Biomedical subjects

Yan-Mei Li

Publications and source records attributed to Yan-Mei Li.

At least 19 recordsLinked to original sources

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

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

Influence of serine O-glycosylation or O-phosphorylation close to the vJun nuclear localisation sequence on nuclear import.

Nuclear import triggered by the nuclear-localisation sequence (NLS) of the viral Jun (vJun) protein is mediated by phosphorylation of a serine close to the NLS. Since phosphorylation and glycosylation of serine residues are often in a reciprocal "yin-yang" relationship, we investigated whether glycosylation of this serine with O-linked N-acetylglucosamine (O-GlcNAc) would also regulate nuclear import via the vJun NLS. Peptides containing the vJun NLS with an adjacent O-phosphorylated, O-GlcNAc-functionalised or unmodified serine, and equipped with an N-terminal biotin or a 7-nitrobenz-2-oxa-1,3-diazolyl (NBD) fluorescent label, were synthesised on the solid phase by means of an Fmoc/Boc strategy and a Pd0-sensitive HYCRON linker. Fluorescence-polarisation measurements on the NBD-labelled peptides indicated that modification with phosphate or O-GlcNAc leads to a decrease in affinity to the import-mediating adapter protein, importin alpha, of about one order of magnitude compared to the unmodified NLS. Microinjection of biotinylated NLS peptide conjugated with fluorescently labelled avidin into NIH/3T3 and MDCK cells, revealed that avidin-unmodified-NLS peptide was rapidly imported into the nucleus. However, either phosphate or O-GlcNAc next to the NLS caused almost complete exclusion of the protein conjugate from nuclear import. These findings indicate that nuclear import by the vJun NLS might not be regulated by a "yin-yang" modification of an adjacent serine with phosphate or O-GlcNAc. Rather, negative regulation of binding between the polybasic NLS and importin by a negatively charged or a bulky, uncharged residue appears likely.

Active Transport, Cell Nucleus↗

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

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

Protective effects of 5,4'-dihydroxy-3',5'-dimethoxy-7-O-beta-D -glucopyranosyloxy-flavone on experimental hepatic injury.

AIM: To investigate the pharmacological effects of rice flavone (5,4'-dihydroxy-3',5'-dimethoxy-7-O-beta-D-glucopyranosyloxy-flavone, RF) separated from panicle-differentiating to flowing rice on rat experimental hepatic injury. METHODS: Models of rat acute hepatic injury induced by carbon tetrachloride (CCl(4)) administration, rat hepatic fibrosis induced by thioacetamide, injury of primary cultured rat hepatocytes induced by CCl(4), respectively, were established. After treated with RF, content of serum alanine transaminase (ALT), aspartate aminotransferase (AST) and albumin (Alb), hyaluronic acid (HA), the activity of glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and hydroxyproline (Hyp) were measured and liver tissue was observed pathologically by hematoxylin-eosin (HE) staining. Effects of RF on pathological changes, function index, enzyme of scavenging free radicals and blood rheology were evaluated. RESULTS: In model of rat acute hepatic injury induced by CCl(4), RF can significantly decrease the contents of serum ALT, AST, increase the content of Alb, improve the dropsy and fat denaturalization of hepatocytes. In model of rat hepatic fibrosis induced by thioacetamide, RF can inhibit the increase of HA, Hyp and whole blood viscosity, and improve the activities of GSH-Px and SOD, and inauricular microcirculation. CONCLUSION: RF has apparent protective effects on hepatic injury by increasing activity of GSH-Px and SOD, scavenging free radicals produced by CCl(4), reducing blood viscosity, and improving microcirculation and blood supply.

Acute Disease↗

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↗

PubMed2005

Analysis of the phosphoryl transfer mechanism of c-AMP dependent protein kinase (PKA) by penta-coodinate phosphoric transition state theory.

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.

Catalysis↗

PubMed2005

[Discussion and analysis on point "Siguan"].

Point "Siguan" is seen in the Miraculous Pivot: Jiuzhen Shieryuan for the first time. From then on the doctors of every dynasties cited point "Siguan" and explained its content. But the authors hold that their explanations do not conform with the meaning in the Huangdi's Internal Classic. Therefore, the authors put forward their explanations for point "Siguan" and indicate that correct understanding of point "Siguan" is very important for treatment of diseases of five-zang organs.

Acupuncture Points↗

PubMed2004

Carbohydrates from Cynanchum otophyllum.

Four new carbohydrates were isolated from the acidic hydrolysis part of the ethyl acetate extract of Cynanchum otophyllum Schneid (Asclepiadaceae). Their structures were determined as methyl 2,6-dideoxy-3-O-methyl-beta-D-arabino-hexopyranosyl-(1-->4)-6-deoxy-3-O-methyl-beta-D-ribo-hexopyranosyl-(1-->4)-6-deoxy-3-O-methyl-alpha-L-ribo-hexopyranoside (1), methyl 6-deoxy-1,3-di-O-methyl-beta-D-ribo-hexosyl-(1-->4)-2,6-dideoxy-3-O-methyl-alpha-D-arabino-hexopyranoside (2), methyl 2,6-dideoxy-3-O-methyl-beta-D-arabino-hexopyranosyl-(1-->4)-6-deoxy-3-O-methyl-alpha-L-ribo-hexopyranoside (3), and 2,6-dideoxy-3-O-methyl-beta-D-arabino-hexopyranosyl-(1-->4)-2,6-dideoxy-3-O-methyl-alpha-D-arabino-hexopyranosyl-(1-->4)-2,6-dideoxy-3-O-methyl-beta-D-lyxo-hexopyranose (4), respectively, by spectral methods.

Carbohydrate Conformation↗

PubMed2004

Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF.

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).

DNA, Single-Stranded↗

PubMed2003

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids.

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.

Aspartic Acid↗