Biomedical subjects
Publications and source records attributed to Yu-Fen Zhao.
Phosphorus oxychloride was found to induce ring opening of tetrahydrofuran (THF) to synthesise THF oligomer incorporated phosphate. ESI multi-stage tandem mass spectrometry was used to study the products and confirm the structures.
This review briefly covers recent literature of research on the phosphoryl transfer mechanism of PKA. Combining experimental and theoretical calculation results on enzymes with experimentally observed biomimic activities of phosphoryl amino acids and a small molecular model of catalytic core in PKA, a novel mechanism was proposed. The cooperative participation roles of both Asp166 and Lys168 via a penta-coodinate phosphoric intermediate was elucidated to conciliate the current different views of the phosphoryl transfer mechanism of PKA. Since many ATP-binding enzymes may share a similar phosphoryl transfer mechanism, this proposed mechanism might also apply to the mechanism of these enzymes, e.g., molecular motor and phosphatase among others.
BACKGROUND & OBJECTIVE: Phosphorylation of protein and peptide plays an important role in life activity. Some phosphoryl peptides are found to have activities to inhibit proliferation of tumor cells, but the involved mechanisms are unclear. This study was designed to investigate cell apoptosis induced by (O,O-diisopropyl phosphoryl-L-tryptophan)(2)-L-lysine methyl ester [(DIPP-L-Trp)(2)-L-Lys-OCH(3)], and its mechanism in K562 cells. METHODS: K562 cells were double stained by AnnexinV-FITC and propidium iodide (PI) to detect (DIPP-L-Trp)(2)-L-Lys-OCH(3)-induced apoptosis by flow cytometry (FCM). After treatment of different concentrations of (DIPP-L-Trp)(2)-L-Lys-OCH(3), K562 cells were stained by rhodamine123 and PI to detect changes in membrane potential (Delta Psi m), or stained by 2',7'-dichlorofluorescein diacetate (DCFH-DA) to detect reactive oxygen species (ROS) of mitochondrial by FCM. RESULTS: When treated with 50 microg/ml of (DIPP-L-Trp)(2)-L-Lys-OCH(3) for 24 h, apoptosis rate of K562 cells was 61.9%, Delta Psi m was decreased in 93.6% of K562 cells,and ROS production was decreased. Both Delta Psi m and ROS production in K562 cells mitochondria were decreased with the increasing concentration and extending treatment time of (DIPP-L-Trp)(2)-L-Lys-OCH(3). CONCLUSION: (DIPP-L-Trp) (2)-L-Lys-OCH(2) could induce apoptosis in K562 cells, which might relate with down-regulation of mitochondrial Delta Psi m and reduction of ROS production.
A series of neutral N-(substituted-benzamido)-N'-phenylthioureas (substituent = p-OC(2)H(5), p-CH(3), m-CH(3), H, p-Cl, p-Br, m-Cl, and p-NO(2)) were designed as anion receptors, in which the thiourea binding site was attached to the benzamido moiety via an N-N bond. The absorption spectra of these N-benzamidothioureas in acetonitrile peaked at ca. 270 nm were found to show unprecedented red shifts by 7 373 to 14 325 cm(-1) in the presence of anions such as AcO(-), F(-), and H(2)PO(4)(-). Under the same conditions, the classic neutral thiourea receptors, N-(substituted-phenyl)-N'-phenylthioureas, showed absorption spectral shifts in most cases of less than 800 cm(-1) with one exception of 6501 cm(-1). Control experiments, effects of protic solvent, and (1)H NMR titration confirmed the formation of hydrogen-bonding complexes between the new N-benzamidothiourea receptors and anions. The binding constants with AcO(-), for example, are at 10(5)-10(7) mol(-1) L order of magnitude, which are 13 to 590 times those of the corresponding classic N-phenylthioureas in the same solvent. It was found that, whereas the absorption of the N-benzamidothiourea receptors showed essentially no dependence on the substituent, the substantially red-shifted new absorption band of the N-benzamidothiourea-anion binding complex was sensitively subject to the substituent. A linear relationship was found between the absorption energies of the N-benzamidothiourea-acetate binding complexes and the Hammett constants of the substituents with a negative slope of -0.34 eV. This led to the assignment that the substantially red-shifted absorption band was the ground-state intramolecular charge-transfer absorption with the substituent locating in the electron acceptor moiety. It was concluded that anion binding to the thiourea moiety of the N-benzamidothiourea receptors switched on their ground-state charge transfer. An anion-binding induced structural change was suggested to occur around the N-N bond in N-benzamidothioureas, which resulted in a substantially increased electron donating ability of the electron donor in the receptor molecules. As a consequence, the ground-state charge transfer takes place in the N-benzamidothiourea-anion binding complexes, leading to unprecedented red shifts in the absorption spectra and substantially enhanced anion binding affinities than those of the corresponding N-phenylthiourea receptors. N-Benzamido-N'-phenylthioureas represent a new generation of neutral thiourea-based anion receptors that show substantially improved anion binding performance important for anion sensing and recognition.
In the work described in this paper, chrysin was phosphorylated by a modified Atheron-Todd reaction. The structure of phosphorylated chrysin was determined by elemental analysis, NMR, ESI-MS/MS, and X-ray data. Electrospray ionization results showed that the phosphorylated flavonoids could form noncovalent complexes with many proteins, such as lysozyme, myoglobin, bovine insulin, and cytochrome c, while noncovalent complexes were not detected in the mixed solution of the chrysin and proteins. The research shows that the phosphorylated flavonoids possess relatively stronger affinities and form noncovalent complexes with the proteins more easily than the non-phosphorylated compounds.
With the introduction of a diisopropyloxyphosphoryl (DIPP) group at the N-terminus of amino acids, the signal response in electrospray ionization mass spectrometry can be enhanced by 10-100-fold in positive mode and even more in negative mode. An enhancement of proton affinity due to the N-terminal DIPP derivatization was considered to be responsible for the sensitivity improvement in positive mode, which was supported by kinetic method studies. Two possible mechanisms, i.e., an increase in gas-phase acidity due to the introduction of the electron-withdrawing DIPP group, and the effect of pH on the formation of anions of amino acids and their phosphorylated derivatives, were considered for the signal response enhancement in negative mode.
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to obtain spectra of peptide-DNA complexes formed by basic domain (BD15) of c-Fos protein and DNA AP-1 site (5'-TGAGTCA-3'). The noncovalent interaction between single stranded DNA and BD15 was observed and confirmed to be an ionic one between the negatively charged sugar-phosphate backbone of DNA and positively charged side chains of Arg- and lys-rich peptides as demonstrated by Vertes and coworkers and Woods and coworkers. But the specific noncovalent interaction between DNA AP-1 site and the dimer of BD15 was firstly detected in this paper. Various different sequence DNAs were studied and it was found that this interaction is a sequence-specific one, and AP-1 site was essential for this interaction. This specific interaction depends on the matrix. It was only observed in the ATT matrix and not in the other two matrixes (CHCA and DHBA).
N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.
Reaction of ADP with amino acid methyl esters mediated by trimethylsilyl chloride in pyridine produced adenosine 5'-phosphoramidates in good yields under mild conditions, it is interesting that nucleophilic attack of amino acid methyl esters only occurred on alpha-phosphorus of ADP.
AZT H-phosphonates conjugated with steroids were synthesized and determined by positive and negative ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated in detail. There are very different characteristic fragment ions in the positive and negative ion MS/MS spectra. The azide group of compounds 6a and 6b underwent either elimination of HN(3) or rearrangement to an amine in both positive and negative ion mass spectrometry.
Amino acid-nucleotide conjugates have important biological functions and therapeutic applications. For example, aminoacyl adenylates are key intermediates in aminoacyl tRNA synthetase reactions. They may also be involved in the prebiotic synthesis of polypeptides. Finally, various amino acid carbomethoxy aryl phosphoramidates of nucleotide prodrugs may be activated through a mechanism involving a pentacoordinated phosphorane intermediates. In order to understand better the chemistry of these compounds, a phenylalanyl adenylate pentacoodinated phosphorane has been synthesized in 72% yield and its decomposition in aqueous solution studied. Hydrolysis gave 2('),3(')-O-isopropylidene adenosine 5(')-monophosphate, 2('),3(')-O-isopropylidene adenosine, and phenylalanine. The results provide model chemistry for the enzymatic degradation mechanism of antiviral aryl amino acid phosphodiester amidates in cells, which leads to their activation.
Serine and alanine phosphoramidates conjugates of 3',5'-TpT 4, 5 were synthesized. The corresponding serine phosphoamidate possesses some unique properties due to the presence of the side chain hydroxyl group.
[structure: see text] A neutral receptor with a rigid hydrazine spacer, N-p-(dimethylamino)benzamido-N'-phenylthiourea, was prepared, and its dual fluorescence in acetonitrile was found to show response toward the presence of anions such as AcO(-), H(2)PO(4)(-), HSO(4)(-), Br(-), Cl(-), F(-), and ClO(4)(-) with high sensitivity and selectivity toward AcO(-).
A novel rearrangement reaction with a carbonyl oxygen migration was observed in the electrospray ionization tandem mass spectra of N-diisopropyloxyphosphoryl dipeptides and their analogues. A possible mechanism was proposed and supported by the MS/MS study, derivatization of different functional groups and deuterium labeling experiments. It was found that metal ions could catalyze the rearrangement through a five-membered ring intermediate. A strong affinity between the phosphoryl group and oxygen atom in the gas phase was proposed to result in this kind of rearrangement reaction, which might provide some basic information on the nature of phosphorylation in biochemistry. The replacement of N-terminal alpha-alanine by beta-alanine stopped the migration, which provides a simple method for differentiating the alpha- and beta-alanine residues at the N-terminus of peptides.
A one-step phosphoryl derivatization method has been used in a peptide sequencing procedure for electrospray ionization tandem mass spectrometry (ESI-MS/MS). The sodiated derivatized peptides exhibit very simple dissociation patterns, in which two kinds of fragment ions, [b(n) + OH + Na]+ and [a(n) + Na]+, are formed. Since the amino acid residues are lost sequentially from the C-terminus, peptide sequences can be identified easily. The fragmentation efficiency of peptides increased as a result of the phosphorylation, and also provided peaks of useful intensity at lower m/z. A peptide with lysine at the C-terminus was derivatized and analyzed by ESI-MS/MS. Similar mass spectra, from which the sequence could be read out, were obtained. This is a novel derivatization method yielding neutral derivatives that should be suitable for peptide sequencing by LC/ESI-MS/MS.
The negative-ions of N-phosphoryl amino acids were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The negative-ion ESI-MS/MS of N-phosphoryl amino acids showed characteristic fragmentation patterns different from those observed in the corresponding positive-ion ESI-MS/MS and negative-ion fast-atom bombardment mass spectra. For negative-ion ESI-MS/MS, a unique fragmentation from the N-terminal of N-phosphoryl amino acids or peptides containing a free beta-OH or CO(2)H group was observed to yield the characteristic fragment ion (RO)(2)P(O)O(-). The ease of the rearrangement depended on the position of the hydroxyl group in amino acids or peptides, and the N --> O rearrangement mechanism was proposed to involve the participation of the hydroxyl group. From previous solution-phase experiments and theoretical calculations, it was found that the beta-OH group was more active than gamma-OH, and the corresponding difference in negative-ion ESI-MS/MS was consistent with those previous findings.
With the assistance of phosphorus oxychloride, alpha-amino acids were assembled into homo-peptides, which were analyzed by electrospray ionization mass spectrometry (ESI-MS) and multistage electrospray ionization mass spectrometry (ESI-MS/MS). On quenching with water or various alcohols, the reaction mixtures yielded the corresponding peptides or peptide esters, respectively. This paper reports a simple method to synthesize the homo-oligo-peptide-ester conjugated library by phosphorus oxychloride activation.
Explore the source record for details and available documents.