Search results for "Sequence"
showing 10 items of 4987 documents
A new strategy for the synthesis of fluorinated 3,4-dihydropyrimidinones
2009
A new family of 3,4-dihydropyrimidinones (DHPMs) bearing fluorinated substituents at C6 have been prepared from gem-difluorinated nitriles, alkyl 3-butenoates and iso(thio)cyanates. This novel Biginelli-type process relies on the gamma-addition of the ester-derived enolate to fluorinated nitriles. A tandem nucleophilic addition aza-Michael reaction sequence completes the synthetic process. (C) 2009 Elsevier B.V. All rights reserved.
Influence of the position of two dehydro-amino acids residues in the oligopeptide sequence on the binding ability towards Cu(II) ions
2005
Abstract Studies on the binding ability of bis-dehydro-hexa- and pentapeptides have shown that the hexapeptides bind Cu+2 with similar efficacy as pentapeptides. The increase of distance between two dehydro-amino acid residues in the peptide backbone has no impact on the efficacy in metal ion binding. The type of isomeration [(Z) or (E)] has an influence on the coordination of the metal ion only to the first amide nitrogen.
A pea nuclear protein that is induced by dehydration belongs to the vicilin superfamily
2000
The purification to homogeneity of p16, a protein with an electrophoretic mobility compatible with an apparent molecular mass of 16 kDa, from nuclei of ungerminated pea embryonic axes is described. A cDNA clone of its gene, which was designated psp54, was also isolated. The psp54 cDNA contains an open reading frame coding for a 54.4-kDa polypeptide (p54). p16 corresponds to the C-terminal third of p54, although the mechanisms by which the primary polypeptide could be processed are not yet known. The sequence of p54 is 60% identical with that of the precursor of a sucrose-binding soybean protein, and, to a lesser extent (31-34%), it shares homology with some storage proteins. p16 is also 30%…
Investigation of α-amino acid N-carboxyanhydrides by X-ray diffraction for controlled ring-opening polymerization
2019
Abstract The need for a scalable synthesis of not sequence defined polypeptides as biomaterials is met by the ring-opening polymerization of α-amino acid N-carboxyanhydrides (NCAs). Even though this polymerization technique appears straight forward, it holds pitfalls in terms of reproducibility and overall control over the polymerization conditions, which depends, beside choice of solvent or initiator, significantly on reagent purity. In addition, the synthesis of monomers can lead to the formation of racemic amino acids. Thus, in this work, we describe the benefits of highly pure monomers in order to control nucleophilic ring-opening polymerization NCAs. Hereby, monomer purity is investiga…
Citrate Sensing by the C 4 -Dicarboxylate/Citrate Sensor Kinase DcuS of Escherichia coli : Binding Site and Conversion of DcuS to a C 4 -Dicarboxylat…
2007
ABSTRACT The histidine protein kinase DcuS of Escherichia coli senses C 4 -dicarboxylates and citrate by a periplasmic domain. The closely related sensor kinase CitA binds citrate, but no C 4 -dicarboxylates, by a homologous periplasmic domain. CitA is known to bind the three carboxylate and the hydroxyl groups of citrate by sites C1, C2, C3, and H. DcuS requires the same sites for C 4 -dicarboxylate sensing, but only C2 and C3 are highly conserved. It is shown here that sensing of citrate by DcuS required the same sites. Binding of citrate to DcuS, therefore, was similar to binding of C 4 -dicarboxylates but different from that of citrate binding in CitA. DcuS could be converted to a C 4 -…
Impact of amino acids 22-27 of Rho-subfamily GTPases on glucosylation by the large clostridial cytotoxins TcsL-1522, TcdB-1470 and TcdB-8864
1999
Here we report data describing some principles of the interaction between small GTP-binding proteins and large Clostridial cytotoxins (LCTs). Our investigation was based on the differential glucosylation of Rac1 versus RhoA by LCTs TcsL-1522, TcdB-1470 and TcdB-8864. Chimeric RhoA/Rac1 proteins and GTPases mutated at defined regions or single amino acids were used as substrates. Starting with chimeric Rac/Rho proteins we demonstrated that proteins containing the N-terminal 73 amino acids of Rac1 (but not those of RhoA) were efficiently glucosylated. Within this stretch, three regions differ significantly in Rac1 and RhoA. Regions containing amino acids 41-45 and 50-54 had no effect on toxin…
Contact sites of peptide-oligoribonucleotide cross-links identified by a combination of peptide and nucleotide sequencing with MALDI MS.
1997
We have investigated peptide–oligoribonucleotide complexes isolated from cross-linked Escherichia coli 30S ribosomal subunits in order to identify the contact sites of these complexes at the molecular level. For this purpose, reversed-phase (RP) HPLC-purified peptide–oligoribonucleotide complexes were submitted to N-terminal amino acid sequencing in order to determine the cross-linked peptide moiety and were analyzed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for calculation of the nucleotide composition of the cross-linked complex. Subsequently, for nucleotide sequence information the complexes were partially hydrolyzed or treated with exonucleases and a…
An ab initio softness metric to measure the similarity between all pairs of amino acids
2010
Abstract The search for quantitative index of similarity between molecular moeties is important for its applications in pharmacology. Similarity is also an important concept in computational biology to measure the exchangeability of an amino acid by another in a protein sequence. In the present work, a distance between two molecules based on local and global softnesses of their fragments is defined. The method proposed is general and could be applied to any molecular library. It is first applied to compute the distance between the 190 pairs of different amino acids in their neutral states. Two amino acids belonging to the one of the biochemical class (aliphatic, sulfur-containing, acidic, ……
Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway
2012
The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect distinctive kinetic characteristics, as well as sequence-dependent properties of the employed enzymes. This study aims to examine possible linkages between kinetic constants and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolytic pathway. The values of Michaelis-Menten constant (K M), turnover number (k cat), and specificity constant (k sp = k cat/K M) were taken from BRENDA (15, 17, and 16 values, respectively) and protein sequences of nine…
Identification of the membrane penetrating domain of Vibrio cholerae cytolysin as a β-barrel structure
2005
Summary Vibrio cholerae cytolysin (VCC) is an oligomerizing pore-forming toxin that is related to cytolysins of many other Gram-negative organisms. VCC contains six cysteine residues, of which two were found to be present in free sulphydryl form. The positions of two intramolecular disulphide bonds were mapped, and one was shown to be essential for correct folding of protoxin. Mutations were created in which the two free cysteines were deleted, so that single cysteine substitution mutants could be generated for site-specific labelling. Employment of polarity-sensitive fluorophores identified amino acid side-chains that formed part of the pore-forming domain of VCC. The sequence commenced at…