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Yu-Fen Zhao

Publications and source records attributed to Yu-Fen Zhao.

At least 19 recordsLinked to original sources
PubMed2006

Application of (31P) NMR in analyzing the degradation efficiency of organic phosphorus degrading-bacteria.

HPLC and HPLC-MS are the fastest and most accurate techniques for analysis of organic phosphorus pesticide (OPP) at the present time. Using these techniques, 14 strains of methamidopho (MAP) degrading-bacteria from the area contaminated with MAP have been identified. The results from HPLC and HPLC-MS analyses showed that the highest degradation rate was 73% after 7 days. In order to determine what metabolites will be formed after degradation, a key issue that has been neglected for a long time, we used ((31)P) NMR to track the degradation process. The results showed that different strains produced different metabolites. Ten strains were divided into three groups (groups A, B and C) by their metabolic profiling. Strains in group A degraded MAP into phosphor acid by breaking down all P-N, P-O and P-S bonds in 7 days. Strains in groups B and C had only broken down partially P-N and P-S bonds at the same time. Therefore, the bacterial strains in group A had a greater application potential than the other two groups. In addition, most metal phosphates are unsolvable in water. The analysis of X-ray showed, that the phosphate radicals generated by bacterial degradation induce crystallogenesis of heavy metal salts in water phase and also cause the chemical sedimentation of their crystals. Furthermore, these crystals are hydrogen phosphates. The results suggested that the MAP-degrading bacteria could be used for cleaning up not only the organic phosphorous pesticide contamination but also the phosphorous and heavy metal contamination in water environment simultaneously.

Bacteria↗
PubMed2006

The self-assembly ability of the first microtubule-binding repeat from tau and its modulation by phosphorylation.

Aggregation of abnormally phosphorylated tau in the form of tangs of paired helical filaments (PHFs) is one of the hallmarks of Alzheimer's disease (AD) and other tauopathies. It is of fundamental importance to study the mechanism of PHF formation and its modulation by phosphorylation. In this work, we have focused on the first microtubule-binding repeat of tau encompassing an abnormal phosphorylation site Ser262. The assembly propensities of this repeat and its corresponding phosphorylated form were investigated by turbidity and electron microscopy. Additionally, conformation of the two peptides is also analyzed through circular dichroism (CD) and NMR spectroscopy. Our results reveal that both of them are capable of self-assembly and phosphorylation at Ser262 could speed up the process of assembly. A possible mechanism of PHF formation is proposed and enhancing effect of phosphorylation on assembly provides an explanation to its toxicity in Alzheimer's disease.

Amino Acid Sequence↗
PubMed2006

Studies of interaction between a new synthesized minor-groove targeting artificial nuclease and DNA.

Nuclease plays an important role in molecular biology, such as DNA sequencing. Synthetic polyamide conjugates can be considered as new tool in the selective inhibition of gene expression and as potential drugs in anticancer or antiviral chemotherapy. In this paper, a new synthesized minor-groove targeting artificial nuclease, oligopyrrol-containing peptide, was reported. It was found that this new compound can bind DNA in AT-riched minor groove with high affinity and site specificity. DNA binding behavior was determined by UV-vis and circular dichroism (CD) methods. It was indicated that compound 6 can enhance the Tm of oligomer DNA from 51.8 to 63.5 degrees C and possesses large binding constant (Kb=8.83x10(4)L/mol).

Animals↗
PubMed2006

A unique NH-spacer for N-benzamidothiourea based anion sensors. Substituent effect on anion sensing of the ICT dual fluorescent N-(p-dimethylaminobenzamido)-N'-arylthioureas.

A series of N-(p-dimethylaminobenzamido)-N'-(substituted-phenyl)thioureas (substituent = p-CH3, H, p-Cl, p-Br, m-Br, m-NO2, and p-NO2) were designed as anion sensors in order to better understand the -NH-spacer via a substituent effect investigation. In these molecules the dual fluorescent intramolecular charge transfer (ICT) fluorophore p-dimethylaminobenzamide as the signal reporter was linked to the anion-binding site, the thiourea moiety, via an N-N single bond. Correlation of the NMR signals of the aromatic and -NH protons with substituents in these molecules indicated that the N-N single bond stopped the ground-state electronic communication between the signal reporter and the anion-binding site. Dual fluorescence was observed in highly polar solvents such as acetonitrile with the former five derivatives. The fact that the CT emission wavelength and the CT to LE emission intensity ratio of the sensors were independent of the substituent existing in the anion-binding moiety suggested that the substituent electronic effect could not be communicated to the CT fluorophore in the excited-state either. Yet in acetonitrile both the CT dual fluorescence and the absorption of the sensors were found to be highly sensitive toward anions. A conformation change around the N-N bond in the sensor molecules was suggested to occur upon anion binding that established the electronic communication between the signal reporter and the anion-binding site. The anion binding constants of the N-(p-dimethylaminobenzamido)thiourea sensors were found higher than those of the corresponding traditional N-phenylthiourea counterparts and the substituent effect on the anion binding constant was much higher than that in the latter. "-NH-" was shown to be a unique spacer that affords N-benzamidothiourea allosteric anion sensors.

Amination↗
PubMed2006

Characterization of copper binding to the peptide amyloid-beta(1-16) associated with Alzheimer's disease.

Amyloid-beta peptide (Abeta) is the principal constituent of plaques associated with Alzheimer's disease (AD) and is thought to be responsible for the neurotoxicity associated with the disease. Copper binding to Abeta has been hypothesized to play an important role in the neruotoxicity of Abeta and free radical damage, and Cu2+ chelators represent a possible therapy for AD. However, many properties of copper binding to Abeta have not been elucidated clearly, and the location of copper binding sites on Abeta is also in controversy. Here we have used a range of spectroscopic techniques to characterize the coordination of Cu2+ to Abeta(1-16) in solution. Electrospray ionization mass spectrometry shows that copper binds to Abeta(1-16) at pH 6.0 and 7.0. The mode of copper binding is highly pH dependent. Circular dichroism results indicate that copper chelation causes a structural transition of Abeta(1-16). UV-visible absorption spectra suggest that three nitrogen donor ligands and one oxygen donor ligand (3N1O) in Abeta(1-16) may form a type II square-planar coordination geometry with Cu2+. By means of fluorescence spectroscopy, competition studies with glycine and L-histidine show that copper binds to Abeta(1-16) with an affinity of Ka approximately 10(7) M(-1) at pH 7.8. Besides His6, His13, and His14, Tyr10 is also involved in the coordination of Abeta(1-16) with Cu2+, which is supported by 1H NMR and UV-visible absorption spectra. Evidence for the link between Cu2+ and AD is growing, and this work has made a significant contribution to understanding the mode of copper binding to Abeta(1-16) in solution.

Alzheimer Disease↗
PubMed2006

Identification of radiation-induced cross-linking between thymine and tryptophan by electrospray ionization-mass spectrometry.

Upon exposure to ionizing radiation, DNA undergoes a variety of modifications including the production of a covalent bond between the nucleobase thymine and aromatic amino acids. In this work, electrospray ionization-mass spectrometry(ESI-MS) was used to identify the gamma radiation-induced covalent cross-linking of model peptides (sequence YPPW and pYPPW) with the nucleobase thymine. Tandem electrospray ionization-mass spectrometry (ESI-MSn) was employed to investigate the cross-linking sites. The results showed that irrespective of whether tyrosine was phosphorylated or not, the nucleobase thymine was cross-linked with the tryptophan residue. Possible cross-linking mechanisms are proposed by investigating the related mass peaks.

Cross-Linking Reagents↗
PubMed2006

Novel acetylation-aided migrating rearrangement of uridine-diphosphate-N-acetylglucosamine in electrospray ionization multistage tandem mass spectrometry.

Uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) is the final product of hexosamine biosynthetic pathway (HSP) and the donor substrate for the modification of nucleocytoplasmic proteins at serine and threonine residues with N-acetylglucosamine (GlcNAc) catalyzed by O-GlcNAc transferase (OGT). Many analogs of UDP-GlcNAc were designed to interfere with the process of protein O-glycosylation by blocking OGT. A novel rearrangement reaction was observed in which phosphate-N-acetylglucosamine moiety migrated to 3' terminus of ribose in ESI-MS(n) of UDP-GlcNAc. Results from tandem mass spectrometry, control experiments and calculation showed that the phosphate-N-acetylglucosamine migration might undergo a pentacoordinate phosphoric intermediate. Furthermore, the acetylation of glucosamine in UDP-GlcNAc was essential in the migration process.

Acetylation↗
PubMed2006

Alternative O-GlcNAcylation/O-phosphorylation of Ser16 induce different conformational disturbances to the N terminus of murine estrogen receptor beta.

Serine and threonine residues in many proteins can be modified by either phosphorylation or GlcNAcylation. To investigate the mechanism of O-GlcNAc and O-phosphate's reciprocal roles in modulating the degradation and activity of murine estrogen receptor beta (mER-beta), the conformational changes induced by O-GlcNAcylation and O-phosphorylation of Ser(16) in 17-mer model peptides corresponding to the N-terminal intrinsically disordered (ID) region of mER-beta were studied by NMR techniques, circular dichroism (CD), and molecular dynamics simulations. Our results suggest that O-phosphorylation discourages the turn formation in the S(15)STG(18) fragment. In contrast, O-GlcNAcylation promotes turn formation in this region. Thus, we postulate that the different changes of the local structure in the N-terminal S(15)STG(18) fragment of mER-beta caused by O-phosphate or O-GlcNAc modification might lead to the disturbances to the dynamic ensembles of the ID region of mER-beta, which is related to its modulatory activity.

Acetylglucosamine↗
PubMed2006

Hydroxylation of 3-nitrotyrosine and its derivatives by gamma irradiation.

Radiation-induced hydroxylation of 3-nitrotyrosine (3-NY) and its derivatives in aqueous solution were investigated as a function of gamma-radiation dose. Irradiated 3-NY, 3-nitrotyrosine ethyl ester (3-NYE) and 3-NY containing peptide Gly-nitroTyr-Gly were separated and analyzed with reverse-phase HPLC and UV-Vis absorption spectroscopy. The structures of the hydroxylated products were confirmed by electrospray ionization mass spectrometry and (1)H-NMR spectrometry. The amounts of the hydroxylated products in irradiated 3-NY and Gly-nitroTyr-Gly solutions increased with increasing radiation dose. Tandem electrospray ionization mass spectrometry (ESI-Mass(2)) was performed to investigate the hydroxylation of peptide Gly-nitroTyr-Gly. These studies showed that the hydroxylation occurred at 3-NY residue. We also found that the identification of 3-NY hydroxylation in peptide could be identified by ion scanning for the specific immonium ion at m/z 197.0.

Dose-Response Relationship, Radiation↗
PubMed2005

Low-barrier hydrogen bond between phosphate and the amide group in phosphopeptide.

As the conversion between the monoionic (1) and diionic (2) form of the phosphate occurs, the phosphorylated peptides or proteins can not only cause the formation of a hydrogen bond between the phosphate group and the amide group but also change the strength of the hydrogen bond to form low-barrier hydrogen bonds (LBHBs). This reversible protonation of the phosphate group, which changes both the electrostatic properties of the phosphate group and the strength of the hydrogen bond, provides a possible mechanism in regulating protein function.

Amides↗
PubMed2005

Binding of copper (II) ion to an Alzheimer's tau peptide as revealed by MALDI-TOF MS, CD, and NMR.

The tau protein plays an important role in some neurodegenerative diseases including Alzheimer's disease (AD). Neurofibrillary tangles (NFTs), a biological marker for AD, are aggregates of bundles of paired helical filaments (PHFs). In general, the alpha-sheet structure favors aberrant protein aggregates. However, some reports have shown that the alpha-helix structure is capable of triggering the formation of aberrant tau protein aggregates and PHFs have a high alpha-helix content. In addition, the third repeat fragment in the four-repeat microtubule-binding domain of the tau protein (residues 306-336: VQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQ, according to the longest tau protein) adopts a helical structure in trifluoroethanol (TFE) and may be a self-assembly model in the tau protein. In the human brain, there is a very small quantity of copper, which performs an important function. In our study, by means of matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy, the binding properties of copper (II) ion to the R3 peptide derived from the third repeat fragment (residues 318-335: VTSKCGSLGNIHHKPGGG) have been investigated. The results show that copper ions bind to the R3 peptide. CD spectra, ultraviolet (UV)-visible absorption spectra, and MALDI-TOF MS show pH dependence and stoichiometry of Cu2+ binding. Furthermore, CD spectra and NMR spectroscopy elucidate the copper binding sites located in the R3 peptide. Finally, CD spectra reveal that the R3 peptide adopts a mixture structure of random structures, alpha-helices, and beta-turns in aqueous solutions at physiological pH. At pH 7.5, the addition of 0.25 mol eq of Cu2+ induces the conformational change from the mixture mentioned above to a monomeric helical structure, and a beta-sheet structure forms in the presence of 1 mol eq of Cu2+. As alpha-helix and beta-sheet structures are responsible for the formation of PHFs, it is hypothesized that Cu2+ is an inducer of self-assembly of the R3 peptide and makes the R3 peptide form a structure like PHF. Hence, it is postulated that Cu2+ plays an important role in the aggregation of the R3 peptide and tau protein and that copper (II) binding may be another possible involvement in AD.

Alzheimer Disease↗
PubMed2005

Studies on the structure behavior of triphenyldichlorophosphorane in different solvents.

Triphenyldichlorophosporane, which was prepared according to Appel reaction, was an efficient reagent for alkyl halide synthesis by virtue of having two replaceable groups on "pentavalent" phosphorus. The reaction of triphenylphosphine with hexachloroethane was investigated in different solvents and 31P NMR traced the processes of these reactions. As results, it was found that there was similar high coordinated phosphorus species formed in aromatic solvents and in ring ether type solvents, which had large 1J(P-C) (about 140 Hz) according to 13C NMR experiments. It is indicated that, for some solvent such as benzene or dioxane, solvent molecules might be locked in the high coordinated phosphorus compounds, which in turn would affect the triphenyl groups situated at the equatorial position.

Ethane↗
PubMed2005

Synthesis and conformational properties of phosphopeptides related to the human tau protein.

In the brains of Alzheimer's disease patients, the tau protein dissociates from the axonal microtubule and abnormally aggregates to form a paired helical filament (PHF). One of the priorities in Alzheimer research is to determine the effects of abnormal phosphorylation on the local structure. A series of peptides corresponding to isolated regions of tau protein have been successfully synthesized using Fmoc-based chemistry and their conformations were determined by 1H NMR spectroscopy and circular dichroism (CD) spectroscopy. Immunodominant peptides corresponding to tau-(256-273), tau-(350-367) and two phosphorylated derivatives in which a single Ser was phosphorylated at positions 262 and 356, respectively, were the main focus of the study. A direct alteration of the local structure after phosphorylation constitutes a new strategy through which control of biological activity can be enforced. In our study on Ser262 in R1 peptide and Ser356 in R4 peptide, phosphorylation modifies both the negative charge and the local conformation nearby the phosphorylation sites. Together, these structural changes indicate that phosphorylation may act as a conformational switch in the binding domain of tau protein to alter specificity and affinity of binding to microtubule, particularly in response to the abnormal phosphorylation events associated with Alzheimer's disease.

Alzheimer Disease↗
PubMed2005

Condensation properties of vesicles formed from an amphiphilic N-phosphorylamino acid.

Stable unilamellar vesicles were formed in water under appropriate pH from dispersions of N-(O,O-di-n-hexadecyl)phosphorylalanine, an amphiphilic N-phosphorylamino acid. We found that condensation occurred in the vesicle solution after incubated at 40 degrees C, which may contribute to the stability of the vesicular system. Dipeptide derivative in the vesicle solution was identified by electrospray ionization mass spectrometry (ESI-MS), which suggests the peptide formation without any coupling reagents. Hydrogen bond and electrostatic interactions play important roles in the process of vesicle formation, while the suitable orientation and packing of the amphiphilic molecules at the vesicle/water interface together with certain conformational freedom in the vesicular bilayer are considered to be most favorable for the condensation in ordered systems as vesicles.

Alanine↗
PubMed2005

Modeling kinase-substrate specificity: implication of the distance between substrate nucleophilic oxygen and attacked phosphorus of ATP analog on binding affinity.

Molecular dynamics simulations were performed on modeled kinase-substrate complexes in an attempt to establish a relationship between structural features and binding ability of the complexes. We found that the monitored distance between substrate nucleophilic oxygen (OG) and attacked phosphorus (PG) of ATP analog correlated closely with the binding affinity. With reference to 3.3 A, the van der Waals sum of oxygen and phosphorus, the calculated distances of good substrates were close to it whereas those of poor substrates were far apart from it. Therefore, it is reasonable to consider the OG-PG distance as a potential criterion to prefigure the kinase-substrate binding specificity and the simple computational techniques may work as an easy approach to distinguish good substrates from weak or poor substrates.

Adenosine Triphosphate↗
PubMed2005

Characterization of electrospray ionization mass spectrometry for N-diisopropyloxyphosphoryl dipeptide methyl esters.

A systematic study of the fragmentation pattern of N-diisopropyloxyphosphoryl (DIPP) dipeptide methyl esters in an electrospray ionization (ESI) tandem mass spectrometry (MS/MS) was presented. A combination of accurate mass measurement and tandem mass spectrometry had been used to characterize the major fragment ions observed in the ESI mass spectrum. It was found that the alkali metal ions acted as a fixed charge site and expelled the DIPP group after transferring a proton to the amide nitrogen. For all the N-phosphoryl dipeptide methyl esters, under the activation of a metal ion, the rearrangement product ion at m/z 163 was observed and confirmed to be the sodium adduct of phosphoric acid mono-isopropyl esters (PAIE), via a specific five-membered penta-co-ordinated phosphorus intermediate. However, no rearrangement ion was observed when a beta-amino acid was at the N-terminal. This could be used to develop a novel method for differentiating isomeric compounds when either alpha- or beta-amino acid are at the N-terminus of peptides. From the [M+Na]+ ESI-MS/MS spectra of N-phosphoryl dipeptide methyl esters (DIPP Xaa1 Xaa2 OMe), the peaks corresponding to the [M+Na Xaa1 C3H6]+ were observed and explained. The [M+Na]+ ESI-MS/MS spectra of N-phosphoryl dipeptide methyl esters with Phe located in the C-terminal, such as DIPPValPheOMe, DIPPLeuPheOMe, DIPPIlePheOMe, DIPPAlaPheOMe and DIPPPhePheOMe, had characteristic fragmentation. Two unusual gas-phase intramolecular rearrangement mechanisms were first proposed for this fragmentation. These rearrangements were not observed in dipeptide methyl ester analogs which did not contain the DIPP at the N-terminal, suggesting that this moiety was critical for the rearrangement.

Cations↗