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General Base (general + base)

Distribution by Scientific Domains
Chemistry80%

Terms modified by General Base

  • general base catalysis
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    Selected Abstracts

    Kinetic evidence for the occurrence of kinetically detectable intermediates in the cleavage of N -ethoxycarbonylphthalimide under N -methylhydroxylamine buffers

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2002
    M. Niyaz Khan
    The kinetics of the aqueous cleavage of N -ethoxycarbonylphthalimide (NCPH) in CH3NHOH buffers of different pH reveals that the cleavage follows the general irreversible consecutive reaction path NCPH ENMBC AB, where ENMBC, A, and B represent ethyl N -[o -(N -methyl- N -hydroxycarbamoyl)benzoyl]carbamate, N -hydroxyl group cyclized product of ENMBC, and o -(N -methyl- N -hydroxycarbamoyl)benzoic acid, respectively. The rate constant k1 obs at a constant pH, obeys the relationship k1 obs = kw + knapp [Am]T + kb[Am]T2, where [Am]T is the total concentration of CH3NHOH buffer and kw is first-order rate constant for pH-independent hydrolysis of NCPH. Buffer-dependent rate constant kb shows the presence of both general base and general acid catalysis. Both the rate constants k2 obs and k3 obs are independent of [Am]T (within the [Am]T range of present study) at a constant pH and increase linearly with the increase in aOH with definite intercepts. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 34: 95,103, 2002 [source]

    Structure,Activity Relationship Studies in Single-Site Esterase Peptide Dendrimers

    ISRAEL JOURNAL OF CHEMISTRY, Issue 1 2009
    Sacha Javor
    We recently reported on peptide dendrimers with a single catalytic site at the dendrimer core catalyzing the hydrolysis of acetoxy- and butyryloxy-pyrene trisulfonate 1a/b in aqueous buffer with Michaelis,Menten kinetics. Substrate binding is mediated by a pair of protonated arginine or histidine residues in the first generation branch, and esterolysis is performed by the imidazole side-chain of a histidine residue in the core acting as a general base or nucleophile. Herein we report on a structure,activity relationship study searching for an optimal combination between amino acid sequence and catalytic machinery. Installation of histidine residues onto the aromatic dendrimer framework "R" leads to 10-fold higher rate acceleration up to kcat/kuncat = 1.5 * 103 at pH 5.5 with dendrimers RG3H (AcYT)8 (BWG)4 (BHS)2BHS and RMG3H (AcYT)8(BWG)4(BHSG)2BHS (one-letter codes for L -amino acids; Ac = acetyl, B = L -2,3-diaminopropionic acid branching point, C-terminus is amide -CONH2). These dendrimers reach the compactness of a native folded protein. [source]

    The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lid

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010
    Javier García-Nafría
    dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). In Bacillus subtilis there are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85,Å resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in the trans conformation and the other three in the active gauche conformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the `Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism. [source]

    Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3,-monophosphate

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010
    Shuji Noguchi
    Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3,-monophosphate have been solved at 0.96 and 0.99,Å resolution. The crystal structures revealed that the C, atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed. [source]

    The effects of kin and familiarity on interactions between fish

    FISH AND FISHERIES, Issue 4 2003
    Ashley J W Ward
    Abstract Fish have been shown to discriminate between individuals on very general bases such as species, body length and colour. More recently, evidence has been accumulating from a number of species that relatedness and familiarity may be extremely important in mediating a range of interactions between individual fish. Studies have shown that fish are able to recognize kin and/or familiars, and that this ability potentially conveys significant benefits, including increased inclusive fitness, reduced inbreeding costs, reduced competition and enhanced antipredator behaviour. Here, we review the literature and consider future directions and applications for this research. [source]