Influence of glycosidic linkage on solution conformational entropy of oligosaccharides: Malto- vs. isomalto- and cello- vs. laminarioligosaccharides

Carbohydrate flexibility can influence a variety of recognition, processing, and end-use properties, at both the polymeric and oligomeric levels. The influence of glycosidic linkage, in particular, on carbohydrate flexibility is manifested in properties such as bacterial selectivity, solution viscosity, and the ability to regulate the spread of disease. Here, we apply size-exclusion chromatography, an entropically controlled technique, to determine the solution conformational entropy (ΔS) of various oligosaccharide series. The aim of the present study is to highlight how, for a given anomeric configuration, glycosidic linkage affects ΔS, and to do so quantitatively as a function of degree of polymerization (DP). To this end, we compare ΔS values for DP 1-7 for malto- and isomaltooligosaccharides, and for DP 1-5 for cello- and laminarioligosaccharides. To do so, we realize previously unattainable separations of disaccharides via a strict size-exclusion mechanism. Also given here are the requirements for extending our method to other oligomers, as well as to biopolymers     

Synthesis of two isomeric pentasaccharides,the possible repeating unit of the beta-glucan from the micro fungus Epicoccum nigrum Ehrenb. ex Schlecht

Two isomeric pentasaccharides, beta-D-Glcp-(1-->3)-[beta-D-Glcp-(1-->6)]-beta-D-Glcp-(1-->3)-[beta-D-Glcp-(1-->6)]-beta-D-Glcp (I) and beta-D-Glcp-(1-->6)-beta-D-Glcp-(1-->3)-[beta-D-Glcp-(1-->3)-beta-D-Glcp-(1-->6)]-beta-D-Glcp (II), the possible repeating unit of the beta-glucan from the micro fungus Epicoccum nigrum Ehrenb. ex Schlecht, were synthesized as their 4-methoxyphenyl glycosides in a regio- and stereoselective manner. The pentasaccharide I was obtained from 3-O-selective glycosylation of 4-methoxyphenyl 4,6-O-benzylidene-beta-D-glucopyranoside (12) with 2,3,4,6-tetra-O-benzoyl-beta-D-glucopyranosyl-(1-->3)-[2,3,4,6-tetra-O-benzoyl-beta-D-glucopyranosyl-(1-->6)]-2,4-di-O-acetyl-alpha-D-glucopyranosyl trichloroacetimidate (6) followed by acetylation, debenzylidenation, and 6-O-selective glucosylation with 2,3,4,6-tetra-O-benzoyl-beta-D-glucopyranosyl trichloroacetimidate (1), and then by deprotection. The pentasaccharide II was obtained from 3-O-selective coupling of 12 with 2,3,4,6-tetra-O-benzoyl-beta-D-glucopyranosyl-(1-->6)-2,4-di-O-acetyl-3-O-allyl-alpha-D-glucopyranosyl trichloroacetimidate (10) followed by acetylation, debenzylidenation, and 6-O-selective glycosylation with 2,3,4,6-tetra-O-benzoyl-beta-D-glucopyranosyl-(1-->3)-2,4,6-tri-O-acetyl-alpha-D-glucopyranosyl trichloroacetimidate (11), and finally by deprotection.     

N-linked glycan structures of mouse interferon-beta produced by Bombyx mori larvae

The full-length mouse interferon-beta (mIFN-beta) cDNA, including the secretion signal peptide coding region under control of the polyhedrin promoter, was introduced into Bombyx mori nucleopolyhedrovirus (BmNPV). Recombinant mIFN-beta (rmIFN-beta) was accumulated in the haemolymph of infected silkworm larvae. Western blot analysis showed isoforms of rmIFN-beta, suggesting that rmIFN-beta is glycosylated. The glycan structures of purified rmIFN-beta were determined. The N-glycans were liberated by hydrazinolysis and the resulting oligosaccharides were labeled with 2-aminopyridine. The pyridylaminated (PA) glycans were purified by gel filtration, reversed-phase HPLC, and size-fractionation HPLC. The structures of the PA-sugar chains were identified by a combination of two-dimensional PA-sugar chain mapping, MS analysis, and exoglycosidase digestions.     

Assessing glycosidic linkage flexibility: Conformational analysis of the repeating trisaccharide unit of Aeromonas salmonicida

Summary A detailed conformational analysis was performed for the synthetic branched trisaccharide -d-Man-NAc-(14)-[-d-Glc-(13)]-l-Rha 1 which represents the repeating unit of the O-antigenic polysaccharide of Aeromonas salmonicida. The study was based on 26 experimental NOE curves from 1D transient NOE experiments, employing Gaussian-shaped inversion pulses at 600 MHz. Eight of the NOE curves were interglycosidic and thus useful for an analysis of glycosidic linkage orientations. Metropolis Monte Carlo (MMC) simulations and minimum-energy calculations with the program GEGOP were used to obtain theoretical NOE curves which were compared to the experimental ones. MMC simulations with different temperature parameters of 310, 600, 900 and 2000 K allowed identification of NOEs which are sensitive towards different conformation distributions-not only different conformations-at both glycosidic linkages in 1. A comparison of trisaccharide 1 with the constituent disaccharides -d-ManNAc-(14)-l-Rha 2 and -d-Glc-(13)-l-Rha 3 revealed effects of branching on glycosidic linkage flexibility. A quantitative evaluation was facilitated by the introduction of entropy-related flexibility parameters. Our study indicates a notable restriction of flexibility, especially at the (13) linkage in 1. Although overall flexibility in 1 is reduced as compared to the constituent disaccharides 2 and 3, it cannot be neglected altogether. In summary, combined transient NOE experiments and MMC simulations provide a simple approach to analyse glycosidic linkage flexibility.     

甲基苯丙氨酸的合成与拆分

用取代的氯苄衍生物以及乙酰氨基丙二酸二乙酯为原料,合成了邻位、对位、间位甲基取代苯基丙氨酸。以上3种混旋氨基酸在37℃、pH值7.0、底物浓度0.1mol·L-1条件下用氨基酰化酶拆分得到6个光学异构体。本实验中采用的合成工艺适合工业化。     

Effect of Molecule Branching and Glycosidic Linkage on the Degradation of Polydextrose by Gut Microbiota

Polydextrose is a randomly linked complex glucose oligomer that is widely used as a sugar replacer, bulking agent, dietary fiber and prebiotic. Polydextrose is poorly utilized by the host and, during gastrointestinal transit, it is slowly degraded by intestinal microbes, although it is not known which parts of the complex molecule are preferred by the microbes. The microbial degradation of polydextrose was assessed by using a simulated model of colonic fermentation. The degradation products and their glycosidic linkages were measured by combined gas chromatography and mass spectrometry, and compared to those of intact polydextrose. Fermentation resulted in an increase in the relative abundance of non-branched molecules with a concomitant decrease in single-branched glucose molecules and a reduced total number of branching points. A detailed analysis showed a preponderance of 1,6 pyranose linkages. The results of this study demonstrate how intestinal microbes selectively degrade polydextrose, and provide an insight into the preferences of gut microbiota in the presence of different glycosidic linkages.     

2-氰基-D,L-苯丙氨酸盐酸盐的合成

合成了非天然氨基酸２－氰基－Ｄ,Ｌ－苯丙氨酸盐以及四个中间体,其结构分别通过红外光谱、核磁共振、元素分析、熔点测试等手段得到确证。     

The alpha-(1-->6) glycosidic linkage as a novel conformational entropic regulator in osmoregulated periplasmic alpha-cyclosophorohexadecaose

Molecular dynamics simulations were performed to explain the conformational effect of an alpha-(1-->6)-glycosidic linkage upon the cyclic osmoregulated periplasmic glucan (OPG) produced by Xanthomonas campestris pv. citri. We suggest that a single alpha-(1-->6)-glycosidic linkage in cyclic OPG functions as a novel entropic regulator, which reduces the conformational entropy of cyclic OPG and increases the motional entropy of solvent water molecules.     

佛波酯能改变细胞表面糖蛋白N－糖链的结构

利用标记Ｎ－糖链的凝集素亲和层析法研究了佛波醇肉桂酸乙酸酯（ＰＭＡ）对人肝癌细胞ＳＭＭＣ－７７２１表面糖蛋白上Ｎ－糖链结构的影响,发现１００ｎｍｏｌ／Ｌ的ＰＭＡ处理５天后,可使细胞表面Ｎ－糖链中高甘露糖型和杂合型以及四天线、Ｃ２Ｃ２,６三天线复杂型的比例增高,而二天线复杂型降低。此结果与我们曾报道的视黄酸（ＲＡ）和双丁配环磷酸腺苷（ｄｂ－ｃＡＭＰ）对该细胞表面Ｎ－糖链的影响相反。因ＲＡ和ｄｂ－ｃＡＭＰ是ＳＭＭＣ－７７２１细胞的分化诱导剂,可抑制细胞生长;而ＰＭＡ是该细胞的增殖促进剂,故细胞表面Ｎ－糖链的变化与细胞的分化和增殖密切相关。     

Synthesis of the glycosidic precursor of isomeric marmelo lactones,volatile components of the quince fruit,Cydonia oblonga

The glucosidic precursor of marmelo lactones was synthesized by employing a common intermediate which had been used for the synthesis of the glucosidic precursor of marmelo oxides. The synthesis was performed by modifying the former procedure. Monochloroacetyl was adopted to protect both the glucose and aglycon hydroxyl groups for selective transesterification in the presence of the glycosyl ester. Glycosylation of the aglycon carboxyl group with 1-alpha-bromopermonochloroacetylglucose and final selective alcoholysis yielded the target glucoside.     

Synthesis of tetra- and pentasaccharides corresponding to the capsular polysaccharide of Streptococcus pneumoniae type 9A&L, 9N and 9A

Two tetrasaccharides, alpha-D-GlcAp-(1-->3)-alpha-D-Galp-(1-->3)-beta-D-ManpNAc-(1-->4)-beta-D-Glcp and alpha-D-GlcAp-(1-->3)-alpha-D-Glcp-(1-->3)-beta-D-ManpNAc-(1-->4)-beta-D-Glcp (protected form), and a pentasaccharide, alpha-D-Glcp-(1-->4)-alpha-D-GlcAp-(1-->3)-alpha-D-Galp-(1-->3)-beta-D-ManpNAc-(1-->4)-beta-D-Glcp have been synthesised from 2-aminoethyl glycoside trisaccharide acceptors in a linear approach via consecutive alpha-glycosylations. Ethyl thioglycosides were used as glycosyl donors and DMTST in Et(2)O or NIS/TfOH in CH(2)Cl(2) were employed as promoters.     

Synthesis,biological activities and docking studies of pleuromutilin derivatives with piperazinyl urea linkage

Antibiotics resistance is becoming increasingly common, involving almost all antibiotics on the market. Diseases caused by drug resistant bacteria, such as MRSA, have high mortality and negatively affect public health. The development of new drugs would be an effective means of solving this problem. Modifications based on bioactive natural products could greatly shorten drug development time and improve success rate. Pleuromutilin, a natural product from the basidiomycete bacterial species, is a promising antibiotic candidate. In this study, a series of novel pleuromutilin derivatives possessing piperazinyl urea linkage were efficiently synthesised, and their antibacterial activities and bactericidal properties were evaluated via MIC, MBC and Time-kill kinetics assays. The results showed that all compounds exhibited potent activities against tested strains, especially MRSA strains with MIC values as low as 0.125 μg/mL; 8 times lower than that of marketed antibiotic Tiamulin. Docking studies indicate substituted piperazinyl urea derivatives could provide hydrogen bonds and initiate π-π stacking between molecules and surrounding residues.     

Side Chain Dynamics and Alternative Hydrogen Bonding in the Mechanism of Protein Thermostabilization

Abstract

To elucidate the mechanism of protein thermostabilization, the thermodynamic properties of small monomeric proteins from mesophilic and thermophilic organisms have been analyzed. Molecular dynamics simulations were employed in the study of dynamic features of charged and polar side chains of amino acid residues. The basic conclusion has been made: surface charged and polar side chains with high conformational mobility can form alternative hydrogen bonded (H-bonded) donor-acceptor pairs. The correlation between the quantitative content of alternative H-bonds per residue and the temperature of maximal thermostability of proteins has been found. The proposed mechanism of protein thermostabilization suggests continuous disruption of the primary H- bonds and formation of alternative ones, which maintain constant the enthalpy value in the native state and prevent a rapid increase of the conformational entropy with the rising temperature. The analysis of the results show that the more residues located in the N- and C-terminal regions and in the extended loops that are capable of forming alternative longer-range H-bonded pairs, the higher the protein thermostability.     

Synthesis and chemical behaviour of D-glucosyl esters of glutamic acid having the side-chain carboxyl group involved in the glycosidic linkage.

Simultaneous and stepwise deprotection of the fully benzylated D-glucosyl esters of 1-benzyl N-benzyloxycarbonyl- and N-tert-butyloxycarbonyl-L-glutamic acid (1 and 5, respectively) have been examined. Catalytic hydrogenation of 1 led to intramolecular aminolysis to give pyroglutamic acid and D-glucose, but similar treatment in the presence of trifluoroacetic acid afforded both anomers of 1-O-(L-gamma-glutamyl)-D-glucopyranose, which were characterized as trifluoroacetates (2alpha and 2beta) and converted into 2,3,4,6-tetra-O-acetyl-1-O-[1-methyl N-(acetyl)-L-glutam-5-oyl]-D-glucopyranose (4) which was also prepared by a definitive method. Hydrogenolysis of 5 gave both anomers of 1-O-[N-(tert-butyloxycarbonyl)-L-gamma-glutamyl]-D-glucopyranose (6), which, upon treatment with trifluoroacetic acid at - 10 degrees, afforded 2alpha and 2beta, respectively. The structure of 6beta was established by its conversion into 2,3,4,6-tetra-O-acetyl-1-O-[1-methyl N-(tert-butyloxycarbonyl)-L-glutam-5-oyl]-beta-D-glucopyranose (7beta), whereas similar treatment of 6alpha gave a mixture of 1,3,4,6-tetra-O-acetyl-2-O-[1-methyl N-(tert-butyloxycarbonyl)-L-glutam-5-oyl]-alpha-D-glucopyranose (9) and 7alpha. A 1 leads to 2 acyl migration occurred during esterification of the aglycon carboxyl group of 6alpha with diazomethane to give 2-O-[1-methyl N-(tert-butyloxycarbonyl)-L-glutam-5-oyl]-alpha-D-glucopyranose (8).     

A comprehensive linkage map of the pig based on a wild pig - Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 type I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1–4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.     

Likelihood ratio testing for admixture models with application to genetic linkage analysis

Summary We consider likelihood ratio tests (LRT) and their modifications for homogeneity in admixture models. The admixture model is a two‐component mixture model, where one component is indexed by an unknown parameter while the parameter value for the other component is known. This model is widely used in genetic linkage analysis under heterogeneity in which the kernel distribution is binomial. For such models, it is long recognized that testing for homogeneity is nonstandard, and the LRT statistic does not converge to a conventional χ² distribution. In this article, we investigate the asymptotic behavior of the LRT for general admixture models and show that its limiting distribution is equivalent to the supremum of a squared Gaussian process. We also discuss the connection and comparison between LRT and alternative approaches such as modifications of LRT and score tests, including the modified LRT ( Fu, Chen, and Kalbfleisch, 2006 , Statistica Sinica 16 , 805–823). The LRT is an omnibus test that is powerful to detect general alternative hypotheses. In contrast, alternative approaches may be slightly more powerful to detect certain type of alternatives, but much less powerful for others. Our results are illustrated by simulation studies and an application to a genetic linkage study of schizophrenia.     

Synthesis of neoglycoenzymes with homogeneous N-linked oligosaccharides using immobilized endo-beta-N-acetylglucosaminidase A

A procedure for the enzymatic synthesis of neoglycoenzymes is described. The gene encoding endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) was overexpressed in Escherichia coli as a fusion protein linked to glutathione S-transferase (GST). GST-Endo-A fusion was extracted as a soluble protein. The fusion protein was purified to homogeneity with glutathione-Sepharose 4B and showed transglycosylation activity toward high-mannose-type glycopeptides without removing the GST moiety. The GST-Endo-A immobilized on glutathione-Sepharose 4B retained its transglycosylation activity. The immobilized enzyme could transfer (Man)(6)GlcNAc en bloc to partially deglycosylated ribonuclease B without damaging its enzyme activity. The immobilized GST-Endo-A should be very useful for synthesizing active neoglycoenzymes attached with homogeneous N-linked oligosaccharides.     

Enhanced intracellular peptide delivery by multivalent cell-penetrating peptide with bioreducible linkage

Multivalent cell-penetrating peptides (CPPs) have been reported to show enhancement in cellular uptake and endosomolytic activity. However, its application was limited to trans-delivery of cargo which is lower in cellular uptake efficiency of cargo than cis-delivery. Here, we tried the cis-delivery of cargo with multivalent CPP by preparing bioreducible dimeric CPP–cargo with apoptotic activity using TatBim peptide, a fusion of Tat CPP and Bim peptide derived from Bim apoptosis-inducing protein. Dimeric TatBim was almost twice as highly internalized by cells and significantly induced apoptosis compared to monomeric TatBim. Contribution of bioreducible linkage of dimeric TatBim towards apoptotic activity was also confirmed.