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  • electrospray ionization
  • We have investigated these properties for Ximelagatran (Xi), which has a high tendency to form doubly charged ions in electrospray ionization (ESI), by studying the percentage of doubly charged species formed when varying the formic acid (FA) concentration, analyte concentration, amount of organic modifier and flow rate. (diva-portal.org)
  • metal ions
  • These metal ions complex to the substrate pyrophosphate, thereby promoting the ionization of the leaving group of FPP, resulting in the generation of a highly reactive allylic cation. (asm.org)
  • 2,3,5,6 Additionally, they can act as siderophores which chelate and transport metal ions essential for cell growth and proliferation. (rsc.org)
  • product ions
  • The fragmentation patterns are to a great extent similar, but the doubly charged species is more inclined to generate low-mass product ions. (diva-portal.org)
  • The influence of the presence and position of a single beta-alanine, gamma-aminobutyric acid, epsilon-aminocaproic acid or 4-aminomethylbenzoic acid residue on the tendency to form b(n)+ -and y(n)+ -type product ions was determined using a group of protonated tetrapeptides with general sequence XAAG, AXAG and AAXG (where X refers to the position of amino acid substitution). (wichita.edu)
  • homology
  • Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. (jcvi.org)
  • Based on both sequence and structure homology ( 4 , 6 ), these β -lactam-forming enzymes show evolutionary roots in the broadly distributed asparagine synthetases, class B (AS-B), which convert the essential amino acid aspartate to asparagine. (pubmedcentralcanada.ca)
  • To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology 1 . (jove.com)
  • amidation
  • Such 'variations' could include incorporation of different pre-curs-ors (for biochemistry experts: methylmalonyl-CoA and/or malonyl-CoA) in the initiation step as well as in the elongation steps of the linear polyketide chain, or skipping some steps entirely, and, lastly, variations in the post-PKS 'tailoring steps' of amidation, cyclization, hydration, and methyl-a-tion of the polyketide chain (Figure 2). (asmblog.org)
  • nucleotides
  • 9. A probe comprising a nucleotide sequence consisting of at least 40 nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 155, SEQ ID NO: 372, SEQ ID NO: 1699, SEQ ID NO: 1891, SEQ ID NO: 1900, SEQ ID NO: 2252, SEQ ID NO: 2335, SEQ ID NO: 2481, and SEQ ID NO: 2673. (patents.com)
  • Fragments
  • Several contingent ion fragments, including reliable mass accuracy, localize a PTM of +28 Da to the initiator methionine of N-AgrD. (nih.gov)
  • genes
  • Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. (pnas.org)
  • Three distinct classes of terpene synthase genes were discerned, from which assumed patterns of sequential intron loss and the loss of an unusual internal sequence element suggest that the ancestral terpenoid synthase gene resembled a contemporary conifer diterpene synthase gene in containing at least 12 introns and 13 exons of conserved size. (genetics.org)
  • Enzymes
  • The clear evolution of these often well-studied enzymes to new, specialized roles is striking but frequently difficult to deduce from their primary sequence alone ( 1 ). (pubmedcentralcanada.ca)
  • substrate
  • The aspartates bind and activate the diphosphate group of the allylic substrate through bridging Mg2+ ions . (grantome.com)
  • precursor ion
  • In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation. (springer.com)
  • Structures
  • Moreover, modified sequences are frequently also present unmodified (heterogeneity), and when occupied, the same site may be modified with different carbohydrate structures (microheterogeneity). (mcponline.org)
  • Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. (springer.com)
  • Furthermore, we are developing improved native MS and ion mobility spectrometry protocols and methodologies to investigate the structures of the protein complex associated with apoptosis and proliferation of cancer cells. (phoenix-center.cn)
  • undergo
  • Terpenes are synthesized from linear isoprene diphosphate precursors with various chain lengths, and their enormous structural diversity is the result of the large number of possible enzyme-catalyzed cyclizations and rearrangements that the double-bond-containing isoprene chains can undergo ( 14 , 49 ). (asm.org)
  • However, [ 32 P]PP i -ATP exchange assays demonstrated Y345A and E380A undergo the first half-reaction, with the remaining active mutants showing decreased forward commitment to β -lactam cyclization. (pubmedcentralcanada.ca)
  • variation
  • DNA Sequencing Variation in Geographic Diverse Samples of Paraorygmatobothrium(Tetraphyllidea: Phyllobothriidae) Collected from the Blacktip Shark,Carcharhinu Limbatus. (wvstateu.edu)
  • diversity
  • Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. (pnas.org)
  • The diagnosis of viral causes of many infectious diseases is difficult due to the inherent sequence diversity of viruses as well as the ongoing emergence of novel viral pathogens, such as SARS coronavirus and 2009 pandemic H1N1 influenza virus, that are not detectable by traditional methods. (jove.com)
  • fragment ion
  • Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b 2 + fragment ion from the protonated PPG tripeptide. (springer.com)
  • This result is in contrast with a recent study of the IRMPD action spectrum of the PP b 2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. (springer.com)
  • accuracy precursor
  • Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. (mcponline.org)
  • similarity
  • The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. (jcvi.org)
  • Abstract
  • http://onlinelibrary.wiley.com/doi/10.1002/cber.19110440309/abstract;jsessionid=88DB9E8643AD7A2A200A0D7E1EDBE471.d01t01 Pictet, Spengler The reaction is a cyclization between an amine that carries an aromatic ring, and an aldehyde, usually catalyzed by acid (Scheme 1911 Pictet Spengler 2). (openwetware.org)
  • substantially
  • Because of the substantially weakened carbon-hydrogen bonds in alkylarene radical cations, the formation of benzylic cation 4, shown in the chair conformation that is relevant to cyclization, either undergoes 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Angew. (docme.ru)
  • Formation
  • The acid or base catalyzed aspartimide formation is sequence dependent. (studyres.com)
  • The amino acid residue, x, immediately following the aspartyl residue in sequence (Asp-x), exerts a significant influence on the rate of imide formation. (studyres.com)
  • Our initial studies focused on the conversion of paramethoxybenzyl (PMB) ether 1 into tetrahydropyrone 2 (Scheme 1) by DDQ-mediated oxocarbenium ion formation. (docme.ru)
  • electron
  • Thus, amino acids in this position, containing either electron donating or nonbulky side chains, are conducive to the cyclization side reaction. (studyres.com)
  • This reaction proceeds by electron transfer from 1 to DDQ to form radical-ion pair 3. (docme.ru)
  • While the electron-transfer dissociation data provided the bulk of the information for both modified sequence and modification site assignment, the higher-energy collision-dissociation data frequently yielded confirmation of the peptide identity, and revealed the presence of some core-2 or core-3 oligosaccharides. (mcponline.org)
  • bias
  • The reduced magnitude of change of the fluorescence intensity of the DyLight dyes, particularly of DY647 in comparison with Cy5, suggests that these dyes are less likely to introduce sequence-dependent bias into experiments based on fluorescent labeling of nucleic acids. (jove.com)
  • amino acids
  • In addition, differences in the relative proton affinities of the alternative amino acids influence the competition between complementary b(n) and y(n) ions. (wichita.edu)
  • hydrophilic
  • This enrichment step was implemented with either protein-level mixed-bed ion-exchange chromatography or with peptide-level electrostatic repulsion hydrophilic interaction chromatography. (mcponline.org)
  • dissociation
  • In addition, ion mobility MS shows that Pt binds to multiple sites in Substance P, generating multiple conformers, which can be partially localized by collisionally activated dissociation (CAD). (springer.com)
  • glycosylation
  • The lack of consensus sequence, common core structure, and universal endoglycosidase for the release of O -linked oligosaccharides makes O -glycosylation more difficult to tackle than N -glycosylation. (mcponline.org)
  • First, N -glycosylation again has a well defined consensus sequence: N X (S/T/C) where the middle amino acid cannot be Pro ( 6 ). (mcponline.org)
  • By contrast, analysis of O -glycosylation is hampered by a lack of (i) a consensus sequence, (ii) a universal core structure, and (iii) a universal endoglycosidase or gentle chemical hydrolysis method to facilitate analysis. (mcponline.org)
  • consensus sequence
  • namely, a consensus sequence for modification and a single core structure for modification. (mcponline.org)
  • A consensus sequence has been defined: W XX W where the first Trp is modified, and the modification, a Man moiety, readily survives sample preparation and mass spectrometric analysis, including collisional activation ( 5 ). (mcponline.org)