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Cleavage Reaction (cleavage + reaction)
Selected AbstractsC(10),C(19) Bond Cleavage Reaction of 19-Oxygenated Androst-4-ene-3,6-dione Steroids under Various Conditions.CHEMINFORM, Issue 3 2005Masao Nagaoka Abstract For Abstract see ChemInform Abstract in Full Text. [source] A General Procedure for a One-Pot Oxidative Cleavage/Wittig Reaction of Glycols.CHEMINFORM, Issue 35 2002Norma K. Dunlap Abstract For Abstract see ChemInform Abstract in Full Text. [source] Significant activity of a modified ribozyme with N7-deazaguanine at G10.1: the double-metal-ion mechanism of catalysis in reactions catalysed by hammerhead ribozymesGENES TO CELLS, Issue 8 2000Yuka Nakamatsu Background Several reports have appeared recently of experimental evidence for a double-metal-ion mechanism of catalysis in reactions catalysed by hammerhead ribozymes. In one case, hammerhead ribozyme-mediated cleavage was analysed as a function of the concentration of La3+ ions in the presence of a fixed concentration of Mg2+ ions so that the role of metal ions that are directly involved in the cleavage reaction could be monitored. The resultant bell-shaped curve for activation of cleavage was used to support the proposed double-metal-ion mechanism of catalysis. However, other studies have demonstrated that the binding of a metal ion (the most conserved P9 metal ion) to the pro-Rp oxygen (P9 oxygen) of the phosphate moiety of nucleotide A9 and to the N7 of nucleotide G10.1 is critical for efficient catalysis, despite the large distance (,20 Å) between the P9 metal ion and the labile phosphodiester group in the ground state. In fact, it was demonstrated that an added Cd2+ ion binds first to the pro-Rp phosphoryl P9 oxygen but not with the pro-Rp phosphoryl oxygen at the cleavage site. Results In earlier discussions, it was difficult to completely exclude the possibility that La3+ ions might have replaced the P9 metal ion and, as a result, created conditions represented by the bell-shaped curve. In order to clarify this situation, we examined a chemically synthesized hammerhead ribozyme (7-deaza-R34) that included a minimal modification, namely, an N7-deazaguanine residue in place of G10.1. We compared the kinetic properties of this ribozyme with those of the parental ribozyme (R34). Kinetic analysis revealed that, unlike the cases of added Cd2+ ions, the added La3+ ions did not replace the pre-existing P9 metal ion, and that the replacement of N7 by C7 at G10.1 reduced the catalytic activity to a limited extent. This result indicates that the binding of a Mg2+ ion to N7 at G10.1 is catalytically important but not indispensable. Most importantly, 7-deaza-R34 also yielded a bell-shaped curve upon addition of La3+ ions to the reaction mixture. Conclusions Since the data based on our experiments with 7-deaza-R34 are completely free from potential artefacts, due to the binding of a La3+ ion to N7 at G10.1, our results, that 7-deaza-R34 yielded a bell-shaped curve following the addition of La3+ ions to the Mg2+ -background reaction mixture, strongly supports the proposal that a double-metal-ion mechanism is operative in the cleavage reaction which is catalysed by hammerhead ribozymes. [source] How to keep V(D)J recombination under controlIMMUNOLOGICAL REVIEWS, Issue 1 2004Marjorie A. Oettinger Summary:, Breaking apart chromosomes is not a matter to be taken lightly. The possible negative outcomes are obvious: loss of information, unstable chromosomes, chromosomal translocations, tumorigenesis, or cell death. Utilizing DNA rearrangement to generate the desired diversity in the antigen receptor loci is a risky business, and it must be carefully controlled. In general, the regulation is so precise that the negative consequences are minimal or not apparent. They are visible only when the process of V(D)J recombination goes awry, as for example in some chromosomal translocations associated with lymphoid tumors. Regulation is imposed not only to prevent the generation of random breaks in the DNA, but also to direct rearrangement to the appropriate locus or subregion of a locus in the appropriate cell at the appropriate time. Antigen receptor rearrangement is regulated essentially at four different levels: expression of the RAG1/2 recombinase, intrinsic biochemical properties of the recombinase and the cleavage reaction, the post-cleavage /DNA repair stage of the process, and accessibility of the substrate to the recombinase. Within each of these broad categories, multiple mechanisms are used to achieve the desired aims. The major focus of this review is on accessibility control and the role of chromatin and nuclear architecture in achieving this regulation, although other issues are touched upon. [source] Determination of binding sites in carboplatin-bound cytochrome c using electrospray ionization mass spectrometry and tandem mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2005Gaosheng Yang Abstract Interaction of carboplatin with cytochrome c (Cyt. c) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). ESI-MS studies revealed that the ring-opened adducts of carboplatin with Cyt. c were formed in the stoichiometric ratio of 1 : 1 and 2 : 1 at pH 5.0 and 37 °C and in the stoichiometric ratio of 1 : 1 only at pH 7.0 and 37 °C. It was also found that Cyt. c could be cleaved by carboplatin at pH 2.5 and 50 °C. The cleaved fragments of Cyt. c were determined by ESI-MS and MS/MS analysis to be Glu66,Met80, Ac-Gly01,Met65, Glu66,Glu104, Ac-Gly01,Met80 and Ile81,Glu104. The carboplatin prefers to anchor to Met65 first, then to Met80. To further confirm the binding site of Met, AcMet-Gly was used as the model molecule to investigate its interaction with carboplatin and its hydrolysis reaction. On the basis of species detected during the reaction monitored by ESI-MS, a possible pathway of the cleavage reaction was proposed. Copyright © 2005 John Wiley & Sons, Ltd. [source] Mechanistic studies of amide bond scission during acidolytic deprotection of Pip containing peptideJOURNAL OF PEPTIDE SCIENCE, Issue 8 2008Chiara Rubini Abstract Unusual TFA catalyzed cleavage reaction is reported for peptide containing pipecolic acid residues. Although the use of TFA under standard cleavage conditions is sufficiently mild to prevent degradation of the desired products, the amide bond between consecutive pipecolic acid residues is unexpectedly hydrolyzed by standard TFA treatment. The hydrolysis is proposed to proceed via an oxazolinium ion intermediate. This mechanism is supported by H/D exchange as observed by ESI-MS and NMR experiments. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Bioactive secondary metabolites from symbiotic marine dinoflagellates: symbiodinolide and durinskiolsTHE CHEMICAL RECORD, Issue 2 2010Masaki Kita Abstract Symbiotic relationships play critical roles in marine ecosystems. Among symbionts, marine dinoflagellates have attracted the attention of natural products chemists, biologists, and ecologists, since they are rich sources of unique bioactive secondary metabolites. The polyol compound symbiodinolide, which was isolated from the symbiotic dinoflagellate Symbiodinium sp., exhibits significant voltage-dependent N -type Ca2+ channel-opening activity and may serve as a defense substance to prevent digestion of the host animals. Durinskiols are also unique long carbon-chain polyol compounds that were isolated from the dinoflagellate Durinskia sp. We found a selective cleavage reaction of allylic 1,2-diol using an olefin metathesis catalyst, and developed a fluorescent-labeling method for MS/MS analysis to achieve the structural elucidation of huge polyol compounds. This review highlights recent advances in structural and biological studies on symbiodinolide, durinskiols, and related polyol compounds. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 57,69; 2010: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.200900007 [source] Tunable DNA Cleavage by Intercalating PeptidoconjugatesCHEMBIOCHEM, Issue 5 2006Kerry P. Mahon Jr. Abstract The properties of a novel family of peptide-based DNA-cleavage agents are described. Examination of the DNA-cleavage activities of a systematic series of peptide,intercalator conjugates revealed trends that show a strong dependence on peptide sequence. Conjugates differing by a single residue displayed reactivities that varied over a wide range. The cleavage activity was modulated by the electrostatic or steric qualities of individual amino acids. Isomeric conjugates that differed in the position of the tether also exhibited different reactivities. The mechanism of DNA cleavage for these compounds was also probed and was determined to involve hydrogen-atom abstraction from the DNA backbone. Previous studies of these compounds indicated that amino acid peroxides were the active agents in the cleavage reaction; in this report, the chemistry underlying the reaction is characterized. The results reported provide insight into how peptide sequences can be manipulated to produce biomimetic compounds. [source] Photoreactivity and Photopolymerization of Silicon-Bridged [1]Ferrocenophanes in the Presence of Terpyridine Initiators: Unprecedented Cleavage of Both Iron,Cyclopentadienyl Bonds in the Presence of ChlorosilanesCHEMISTRY - A EUROPEAN JOURNAL, Issue 31 2007Yan Chan Abstract The photopolymerisation of sila[1]ferrocenophane [Fe(,-C5H4)2SiMe2] (3) with 4,4,,4,,-tri- tert -butyl-2,2,:6,,2,,-terpyridine (tBu3terpy) as initiator has been explored. High-molecular-weight polyferrocenylsilane (PFS) [{Fe(,-C5H4)2SiMe2}n] (5) was formed in high yield when a stoichiometric amount of tBu3terpy was used at 5,°C. Photopolymerisation of ferrocenophane 3 at higher temperatures gave PFS 5 in lower yield and with a reduced molecular weight as a result of a slower propagation rate. Remarkably, when Me3SiCl was added as a capping agent before photopolymerisation, subsequent photolysis of the reaction mixture resulted in the unprecedented cleavage of both iron,Cp bonds in ferrocenophane 3: iron(II) complex [Fe(tBu3terpy)2Cl2] (7Cl) was formed and the silane fragment (C5H4SiMe3)2SiMe2 (8) was released. The iron,Cp bond cleavage reaction also proceeded in ambient light, although longer reaction times were required. In addition, the unexpected cleavage chemistry in the presence of Me3SiCl was found to be applicable to other photoactive ferrocenes such as benzoylferrocene. For benzoylferrocene and ferrocenophane 3, the presence of metal-to-ligand charge transfer (MLCT) character in their low-energy transitions in the visible region probably facilitates photolytic iron,Cp bond cleavage, but this reactivity is suppressed when the strength of the iron,Cp bond is increased by the presence of electron-donating substituents on the cyclopentadienyl rings. [source] Poly(ADP-Ribose)-Polymerase-Catalyzed Hydrolysis of NAD+: QM/MM Simulation of the Enzyme ReactionCHEMMEDCHEM, Issue 5 2006Daniele Bellocchi Dr. Abstract Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme which uses NAD+ as substrate and catalyzes the transfer of multiple units of ADP-ribose to target proteins. PARP is an attractive target for the discovery of novel therapeutic agents and PARP inhibitors are currently evaluated for the treatment of a variety of pathological conditions such as brain ischemia, inflammation, and cancer. Herein, we use the PARP-catalyzed reaction of NAD+ hydrolysis as a model for gaining insight into the molecular details of the catalytic mechanism of PARP. The reaction has been studied in both the gas-phase and in the enzyme environment through a QM/MM approach. Our results indicate that the cleavage reaction of the nicotinamide-ribosyl bond proceeds through an SN2 dissociative mechanism via an oxacarbenium transition structure. These results confirm the importance of the structural water molecule in the active site and may constitute the basis for the design of transition-state-based PARP inhibitors. [source] Photooxidation and Photoconductivity of Polyferrocenylsilane Thin FilmsMACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 7 2003Paul W. Cyr Abstract Irradiation of thin films of poly(ferrocenylmethylphenylsilane) ([Fe(,5 -C5H4)2SiMePh]n) cast from chloroform solution with UV light leads to photooxidation of ferrocene centers in the polymer main chain. The extent of the polymer oxidation can be controlled in the range ca. 0,5% by the duration of the irradiation exposure and by the concentration of chloroform. The photooxidized polyferrocenylsilane material is conductive, with an increased conductivity of greater than three orders of magnitude relative to the unoxidized material. In addition, the photooxidized polymers have been found to be photoconductive. The photooxidation process can be reversed by means of chemical reduction using hydrazine or decamethylferrocene, leading to the regeneration of the neutral polymers. However, substantial molecular weight decline was detected during the photooxidation/reduction process, presumably as a result of chain cleavage reactions induced by the anionic or radical chlorinated photoproducts. Methylation of the cyclopentadienyl rings of the ferrocene moiety in the polymer was found to lead to materials which are significantly more stable. Time trace of the current at constant applied voltage of 100 V for a PFS film upon illumination. The ON and OFF states were created by using a mechanical shutter. [source] Die facettenreiche Welt der Apocarotinoide.BIOLOGIE IN UNSERER ZEIT (BIUZ), Issue 5 2009Aromen und Hormone, Düfte, Farben Abstract Apocarotinoide werden durch hochspezifische Spaltungsreaktionen oxidativer Enzyme an den Doppelbindungen von Carotinoiden maßgeschneidert. Es können neue Chromophore entstehen, die zusätzliche Nuancen des gelb-roten Farbspektrums eröffnen. Farblose C13-Apocarotinoide können potente Duft- und Aromastoffe sein. Viele Apocarotinoidfunktionen mit Hormoncharakter sind lange bekannt (Abszisinsäure in Pflanzen, Trisporsäure in Pilzen, Retinsäure in Säugern). Eine neue Klasse von Apocarotinoid-Pflanzenhormonen, die die Sprossverzweigung der Pflanzen mitbestimmen, wurde kürzlich als Strigolactone identifiziert. In ihrer Biosynthese wie auch in der von mykorrhizainduzierten C13/C14-Apocarotinoiden treten mehrstufige aufeinanderfolgende Carotinoidspaltungsreaktionen auf. Das Wissen über Synthesewege und Funktionen von Apocarotinoiden eröffnet neue Perspektiven für Anwendungen im Zierpflanzenbau, bei der Bekämpfung parasitischer Unkräuter und in der Beeinflussung von Blütendüften und Fruchtaromen. Apocarotenoids are tailored from carotenoids by highly specific oxidative enzymes cleaving different double bonds. New chromophores can be generated, which make additional nuances of the yellow-red color spectrum available. Colorless C13 apocarotenoids can constitute potent scent and aroma compounds. Many apocarotenoid hormone functions are well-known (abscisic acid in plants, trisporic acid in fungi, retinoic acid in mammals). A new class of apocarotenoid plant hormones, which take part in determining shoot branching has recently been identified as strigolactones. In the biosyntheses of strigolactones and mycorrhiza-induced C13/C14 apocarotenoids several sequential cleavage reactions occur. The knowledge about biosynthetic pathways and functions of apocarotenoids opens up new perspectives for its application in horticulture and in the control of parasitic weeds as well as in the manipulation of flower scents and fruit aromas. [source] Expression of antibodies using single-open reading frame vector design and polyprotein processing from mammalian cellsBIOTECHNOLOGY PROGRESS, Issue 3 2009Yune Z. Kunes Abstract We describe a novel polyprotein precursor-based approach to express antibodies from mammalian cells. Rather than expressing heavy and light chain proteins from separate expression units, the antibody heavy and light chains are contained in one single-open reading frame (sORF) separated by an intein gene fused in frame. Inside mammalian cells this ORF is transcribed into a single mRNA, and translated into one polypeptide. The antibody heavy and light chains are separated posttranslationally, assembled into the functional antibody molecule, and secreted into culture medium. It is demonstrated that Pol I intein from P. horikoshii mediates protein splicing and cleavage reactions in mammalian cells, in the context of antibody heavy and light chain amino acid sequences. To allow the separation of antibody heavy chain, light chain, and the intein, we investigated a number of intein mutations designed to inhibit intein-mediated splicing but preserve cleavage reactions. We have also designed constructs in which the signal peptide downstream from intein has altered hydrophobicity. The use of some of these mutant constructs resulted in more efficient antibody secretion, highlighting areas that can be further explored in improving such an expression system. An antibody secreted using one of the sORF constructs was characterized. This antibody has correct N-terminal sequences for both of its heavy and light chains, correct heavy and light chain MW as well as intact MW as measured by mass spectrometry. Its affinity to antigen, as measured by surface plasmon resonance (SPR), is indistinguishable from that of the same antibody produced using conventional method. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Study of Protein Splicing and Intein-Mediated Peptide Bond Cleavage under High-Cell-Density ConditionsBIOTECHNOLOGY PROGRESS, Issue 3 2003Shamik Sharma Protein splicing elements (inteins), capable of catalyzing controllable peptide bond cleavage reactions, have been used to separate recombinant proteins from affinity tags during affinity purification. Since the inteins eliminate the use of a protease in the recovery process, the intein-mediated purification system has the potential to significantly reduce recovery costs for the industrial production of recombinant proteins. Thus far, the intein system has only been examined and utilized for expression and purification of recombinant proteins at the laboratory scale for cells cultivated at low cell densities. In this study, protein splicing and in vitro cleavage of intein fusion proteins expressed in high-cell-density fed-batch fermentations of recombinant Escherichia coli were examined. Three model intein fusion constructs were used to examine the stability and splicing/cleavage activities of the fusion proteins produced under high-cell-density conditions. The data indicated that the intein fusion protein containing the wild-type intein catalyzed efficient in vivo protein splicing during high-cell-density cultivation. Also, the intein fusion proteins containing modified inteins catalyzed efficient thiol-induced in vitro cleavage reactions. The results of this study demonstrated the potential feasibility of using the intein-mediated protein purification system for industrial-scale production of recombinant proteins. [source] | |||||||||||||