine task in Computational Biology and Bioinformatics. Classically, alignment methods are the de facto standard for such an assessment. In fact, considerable research efforts for the development of efficient algorithms, both on classic and parallel architectures, has been carried out in the past 50 years. Due to the growing amount of sequence data being produced, a new class of methods has emerged: Alignment-free methods. Research in this ares has become very intense in the past few years, stimulated by the advent of Next Generation Sequencing technologies, since those…