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Yufen Zhao - One of the best experts on this subject based on the ideXlab platform.
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Phosphoryl transfer reaction regulated by amino acid side chains: A model for phosphoproteins
International journal of peptide and protein research, 2009Co-Authors: Yufen Zhao, Qing-jin Yan, Qian WangAbstract:Through a kinetic study of the reaction of phosphoamino acids as incubated in alcohol, it was found that the inter- and intramolecular Phosphoryl transfer reactions were regiospecific and stereoselective. First, the Phosphoryl transfer reaction required the regio-specifically neighboring α-carboxy group activation of amino acid but not 8-carboxy group. The intramolecular side chain catalytic effects relative to hydrogen for N-phosphoamino acids compared to N-phosphoglycine were a 119- to 4-times enhancement of the Phosphoryl transfer reaction, respectively. Secondly, the intramolecular NO Phosphoryl transfer migration was highly stereoselective, since the reaction rate constant of phosphoallothreonine relative to its diastereomeric threonine was reduced to half. The pentacoordinate transition states modulated by the amino acid side chains were demonstrated by the formation rates of intramolecular pentacoordinate spiro mixed anhydride compounds. © Munksgaard 1996.
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Synthesis of Phosphoryl Amino Acids Chrysin Esters
Phosphorus Sulfur and Silicon and The Related Elements, 2008Co-Authors: Xiaolan Chen, Jinwei Yuan, Wenfeng Li, Lingbo Qu, Yufen ZhaoAbstract:The N-Phosphoryl amino acids are coupled with chrysin to form Phosphoryl amino acids chrysin esters. Five of its new analogs have been synthesized. The structures of all the newly synthesized chrysin derivatives were confirmed by ESI-MS, NMR and IR.
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Interaction between N-Phosphoryl-α-, β- and γ-amino acids and nucleosides
Chinese Chemical Letters, 2007Co-Authors: Li Ming Qiang, Shu Xia Cao, Yan Chun Guo, Xin Cheng Liao, Yufen ZhaoAbstract:Abstract The reactions of four different N-(O,O′-diisopropyl) phosphoamino acids (DIPP-aa), such as N-Phosphoryl- l -α-alanine (DIPP- l -α-Ala), N-Phosphoryl- d -α-alanine (DIPP- d -α-Ala), N-Phosphoryl-β-alanine (DIPP-β-Ala) and N-Phosphoryl-γ-amino butyric acid (DIPP-γ-Aba), and four nucleosides, adenosine (A), guanosine (G), cytidine (C) and uridine (U), were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and HPLC/ESI-MS. DIPP- l -α-Ala and DIPP- d -α-Ala produced the same Phosphorylated nucleosides, dinucleotides and phosphoroligopeptide. However, DIPP-β-Ala and DIPP-γ-Aba gave no relevant products.
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Studies on cleavage of DNA by N-Phosphoryl branched peptides.
Peptides, 2006Co-Authors: Yu-ping Feng, Shengli Cao, Anshan Xiao, Wenjun Xie, Yufen ZhaoAbstract:Abstract It was found that N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -leucy]- l -lysyl-methyl ester ( 1 ) and N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -phenylalanyl]- l -lysyl-methyl ester ( 2 ) could cleave supercoiled DNA such as PUC19 efficiently in 40 mM Britton-Robinson buffer. The cleavage activities for both were investigated by agarose gel electrophoresis. The T4 ligase experiments implied that the cleavage of DNA occurs via a hydrolytic path. The results showed that the cleavage reaction of DNA is dependent on the value of pH and ionic strength in the solution. DNA cleavage is more efficient by N -Phosphoryl branched peptide 2 than by N -Phosphoryl branched peptide 1 . The experiments also show that hydrolysis of DNA by N -Phosphoryl branched peptide 1 was accelerated in the presence of Mg 2+ or Zn 2+ ions. The interactions of DNA with N -Phosphoryl branched peptides were also characterized by melting temperature measurements and circular dichroism (CD) techniques. On the basis of experimental data, the possible mechanism of interactions between DNA with N -Phosphoryl branched peptides was discussed.
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Structural characterization of N-Phosphoryl branched peptides
Journal of Molecular Structure, 2005Co-Authors: Yu-ping Feng, Shengli Cao, Yufen ZhaoAbstract:Abstract The structural characteristics of N -Phosphoryl branched peptides 2 – 5 in solution were investigated by NMR spectroscopy. We observed diastereotopic phenomena, interactions between hydrogen bonds and lack of regular secondary structure in these peptides. We also conducted conformational analysis on the amino acids binding Phosphoryl groups in compounds 2 – 5 .
Yu-ping Feng - One of the best experts on this subject based on the ideXlab platform.
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Studies on cleavage of DNA by N-Phosphoryl branched peptides.
Peptides, 2006Co-Authors: Yu-ping Feng, Shengli Cao, Anshan Xiao, Wenjun Xie, Yufen ZhaoAbstract:Abstract It was found that N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -leucy]- l -lysyl-methyl ester ( 1 ) and N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -phenylalanyl]- l -lysyl-methyl ester ( 2 ) could cleave supercoiled DNA such as PUC19 efficiently in 40 mM Britton-Robinson buffer. The cleavage activities for both were investigated by agarose gel electrophoresis. The T4 ligase experiments implied that the cleavage of DNA occurs via a hydrolytic path. The results showed that the cleavage reaction of DNA is dependent on the value of pH and ionic strength in the solution. DNA cleavage is more efficient by N -Phosphoryl branched peptide 2 than by N -Phosphoryl branched peptide 1 . The experiments also show that hydrolysis of DNA by N -Phosphoryl branched peptide 1 was accelerated in the presence of Mg 2+ or Zn 2+ ions. The interactions of DNA with N -Phosphoryl branched peptides were also characterized by melting temperature measurements and circular dichroism (CD) techniques. On the basis of experimental data, the possible mechanism of interactions between DNA with N -Phosphoryl branched peptides was discussed.
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Structural characterization of N-Phosphoryl branched peptides
Journal of Molecular Structure, 2005Co-Authors: Yu-ping Feng, Shengli Cao, Yufen ZhaoAbstract:Abstract The structural characteristics of N -Phosphoryl branched peptides 2 – 5 in solution were investigated by NMR spectroscopy. We observed diastereotopic phenomena, interactions between hydrogen bonds and lack of regular secondary structure in these peptides. We also conducted conformational analysis on the amino acids binding Phosphoryl groups in compounds 2 – 5 .
Osnat Herzberg - One of the best experts on this subject based on the ideXlab platform.
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Dissociative Phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants.
Biochemistry, 2002Co-Authors: Sijiu Liu, Yong Jia, Debra Dunaway-mariano, Osnat HerzbergAbstract:The crystal structure of PEP mutase from Mytilus edulis in complex with a substrate-analogue inhibitor, sulfopyruvate S-pyr (Ki = 22 μM), has been determined at 2.25 A resolution. Mg(II)-S-pyr binds in the α/β barrel's central channel, at the C-termini of the β-strands. The binding mode of S-pyr's pyruvyl moiety resembles the binding mode of oxalate seen earlier. The location of the sulfo group of S-pyr is postulated to mimic the phosphonyl group of the product phosphonopyruvate (P-pyr). This sulfo group interacts with the guanidinium group of Arg159, but it is not aligned for nucleopilic attack by neighboring basic amino side chains. Kinetic analysis of site directed mutants, probing the key active site residues Asp58, Arg159, Asn122, and His190 correlate well with the structural information. The results presented here rule out a Phosphoryl transfer mechanism involving a double displacement, and suggest instead that PEP mutase catalysis proceeds via a dissociative mechanism in which the pyruvyl C(3) adds...
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structure of a phosphonate inhibited beta lactamase an analog of the tetrahedral transition state intermediate of beta lactam hydrolysis
Journal of Molecular Biology, 1994Co-Authors: Celia C H Chen, Jubrail Rahil, R F Pratt, Osnat HerzbergAbstract:Abstract The crystal structure of β-lactamase from Staphylococcus aureus inactivated by p -nitrophenyl[[N-(benzyloxycarbonyl)amino]methyl]phosphonate, a methylphosphonate monoester monoanion inhibitor, has been determined and refined at 2·3 A resolution. The structure reveals a tetrahedral phosphorus covalently bonded to the Oγ atom of the active site serine, Ser70. One of the oxygen atoms bonded to phosphorus is located in the oxyanion hole formed by the two main-chain nitrogen atoms of Ser70 and Gln237, and the second bonded oxygen is solvated. The (benzyloxycarbonyl)aminomethyl group is oriented towards the active site gully such that the peptide group forms compensating electrostatic interactions with polar groups on the enzyme. The benzyl group forms a hydrophobic interaction with Ile239 and an aromatic-aromatic edge-to-face interaction with Tyr105, which has undergone a conformational transition relative to the native structure. The mode of binding supports the proposal that on reaction with the enzyme, the phosphonate generates a structure analogous to the tetrahedral transition state/intermediate associated with the acylation step of a normal substrate. The disposition of the phosphonyl group in this complex is the same as that of the corresponding Phosphoryl group in the complex resulting from the inhibition of trypsin by diisopropylphosphofluoridate. The structure is consistent with a mechanism of inactivation that follows an associative pathway, proceeding via a transition state/intermediate in which phosphorus is penta-co-ordinated, forming a trigonal bipyramidal geometry with the phosphonyl donor (p-nitrophenol) and acceptor (Ser70 Oγ atom) in apical positions. A model of this transition state can be accommodated in the active site of β-lactamase without any steric hindrance. A model of the tetrahedral transition state associated with the acylation step by benzyl penicillin has been derived. Because of the conformational rigidity of the fused rings of penicillin molecules, the orientation of the substrate is fixed once the tetrahedral carbonyl carbon and its ligands are superimposed on the phosphonate group. The outcome is that the carboxylate substituent on the thiazolidine ring forms a salt bridge with Lys234, and the preferred puckering of the ring is that observed in the crystal structure of ampicillin, the so-called "open" conformer.
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An atomic model for protein-protein Phosphoryl group transfer.
The Journal of biological chemistry, 1992Co-Authors: Osnat HerzbergAbstract:Abstract The high resolution crystal structures of two interacting proteins from the phosphoenolpyruvate:sugar phosphotransferase system, the histidine-containing phosphocarrier protein (HPr) and the IIA domain of glucose permease (IIA(Glc)) from Bacillus subtilis, provide the basis for modeling the transient binary complex formed during the Phosphoryl group transfer. The complementarity of the interacting surfaces implies that no major conformational transition is required. The negatively charged Phosphoryl group is buried in the interface, suggesting a key role for electrostatic interactions. It is proposed that the Phosphoryl transfer is triggered by a switch between two salt bridges involving Arg-17 of the HPr. The first, prior to Phosphoryl group transfer, is intramolecular, with the Phosphorylated His-15. The second, during the transfer, is intermolecular, with 2 aspartate residues associated with the active site of IIA(Glc). Such alternating ion pairs may be mechanistically important in other protein-protein phosphotransfer reactions.
Shengli Cao - One of the best experts on this subject based on the ideXlab platform.
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Studies on cleavage of DNA by N-Phosphoryl branched peptides.
Peptides, 2006Co-Authors: Yu-ping Feng, Shengli Cao, Anshan Xiao, Wenjun Xie, Yufen ZhaoAbstract:Abstract It was found that N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -leucy]- l -lysyl-methyl ester ( 1 ) and N α , N ɛ -di[ N -( O , O -diisopropyl)Phosphoryl- l -phenylalanyl]- l -lysyl-methyl ester ( 2 ) could cleave supercoiled DNA such as PUC19 efficiently in 40 mM Britton-Robinson buffer. The cleavage activities for both were investigated by agarose gel electrophoresis. The T4 ligase experiments implied that the cleavage of DNA occurs via a hydrolytic path. The results showed that the cleavage reaction of DNA is dependent on the value of pH and ionic strength in the solution. DNA cleavage is more efficient by N -Phosphoryl branched peptide 2 than by N -Phosphoryl branched peptide 1 . The experiments also show that hydrolysis of DNA by N -Phosphoryl branched peptide 1 was accelerated in the presence of Mg 2+ or Zn 2+ ions. The interactions of DNA with N -Phosphoryl branched peptides were also characterized by melting temperature measurements and circular dichroism (CD) techniques. On the basis of experimental data, the possible mechanism of interactions between DNA with N -Phosphoryl branched peptides was discussed.
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Structural characterization of N-Phosphoryl branched peptides
Journal of Molecular Structure, 2005Co-Authors: Yu-ping Feng, Shengli Cao, Yufen ZhaoAbstract:Abstract The structural characteristics of N -Phosphoryl branched peptides 2 – 5 in solution were investigated by NMR spectroscopy. We observed diastereotopic phenomena, interactions between hydrogen bonds and lack of regular secondary structure in these peptides. We also conducted conformational analysis on the amino acids binding Phosphoryl groups in compounds 2 – 5 .
Milton H Saier - One of the best experts on this subject based on the ideXlab platform.
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biochemical characterization of Phosphoryl transfer involving hpr of the phosphoenolpyruvate dependent phosphotransferase system in treponema denticola an organism that lacks pts permeases
Biochemistry, 2005Co-Authors: Claudio F Gonzalez, Aaron J Stonestrom, Graciela L Lorca, Milton H SaierAbstract:Treponema pallidum and Treponema denticola encode within their genomes homologues of energy coupling and regulatory proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) but no recognizable homologues of PTS permeases. These homologues include (1) Enzyme I, (2) HPr, (3) two IIA(Ntr)-like proteins, and (4) HPr(Ser) kinase/Phosphorylase (HprK). Because the Enzyme I-encoding gene in T. pallidum is an inactive pseudogene and because all other pts genes in both T. pallidum and T. denticola are actively expressed, the primary sensory transduction mechanism for signal detection and transmission appears to involve HprK rather than EI. We have overexpressed and purified to near homogeneity four of the five PTS proteins from T. denticola. Purified HprK Phosphorylates HPr with ATP, probably on serine, while Enzyme I Phosphorylates HPr with PEP, probably on histidine. Furthermore, HPr(His)-P can transfer its Phosphoryl group to IIA(Ntr)-1. Factors and conditions regulating Phosphoryl transfer prove to differ from those described previously for Bacillus subtilis, but cross-enzymatic activities between the Treponema, Salmonella, and Bacillus Phosphoryl-transfer systems could be demonstrated. Kinetic analyses revealed that the allosterically regulated HPr kinase/Phosphorylase differs from its homologues in Bacillus subtilis and other low G+C Gram-positive bacteria in being primed for kinase activity rather than Phosphorylase activity in the absence of allosteric effectors. The characteristics of this enzyme and the Treponema Phosphoryl-transfer chain imply unique modes of signal detection and sensory transmission. This paper provides the first biochemical description of PTS Phosphoryl-transfer chains in an organism that lacks PTS permeases.
