glycosidic bond stability: Topics by Science.gov

Sample records for glycosidic bond stability

Structual Effects of Cytidine 2^' Ribose Modifications as Determined by Irmpd Action Spectroscopy

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; He, Chenchen; Fan, Lin; Wu, Ranran; Yang, Bo; Rodgers, M. T.; Berden, Giel; Oomens, J.

2015-06-01

Modified nucleosides, both naturally occurring and synthetic play an important role in understanding and manipulating RNA and DNA. Naturally occurring modified nucleosides are commonly found in functionally important regions of RNA and also affect antibiotic resistance or sensitivity. Synthetic modifications of nucleosides such as fluorinated and arabinosyl nucleosides have found uses as anti-virals and chemotherapy agents. Understanding the effect that modifications have on structure and glycosidic bond stability may lend insight into the functions of these modified nucleosides. Modifications such as the naturally occurring 2^'-O-methylation and the synthetic 2^'-fluorination are believed to help stabilize the nucleoside through the glycosidic bond stability and intramolecular hydrogen bonding. Changing the sugar from ribose to arabinose alters the stereochemistry at the 2^' position and thus shifts the 3D orientation of the 2^'-hydroxyl group, which also affects intramolecular hydrogen bonding and glycosidic bond stability. The structures of 2^'-deoxy-2^'-fluorocytidine, 2^'-O-methylcytidine and cytosine arabinoside are examined in the current work by measuring the infrared spectra in the IR fingerprint region using infrared multiple photon dissociation (IRMPD) action spectroscopy. The structures accessed in the experiments were determined via comparison of the measured IRMPD action spectra to the theoretical linear IR spectra determined by density functional theory and molecular modeling for the stable low-energy structures. Although glycosidic bond stability cannot be quantitatively determined from this data, complementary TCID studies will establish the effect of these modifications. Comparison of these modified nucleosides with their RNA and DNA analogues will help elucidate differences in their intrinsic chemistry.
Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis.

PubMed

Lenz, Stefan A P; Kohout, Johnathan D; Wetmore, Stacey D

2016-12-22

Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO - ···H 2 O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol -1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO - as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H 2 O nucleophile) by ∼15-20 kJ mol -1 , the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH - nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol -1 . Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol -1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.
Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.
Structural and electronic properties of barbituric acid and melamine-containing ribonucleosides as plausible components of prebiotic RNA: implications for prebiotic self-assembly.

PubMed

Kaur, Sarabjeet; Sharma, Purshotam; Wetmore, Stacey D

2017-11-22

The RNA world hypothesis assumes that RNA was the first informational polymer that originated from prebiotic chemical soup. However, since the reaction of d-ribose with canonical nucleobases (A, C, G and U) fails to yield ribonucleosides (rNs) in substantial amounts, the spontaneous origin of rNs and the subsequent synthesis of RNA remains an unsolved mystery. To this end, it has been suggested that RNA may have evolved from primitive genetic material (preRNA) composed of simpler prebiotic heterocycles that spontaneously form glycosidic bonds with ribose. As an effort toward evaluating this hypothesis, the present study uses density functional theory (DFT) to assess the suitability of barbituric acid (BA) and melamine (MM) to act as prebiotic nucleobases, both of which have recently been shown to spontaneously form a glycosidic bond with ribose and organize into supramolecular assemblies in solution. The significant strength of hydrogen bonds involving BA and MM indicates that such interactions may have played a crucial role in their preferential selection over competing heterocycles that interact solely through stacking interactions from the primordial soup during the early phase of evolution. However, the greater stability of stacked dimers involving BA or MM and the canonical nucleobases compared to those consisting solely of BA and/or MM points towards the possible evolution of intermediate informational polymers consisting of prebiotic and canonical nucleobases, which could have eventually evolved into RNA. Analysis of the associated rNs reveals an anti conformational preference for the biologically-relevant β-anomer of both BA and MM rNs, which will allow complementary WC-like hydrogen bonding that can stabilize preRNA polymers. Large calculated deglycosylation barriers suggest BA rNs containing C-C glycosidic bonds are relevant in challenging prebiotic environments such as volcanic geotherms, while lower barriers indicate the MM rNs containing C-N-C glycosidic linkages may have been more likely synthesized from simple precursors such as urea-ice in icy (polar) regions. Together, our quantum chemical data clarifies the physicochemical interactions and stability of potential prebiotically-relevant constituents of BA and MM polymeric assemblies, and complements information from previous experimental studies to bolster the candidature of these heterocycles as prebiotic nucleobases.
Microsolvated Model for the Kinetics and Thermodynamics of Glycosidic Bond Dissociative Cleavage of Nucleoside D4G.

PubMed

Jiang, Yang; Xue, Ying; Zeng, Yi

2018-02-15

Using the microsolvated model that involves explicit water molecules and implicit solvent in the optimization, two proposed dissociative hydrolysis mechanisms of 2',3'-didehydro-2',3'-dideoxyguanosine (d4G) have been first investigated by means of M06-2X(CPCM, water)/6-31++G(d,p) method. The glycosidic bond dissociation for the generation of the oxacarbenium ion intermediate is the rate-determining step (RDS). The subsequent nucleophilic water attack from different side of the oxacarbenium ion intermediate gives either the α-product [(2S,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] or β-product [(2R,5S)-5-(hydroxymethyl)-2,5-dihydrofuran-2-ol] and is thus referred to as α-path (inversion) and β-path (retention). Two to five explicit water molecules (n = 2-5) are considered in the microsolvated model, and n = 3 or 4 is the smallest model capable of minimizing the activation energy for α-path and β-path, respectively. Our theoretical results suggest that α-path (n = 3) is more kinetically favorable with lower free energy barrier (RDS) of 27.7 kcal mol -1 , in contrast to that of 30.7 kcal mol -1 for the β-path (n = 4). The kinetic preference of the α-path is rationalized by NBO analysis. Whereas thte β-path is more thermodynamically favorable over the α-path, where the formation of β-product and α-product are exergonic and endergonic, respectively, providing theoretical support for the experimental observation that the β-cleavage product was the major one after sufficient reaction time. Comparisons of d4G with analogous cyclo-d4G and dG from kinetic free energy barriers and thermodynamic heterolytic dissociation energies were also carried out. Our kinetic and thermodynamic results manifest that the order of glycosidic bond stability should be d4G < cyclo-d4G < dG, which agrees well with the reported experimental stability order of d4G compounds and analogues and gives further understanding on the influence of 6-cyclopropylamino and unsaturated ribose to the glycosidic bond instability of d4G.
A novel pyrimidine tetrad contributing to stabilize tetramolecular G-quadruplex structures.

PubMed

Esposito, V; Pepe, A; Filosa, R; Mayol, L; Virgilio, A; Galeone, A

2016-03-14

G-quadruplex structures formed by oligodeoxyribonucleotides TGGU(NH2)GGT (AM, U(NH2) = 5-amino-2'-deoxyuridine), TGGU(Br)GGT (BR, U(Br) = 5-bromo-2'-deoxyuridine) and TGGTGGT (TH) have been investigated through circular dichroism, nuclear magnetic resonance, gel electrophoresis and molecular modeling techniques. Collected data indicate that all 7-mer oligonucleotides form tetramolecular parallel G-quadruplex structures with all residues adopting anti glycosidic bonds. In the case of AM, data suggest the occurrence of a novel U(NH2)-tetrad characterized by eight hydrogen bonds that stabilizes the G-quadruplex structure more efficiently than U(Br)- and T-tetrads.
Phystosterols and their derivatives: structural diversity, distribution, metabolism, analysis, and health promoting uses

USDA-ARS?s Scientific Manuscript database

Phytosterols (plant sterols) occur in the cells of all plants. They are important structural components that stabilize the biological membranes of plants. Sterols can occur in the “free” unbound form or they can be covalently bound via an ester or glycosidic bond. Since our previous 2002 review o...
The fate of H atom adducts to 3'-uridine monophosphate.

PubMed

Wang, Ran; Zhang, Ru Bo; Eriksson, Leif A

2010-07-29

The stabilities of the adducts deriving from H free radical addition to the O2, O4, and C5 positions of 3'-uridine monophosphate (3'UMP) are studied by the hybrid density functional B3LYP approach. Upon H atom addition at the O2 position, a concerted low-barrier proton-transfer process will initially occur, followed by the potential ruptures of the N-glycosidic or beta-phosphate bonds. The rupture barriers are strongly influenced by the rotational configuration of the phosphate group at the 3' terminal, and are influenced by bulk solvation effects. The O4-H adduct has the highest thermal stability, as the localization of the unpaired electron does not enable cleavage of either the C1'-N1 or the C3'-O(P) bonds. For the most stable adduct, with H atom added to the C5 position, the rate-controlled step is the H2'a abstraction by the C6 radical site, after which the subsequent strand rupture reactions proceed with low barriers. The main unpaired electron densities are presented for the transient species. Combined with previous results, it is concluded that the H atom adducts are more facile to drive the strand scission rather than N-glycosidic bond ruptures within the nucleic acid bases.
Antivirulence C-Mannosides as Antibiotic-Sparing, Oral Therapeutics for Urinary Tract Infections.

PubMed

Mydock-McGrane, Laurel; Cusumano, Zachary; Han, Zhenfu; Binkley, Jana; Kostakioti, Maria; Hannan, Thomas; Pinkner, Jerome S; Klein, Roger; Kalas, Vasilios; Crowley, Jan; Rath, Nigam P; Hultgren, Scott J; Janetka, James W

2016-10-27

Gram-negative uropathogenic Escherichia coli (UPEC) bacteria are a causative pathogen of urinary tract infections (UTIs). Previously developed antivirulence inhibitors of the type 1 pilus adhesin, FimH, demonstrated oral activity in animal models of UTI but were found to have limited compound exposure due to the metabolic instability of the O-glycosidic bond (O-mannosides). Herein, we disclose that compounds having the O-glycosidic bond replaced with carbon linkages had improved stability and inhibitory activity against FimH. We report on the design, synthesis, and in vivo evaluation of this promising new class of carbon-linked C-mannosides that show improved pharmacokinetic (PK) properties relative to O-mannosides. Interestingly, we found that FimH binding is stereospecifically modulated by hydroxyl substitution on the methylene linker, where the R-hydroxy isomer has a 60-fold increase in potency. This new class of C-mannoside antagonists have significantly increased compound exposure and, as a result, enhanced efficacy in mouse models of acute and chronic UTI.
Replication of N[superscript 2],3-Ethenoguanine by DNA Polymerases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Linlin; Christov, Plamen P.; Kozekov, Ivan D.

2014-10-02

The unstable DNA adduct N2,3-ethenoguanine, a product of both exposure to the carcinogen vinyl chloride and of oxidative stress, was built into an oligonucleotide, using an isostere strategy to stabilize the glycosidic bond. This modification was then used to examine the cause of mutations by DNA polymerases, in terms of both the biochemistry of the lesion and a structure of the lesion within a polymerase.
Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

PubMed

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.
Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

PubMed Central

Gu, Jiande; Wang, Jing; Leszczynski, Jerzy

2010-01-01

To elucidate the contribution of pyrimidine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced C3′–O3′, and C5′–O5′ σ bond as well as N-glycosidic bond breaking of 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate were performed using the B3LYP/DZP++ approach. The base-centered radical anions are electronically stable enough to assure that either the C–O or glycosidic bond breaking processes might compete with the electron detachment and yield corresponding radical fragments and anions. In the gas phase, the computed glycosidic bond breaking activation energy (24.1 kcal/mol) excludes the base release pathway. The low-energy barrier for the C3′–O3′ σ bond cleavage process (∼6.0 kcal/mol for both cytidine and thymidine) suggests that this reaction pathway is the most favorable one as compared to other possible pathways. On the other hand, the relatively low activation energy barrier (∼14 kcal/mol) for the C5′–O5′ σ bond cleavage process indicates that this bond breaking pathway could be possible, especially when the incident electrons have relatively high energy (a few electronvolts). The presence of the polarizable medium greatly increases the activation energies of either C–O σ bond cleavage processes or the N-glycosidic bond breaking process. The only possible pathway that dominates the LEE-induced DNA single strands in the presence of the polarizable surroundings (such as in an aqueous solution) is the C3′–O3′ σ bond cleavage (the relatively low activation energy barrier, ∼13.4 kcal/mol, has been predicted through a polarizable continuum model investigation). The qualitative agreement between the ratio for the bond breaks of C5′–O5′, C3′–O3′ and N-glycosidic bonds observed in the experiment of oligonucleotide tetramer CGAT and the theoretical sequence of the bond breaking reaction pathways have been found. This consistency between the theoretical predictions and the experimental observations provides strong supportive evidences for the base-centered radical anion mechanism of the LEE-induced single-strand bond breaking around the pyrimidine sites of the DNA single strands. PMID:20430827
Synthetic study on the relationship between structure and sweet taste properties of steviol glycosides.

PubMed

Upreti, Mani; Dubois, Grant; Prakash, Indra

2012-04-05

The structure activity relationship between the C₁₆-C₁₇ methylene double bond on the aglycone of steviol glycosides and the corresponding impact on their sweet taste has been reported here for the first time. It has been observed that converting stevioside and rebaudioside A to their corresponding ketones by switching the doubly bonded methylene on C-17 for a ketone group actually removes the sweet taste properties of these molecules completely. Regenerating the original molecules tends to restore the sweet taste of both the steviol glycosides. Thus this C₁₆-C₁₇ methylene double bond in rebaudioside A and stevioside can be regarded as a pharmacophore essential for the sweetness property of these molecules.
Molecular insights into the mechanism of thermal stability of actinomycete mannanase.

PubMed

Kumagai, Yuya; Uraji, Misugi; Wan, Kun; Okuyama, Masayuki; Kimura, Atsuo; Hatanaka, Tadashi

2016-09-01

Streptomyces thermolilacinus mannanase (StMan), which requires Ca(2+) for its enhanced thermal stability and hydrolysis activity, possesses two Ca(2+) -binding sites in loop6 and loop7. We evaluated the function of the Ca(2+) -binding site in loop7 and the hydrogen bond between residues Ser247 in loop6 and Asp279 in loop7. The Ca(2+) -binding in loop7 was involved only in thermal stability. Mutations of Ser247 or Asp279 retained the Ca(2+) -binding ability; however, mutants showed less thermal stability than StMan. Phylogenetic analysis indicated that most glycoside hydrolase family 5 subfamily 8 mannanases could be stabilized by Ca(2+) ; however, the mechanism of StMan thermal stability was found to be quite specific in some actinomycete mannanases. © 2016 Federation of European Biochemical Societies.
Nucleotides containing variously modified sugars: energetics, structure, and mechanical properties.

PubMed

Yurenko, Yevgen P; Novotný, Jan; Nikolaienko, Tymofii Yu; Marek, Radek

2016-01-21

The influence of various sugar residue modifications on intrinsic energetic, conformational, and mechanical properties of 2'-deoxyribonucleotide-5'-monophosphates (dNs) was comprehensively investigated using modern quantum chemical approaches. In total, fourteen sugar modifications, including double bonds and heteroatoms (S and N) inside the sugar ring, as well as fluorination in various positions, were analyzed. Among hundreds of possible conformational states of dNs, only two - AI and BI, corresponding to the most biologically significant forms of a double-helical DNA, were considered for each dN. It was established that the most of the studied modifications tend to strongly stabilize either AI or BI conformation of dNs both in the gas phase and in aqueous solution (modelled by implicit solvent models). Therefore, some of these modifications can be used as a tool for reducing structural polymorphism of nucleic acids in solution as well as for designing oligonucleotides with specific structural features. The evaluation of relaxed force constants (RFC) for glycosidic bonds suggests that the majority of the studied modifications of the sugar residue yield increased strengths of glycosidic bonds in dNs, and can therefore be used for designing modified nucleic acids with an increased resistance to abasic lesions. The most significant reinforcement of the glycosidic bond occurs in dNs containing the CF2 group instead of the O4' oxygen and the fluorine atom at the 2'-α-position. The calculation of the RFC and vibrational root-mean-square (VRMS) deviations for conformational degrees of freedom revealed a strong dependence between mechanical properties of dNs and their energetic characteristics. In particular, electronic energies of AI and BI conformers of dNs calculated in vacuo are closely connected with the values of relaxed force constants (RFC) for the δ angle: the higher RFC(δ) values correspond to more energetically favorable conformers.
Relaxation processes in disaccharide sugar glasses

NASA Astrophysics Data System (ADS)

Hwang, Yoon-Hwae; Kwon, Hyun-Joung; Seo, Jeong-Ah; Shin, Dong-Myeong; Ha, Ji-Hye; Kim, Hyung-Kook

2013-02-01

We represented relaxation processes of disaccharide sugars (anhydrous trehalose and maltose) in supercooled and glassy states by using several spectroscopy techniques which include a broadband dielectric loss spectroscopy, photon correlation spectroscopy and X-ray diffraction (Retvield analysis) methods which are powerful tools to measure the dynamics in glass forming materials. In a dielectric loss spectroscopy study, we found that anhydrous trehalose and maltose glasses have an extra relaxation process besides α-, JG β- and γ-relaxations which could be related to a unique property of glycoside bond in disaccharides. In photon correlation spectroscopy study, we found an interesting compressed exponential relaxation at temperatures above 140°C. The q-1 dependence of its relaxation time corresponds to an ultraslow ballistic motion due to the local structure rearrangements. In the same temperature range, we found the glycosidic bond structure changes in trehalose molecule from the Raman and the Retvield X-ray diffraction measurements indicating that the observed compressed exponential relaxation in supercooled liquid trehalose could be resulted in the glycosidic bond structure change. Therefore, the overall results from this study might support the fact that the superior bioprotection ability of disaccharide sugar glasses might originate from this unique relaxation process of glycosidic bond.
Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran, Renjith; Sarma, Manabendra, E-mail: msarma@iitg.ernet.in

2014-09-14

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed aftermore » impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.« less
The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

PubMed

Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S

2017-04-01

Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, T m , and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (T m (F/T) < T m (εA/T) < T m (Hx/T) < T m (A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.
Engineering improved thermostability of the GH11 xylanase from Neocallimastix patriciarum via computational library design.

PubMed

Bu, Yifan; Cui, Yinglu; Peng, Ying; Hu, Meirong; Tian, Yu'e; Tao, Yong; Wu, Bian

2018-04-01

Xylanases, which cleave the β-1,4-glycosidic bond between xylose residues to release xylooligosaccharides (XOS), are widely used as food additives, animal feeds, and pulp bleaching agents. However, the thermally unstable nature of xylanases would hamper their industrial application. In this study, we used in silico design in a glycoside hydrolase family (GH) 11 xylanase to stabilize the enzyme. A combination of the best mutations increased the apparent melting temperature by 14 °C and significantly enhanced thermostability and thermoactivation. The variant also showed an upward-shifted optimal temperature for catalysis without compromising its activity at low temperatures. Moreover, a 10-fold higher XOS production yield was obtained at 70 °C, which compensated the low yield obtained with the wild-type enzyme. Collectively, the variant constructed by the computational strategy can be used as an efficient biocatalyst for XOS production at industrially viable conditions.
Stability of steviol glycosides in several food matrices.

PubMed

Jooken, Etienne; Amery, Ruis; Struyf, Tom; Duquenne, Barbara; Geuns, Jan; Meesschaert, Boudewijn

2012-10-24

As steviol glycosides are now allowed as a food additive in the European market, it is important to assess the stability of these steviol glycosides after they have been added to different food matrices. We analyzed and tested the stability of steviol glycosides in semiskimmed milk, soy drink, fermented milk drink, ice cream, full-fat and skimmed set yogurt, dry biscuits, and jam. The fat was removed by centrifugation from the dairy and soy drink samples. Proteins were precipitated by the addition of acetonitrile and also removed by centrifugation. Samples of jam were extracted with water. Dry biscuits were extracted with ethanol. The resulting samples were concentrated with solid-phase extraction and analyzed by high-performance liquid chromatography on a C18 stationary phase and a gradient of acetonitrile/aqueous 25 mM phosphoric acid. The accuracy was checked using a standard addition on some samples. For assessing the stability of the steviol glycosides, samples were stored in conditions relevant to each food matrix and analyzed periodically. The results indicate that steviol glycosides can be analyzed with good precision and accuracy in these food categories. The recovery was between 96 and 103%. The method was also validated by standard addition, which showed excellent agreement with the external calibration curve. No sign of decomposition of steviol glycosides was found in any of the samples.

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

PubMed

Perić-Hassler, Lovorka; Hansen, Halvor S; Baron, Riccardo; Hünenberger, Philippe H

2010-08-16

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed. Copyright 2010 Elsevier Ltd. All rights reserved.
A comparison of flavonoid glycosides by electrospray tandem mass spectrometry

NASA Astrophysics Data System (ADS)

March, Raymond E.; Lewars, Errol G.; Stadey, Christopher J.; Miao, Xiu-Sheng; Zhao, Xiaoming; Metcalfe, Chris D.

2006-01-01

A comparison is presented of product ion mass spectra of protonated and deprotonated molecules of kaempferol-3-O-glucoside, quercitin-3-O-glucoside (isoquercitrin), quercitin-3-O-galactoside (hyperoin), apigenin-7-O-glucoside, luteolin-7-O-glucoside, genistein-7-O-glucoside, naringenin-7-O-glucoside (prunin), luteolin-4'-O-glucoside, luteolin-6-C-glucoside (homoorientin, known also as isoorientin), apigenin-8-C-glucoside (vitexin), and luteolin-8-C-glucoside (orientin) together with the product ion mass spectrum of deprotonated kaempferol-7-O-glucoside. All isomeric ions were distinguishable on the basis of their product ion mass spectra. For protonated 3-O-, 7-O-, and 4'-O-glycosides at a collision energy of 46-47 eV, homolytic cleavage of the O-glycosidic bond yielded aglycon Y+ ions, whereas in deprotonated 3-O-, 7-O-, and 4'-O-glycosides, heterolytic and homolytic cleavage of the O-glycosidic bond yielded radical aglycon (Y-H)- and aglycon (Y-) ions. In each case, fragmentation of either the glycan or the aglycon or both was observed. For 6-C- and 8-C-glycosides at a collision energy of 46-47 eV, fragmentation was restricted almost exclusively to the glycan. For luteolin-6-C-glucoside, the integrity of the aglycon structure is preserved at the expense of the glycan for which some 30 fragmentations were observed. Breakdown curves were determined as a function of collision energy for protonated and deprotonated luteolin-6-C-glucoside. An attempt has been made to rationalize the product ion mass spectra derived from C-O- and C-C-luteolin glucosides in terms of computed structures that indicate significant intramolecular hydrogen bonding and rotation of the B-ring to form a coplanar luteolin structure. It is proposed that protonated and deprotonated luteolin-6-C-glucoside may afford examples of cooperative interactive bonding that plays a major role in directing fragmentation.
Enzymes that cleave non-glycosidic ether bonds between lignins or derivatives thereof and saccharides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kravit, Nancy G.; Schmidt, Katherine A.

The patent application relates to isolated polypeptides that specifically cleave non-glycosidic ether bonds between lignins or derivatives thereof and saccharides, and to cDNAs encoding the polypeptides. The patent application also relates to nucleic acid constructs, expression vectors and host cells comprising the cDNAs, as well as methods of producing and using the isolated polypeptides for treating pulp and biomass to increase soluble saccharide yield and enrich lignin fractions.
Hillasides A and B, two new cytotoxic triterpene glycosides from the sea cucumber Holothuria hilla Lesson.

PubMed

Wu, Jun; Yi, Yang-Hua; Tang, Hai-Feng; Wu, Hou-Ming; Zhou, Zhen-Rong

2007-01-01

Two new triterpene glycosides, hillasides A (1) and B (2), were isolated from the sea cucumber H. hilla Lesson, together with one known glycoside holothuria B (3). Their structures were deduced by extensive spectral analysis and chemical evidences. The presence of conjugated double bonds [22E,24-diene] in the aglycone of 1 is a rare structural feature among sea cucumber glycosides. The two glycosides showed significant cytotoxicity against eight human tumour cell lines (A-549, MCF-7, IA9, CAKI-1, PC-3, KB, KB-VIN and HCT-8) with IC(50) in the range of 0.1-3.8 microg/ml.
Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment.

PubMed

Zhang, Ru Bo; Zhang, Ke; Eriksson, Leif A

2008-01-01

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.
Laser-induced hydrogen radical removal in UV MALDI-MS allows for the differentiation of flavonoid monoglycoside isomers.

PubMed

Yamagaki, Tohru; Watanabe, Takehiro; Tanaka, Masaki; Sugahara, Kohtaro

2014-01-01

Negative-ion matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectra and tandem mass spectra of flavonoid mono-O-glycosides showed the irregular signals that were 1 and/or 2 Da smaller than the parent deprotonated molecules ([M - H](-)) and the sugar-unit lost fragment ions ([M - Sugar - H](-)). The 1 and/or 2 Da mass shifts are generated with the removing of a neutral hydrogen radical (H*), and/or with the homolytic cleavage of the glycosidic bond, such as [M - H* - H](-), [M - Sugar - H* - H](-), and [M - Sugar - 2H* - H](-). It was revealed that the hydrogen radical removes from the phenolic hydroxy groups on the flavonoids, not from the sugar moiety, because the flavonoid backbones themselves absorb the laser. The glycosyl positions depend on the extent of the hydrogen radical removals and that of the homolytic cleavage of the glycosidic bonds. Flavonoid mono-glycoside isomers were distinguished according to their TOF MS and tandem mass spectra.
Separation of Rebaudiana A from Steviol glycoside using a polymeric adsorbent with multi-hydrogen bonding in a non-aqueous system.

PubMed

Ba, Jing; Zhang, Na; Yao, Lijuan; Ma, Ning; Wang, Chunhong

2014-11-15

Rebaudioside A (RA) and stevioside (SS) are the primary effective glycoside components in Stevia Rebaudiana. The RA glycoside is sweeter, and it tastes similarly to sucrose. Because extracts with a high RA content can be used as natural sweeteners for food additives approved by the FAO and FDA, RA should generate high market demand. In this study, an efficient method for separating RA was established based on the synergistic multi-hydrogen bonding interaction between a polymeric adsorbent and the RA glycoside. To overcome the destruction of the hydrophobic affinity required for the selective adsorption of RA, an innovative non-aqueous environment was established for adsorption and separation. To this end, an initial polymeric adsorbent composed of a glycidyl methacrylate and trimethylolpropane trimethacrylate (GMA-co-TMPTMA) copolymer matrix was synthesized, and polyethylene polyamine was employed as a functional reagent designed to react with the epoxy group on GME-co-TMPTMA to form a highly selective macroporous adsorbent. The effects of the different functional reagents and the solvent polarity on the adsorption selectivity for RA and SS, respectively, were investigated. Matching the structure of the polyethylene polyamine and sugar ligand on the glycoside molecule was essential in ensuring that the maximum synergistic interaction between adsorbent and adsorbate would be achieved. Moreover, the hydrogen-bonding force was observed to increase when the polarity of the adsorption solvent decreased. Therefore, among the synthesized macroporous polymeric adsorbents, the GTN4 adsorbent-bonding tetraethylenepentamine functional group provided the best separation in an n-butyl alcohol solution. Under the optimized gradient elution conditions, RA and SS can be effectively separated, and the contents of RA and SS increased from 33.5% and 51.5% in the initial crude extract to 95.4% and 78.2% after separation, respectively. Compared to conventional methods, the adsorption-desorption process is more advanced due to its procedural simplicity, low cost and adaptability for industrial production. Copyright © 2014 Elsevier B.V. All rights reserved.
Synthesis and binding affinity analysis of α1-2- and α1-6-O/S-linked dimannosides for the elucidation of sulfur in glycosidic bonds using quartz crystal microbalance sensors.

PubMed

Norberg, Oscar; Wu, Bin; Thota, Niranjan; Ge, Jian-Tao; Fauquet, Germain; Saur, Ann-Kathrin; Aastrup, Teodor; Dong, Hai; Yan, Mingdi; Ramström, Olof

2017-11-27

The role of sulfur in glycosidic bonds has been evaluated using quartz crystal microbalance methodology. Synthetic routes towards α1-2- and α1-6-linked dimannosides with S- or O-glycosidic bonds have been developed, and the recognition properties assessed in competition binding assays with the cognate lectin concanavalin A. Mannose-presenting QCM sensors were produced using photoinitiated, nitrene-mediated immobilization methods, and the subsequent binding study was performed in an automated flow-through instrumentation, and correlated with data from isothermal titration calorimetry. The recorded K d -values corresponded well with reported binding affinities for the O-linked dimannosides with affinities for the α1-2-linked dimannosides in the lower micromolar range. The S-linked analogs showed slightly disparate effects, where the α1-6-linked analog showed weaker affinity than the O-linked dimannoside, as well as positive apparent cooperativity, whereas the α1-2-analog displayed very similar binding compared to the O-linked structure. Copyright © 2017 Elsevier Ltd. All rights reserved.
Cellulase variants

DOEpatents

Blazej, Robert; Toriello, Nicholas; Emrich, Charles; Cohen, Richard N.; Koppel, Nitzan

2015-07-14

This invention provides novel variant cellulolytic enzymes having improved activity and/or stability. In certain embodiments the variant cellulotyic enzymes comprise a glycoside hydrolase with or comprising a substitution at one or more positions corresponding to one or more of residues F64, A226, and/or E246 in Thermobifida fusca Cel9A enzyme. In certain embodiments the glycoside hydrolase is a variant of a family 9 glycoside hydrolase. In certain embodiments the glycoside hydrolase is a variant of a theme B family 9 glycoside hydrolase.
Hydrogenation of the Exocyclic Olefinic Bond at C-16/C-17 Position of ent-Kaurane Diterpene Glycosides of Stevia rebaudiana Using Various Catalysts

PubMed Central

Chaturvedula, Venkata Sai Prakash; Prakash, Indra

2013-01-01

Catalytic hydrogenation of the exocyclic double bond present between C16 and C17 carbons of the four ent-kaurane diterpene glycosides namely rebaudioside A, rebaudioside B, rebaudioside C, and rebaudioside D isolated from Stevia rebaudiana has been carried out using Pt/C, Pd(OH)2, Rh/C, Raney Ni, PtO2, and 5% Pd/BaCO3 to their corresponding dihydro derivatives with 17α and 17β methyl group isomers. Reactions were performed using the above-mentioned catalysts with the solvents methanol, water, and ethanol/water (8:2) under various conditions. Synthesis of reduced steviol glycosides was performed using straightforward chemistry and their structures were characterized on the basis of 1D and 2D NMR spectral data, including a comparison with reported spectral data. PMID:23896597
A general synthesis of C8-arylpurine phosphoramidites.

PubMed

Vongsutilers, Vorasit; Daft, Jonathan R; Shaughnessy, Kevin H; Gannett, Peter M

2009-09-02

A general scheme for the synthesis of C8-arylpurine phosphoramidites has been developed. C8-Arylation of C8-bromo-2'-deoxyguanosine is the key step and has been achieved through the use of a Suzuki coupling. Since the coupling reaction is conducted under aqueous conditions, it is unnecessary to protect and then deprotect the hydroxyl groups, thus saving several steps and improving overall yields. Once the C8-arylgroup is introduced, the glycosidic bond becomes very sensitive to acid catalyzed cleavage. Protection of the amino groups as the corresponding N,N-dimethylformamidine derivative improves stability of the derivatives. Synthetic C8-arylpurines were successfully used to prepare synthetic oligonucleotides.
Bioaccessibility, Intestinal Permeability and Plasma Stability of Isorhamnetin Glycosides from Opuntia ficus-indica (L.).

PubMed

Antunes-Ricardo, Marilena; Rodríguez-Rodríguez, César; Gutiérrez-Uribe, Janet A; Cepeda-Cañedo, Eduardo; Serna-Saldívar, Sergio O

2017-08-22

Isorhamnetin glycosides are representative compounds of Opuntia ficus-indica that possess different biological activities. There is slight information about the changes in bioaccessibility induced by the glycosylation pattern of flavonoids, particularly for isorhamnetin. In this study, the bioaccessibility and permeability of isorhamnetin glycosides extracted from O. ficus-indica were contrasted with an isorhamnetin standard. Also, the plasma stability of these isorhamnetin glycosides after intravenous administration in rats was evaluated. Recoveries of isorhamnetin after oral and gastric digestion were lower than that observed for its glycosides. After intestinal digestion, isorhamnetin glycosides recoveries were reduced to less than 81.0%. The apparent permeability coefficient from apical (AP) to basolateral (BL) direction (Papp (AP-BL) ) of isorhamnetin was 2.6 to 4.6-fold higher than those obtained for its glycosides. Isorhamnetin diglycosides showed higher Papp (AP-BL) values than triglycosides. Sugar substituents affected the Papp (AP-BL) of the triglycosides. Isorhamnetin glycosides were better retained in the circulatory system than the aglycone. After intravenous dose of the isorhamnetin standard, the elimination half-life was 0.64 h but increased to 1.08 h when the O. ficus-indica extract was administered. These results suggest that isorhamnetin glycosides naturally found in O. ficus-indica could be a controlled delivery system to maintain a constant plasmatic concentration of this important flavonoid to exert its biological effects in vivo.
Bioaccessibility, Intestinal Permeability and Plasma Stability of Isorhamnetin Glycosides from Opuntia ficus-indica (L.)

PubMed Central

Antunes-Ricardo, Marilena; Rodríguez-Rodríguez, César; Cepeda-Cañedo, Eduardo

2017-01-01

Isorhamnetin glycosides are representative compounds of Opuntia ficus-indica that possess different biological activities. There is slight information about the changes in bioaccessibility induced by the glycosylation pattern of flavonoids, particularly for isorhamnetin. In this study, the bioaccessibility and permeability of isorhamnetin glycosides extracted from O. ficus-indica were contrasted with an isorhamnetin standard. Also, the plasma stability of these isorhamnetin glycosides after intravenous administration in rats was evaluated. Recoveries of isorhamnetin after oral and gastric digestion were lower than that observed for its glycosides. After intestinal digestion, isorhamnetin glycosides recoveries were reduced to less than 81.0%. The apparent permeability coefficient from apical (AP) to basolateral (BL) direction (Papp(AP-BL)) of isorhamnetin was 2.6 to 4.6-fold higher than those obtained for its glycosides. Isorhamnetin diglycosides showed higher Papp(AP-BL) values than triglycosides. Sugar substituents affected the Papp(AP-BL) of the triglycosides. Isorhamnetin glycosides were better retained in the circulatory system than the aglycone. After intravenous dose of the isorhamnetin standard, the elimination half-life was 0.64 h but increased to 1.08 h when the O. ficus-indica extract was administered. These results suggest that isorhamnetin glycosides naturally found in O. ficus-indica could be a controlled delivery system to maintain a constant plasmatic concentration of this important flavonoid to exert its biological effects in vivo. PMID:28829356
Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism

DOE PAGES

Lee, Brady D.; Apel, William A.; Sheridan, Peter P.; ...

2018-04-16

Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Here, experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX.
Phenylethanoid Glycosides: Research Advances in Their Phytochemistry, Pharmacological Activity and Pharmacokinetics.

PubMed

Xue, Zhenzhen; Yang, Bin

2016-07-29

Phenylethanoid glycosides (PhGs) are widely distributed in traditional Chinese medicines as well as in other medicinal plants, and they were characterized by a phenethyl alcohol (C₆-C₂) moiety attached to a β-glucopyranose/β-allopyranose via a glycosidic bond. The outstanding activity of PhGs in diverse diseases proves their importance in medicinal chemistry research. This review summarizes new findings on PhGs over the past 10 years, concerning the new structures, their bioactivities, including neuroprotective, anti-inflammatory, antioxidant, antibacterial and antivirus, cytotoxic, immunomodulatory, and enzyme inhibitory effects, and pharmacokinetic properties.
Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Brady D.; Apel, William A.; Sheridan, Peter P.

Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Here, experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX.
Change in the Chemical Profile of Mangifera indica Leaves after their Metabolism in the Tropidacris collaris Grasshopper.

PubMed

da Silva, Rodolfo R; Moraes, Marcilio M; Camara, Claudio A G; Ramos, Clécio S

2015-11-01

This present work addresses research on the discovery of new compounds from natural sources. It is based on a study of Mangifera indica leaf metabolism by the Tropidacris collaris grasshopper. We found that the grasshopper hydrolyzed the flavonoid isoquercitrin to quercetin when the O-glycosidic bond was broken and sugar released as a probable energy source for the insect. There was not, however, hydrolysis of the major compound in the leaves, mangiferin, which contains the C-glycosidic bond. All compounds were isolated and their chemical structure determined by UV, IR, MS, 1H and 13C NMR.
Identifying the Tautomeric Form of a Deoxyguanosine-Estrogen Quinone Intermediate.

PubMed

Stack, Douglas E

2015-09-10

Mechanistic insights into the reaction of an estrogen o-quinone with deoxyguanosine has been further investigated using high level density functional calculations in addition to the use of 4-hyroxycatecholestrone (4-OHE₁) regioselectivity labeled with deuterium at the C1-position. Calculations using the M06-2X functional with large basis sets indicate the tautomeric form of an estrogen-DNA adduct present when glycosidic bonds cleavage occurs is comprised of an aromatic A ring structure. This tautomeric form was further verified by use of deuterium labelling of the catechol precursor use to form the estrogen o-quinone. Regioselective deuterium labelling at the C1-position of the estrogen A ring allows discrimination between two tautomeric forms of a reaction intermediate either of which could be present during glycosidic bond cleavage. HPLC-MS analysis indicates a reactive intermediate with a m/z of 552.22 consistent with a tautomeric form containing no deuterium. This intermediate is consistent with a reaction mechanism that involves: (1) proton assisted Michael addition; (2) re-aromatization of the estrogen A ring; and (3) glycosidic bond cleavage to form the known estrogen-DNA adduct, 4-OHE₁-1-N7Gua.
A Novel Diterpene Glycoside with Nine Glucose Units from Stevia rebaudiana Bertoni.

PubMed

Prakash, Indra; Ma, Gil; Bunders, Cynthia; Charan, Romila D; Ramirez, Catherine; Devkota, Krishna P; Snyder, Tara M

2017-01-31

Following our interest in new diterpene glycosides with better taste profiles than that of Rebaudioside M, we have recently isolated and characterized Rebaudioside IX-a novel steviol glycoside-from a commercially-supplied extract of Stevia rebaudiana Bertoni. This molecule contains a hexasaccharide group attached at C-13 of the central diterpene core, and contains three additional glucose units when compared with Rebaudioside M. Here we report the complete structure elucidation-based on extensive Nuclear Magnetic Resonance (NMR) analysis (1H, 13C, Correlation Spectroscopy (COSY), Heteronuclear Single Quantum Coherence-Distortionless Enhancement Polarization Transfer (HSQC-DEPT), Heteronuclear Multiple Bond Correlation (HMBC), 1D Total Correlation Spectroscopy (TOCSY), Nuclear Overhauser Effect Spectroscopy (NOESY)) and mass spectral data-of this novel diterpene glycoside with nine sugar moieties and containing a relatively rare 16 α-linked glycoside. A steviol glycoside bearing nine glucose units is unprecedented in the literature, and could have an impact on the natural sweetener catalog.
Synthesis and Photochromic Properties of Configurationally Varied Azobenzene Glycosides

PubMed Central

Chandrasekaran, Vijayanand; Johannes, Eugen; Kobarg, Hauke; Sönnichsen, Frank D; Lindhorst, Thisbe K

2014-01-01

Spatial orientation of carbohydrates is a meaningful parameter in carbohydrate recognition processes. To vary orientation of sugars with temporal and spatial resolution, photosensitive glycoconjugates with favorable photochromic properties appear to be opportune. Here, a series of azobenzene glycosides were synthesized, employing glycoside synthesis and Mills reaction, to allow “switching” of carbohydrate orientation by reversible E/Z isomerization of the azobenzene N=N double bond. Their photochromic properties were tested and effects of azobenzene substitution as well as the effect of anomeric configuration and the orientation of the sugars 2-hydroxy group were evaluated. PMID:25050228

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

NASA Astrophysics Data System (ADS)

Tan, Yanglan; Polfer, Nicolas C.

2015-02-01

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.
Thermal degradation of onion quercetin glucosides under roasting conditions.

PubMed

Rohn, Sascha; Buchner, Nadja; Driemel, Gregor; Rauser, Morten; Kroh, Lothar W

2007-02-21

Flavonoids are an important constituent of the human diet. In recent years, they have gained much attention due to their physiological properties, leading to an enormous increase in research on cancer prevention and reduction of cardiovascular diseases. Unfortunately, there is limited information about the fate of flavonoid glycosides during thermal treatment such as cooking, frying, roasting, etc. Such processing techniques may have an impact on the flavonoid structure, resulting in changes of the bioavailability and activity of the flavonoids. In this study, the stability of selected model and onion quercetin glycosides under roasting conditions (180 degrees C) was determined. The influence of the kind and position of the sugar moiety was investigated. As onions contain large amounts of quercetin glycosides and are often subject to thermal processes in food production, their major glycosides were isolated using counter current chromatography and roasted. The thermal treatment led to a degradation of the quercetin glycosides. The main product is the aglycone quercetin, which remained stable during further roasting. During the roasting process of the quercetin diglucoside isolated from onion, the formation of a monoglycoside as an intermediate product was observed. This underlined that the stability of the glycosides is dependent on the kind and position of the sugar moiety.
Effect of microwave argon plasma on the glycosidic and hydrogen bonding system of cotton cellulose.

PubMed

Prabhu, S; Vaideki, K; Anitha, S

2017-01-20

Cotton fabric was processed with microwave (Ar) plasma to alter its hydrophilicity. The process parameters namely microwave power, process gas pressure and processing time were optimized using Box-Behnken method available in the Design Expert software. It was observed that certain combinations of process parameters improved existing hydrophilicity while the other combinations decreased it. ATR-FTIR spectral analysis was used to identify the strain induced in inter chain, intra chain, and inter sheet hydrogen bond and glycosidic covalent bond due to plasma treatment. X-ray diffraction (XRD) studies was used to analyze the effect of plasma on unit cell parameters and degree of crystallinity. Fabric surface etching was identified using FESEM analysis. Thus, it can be concluded that the increase/decrease in the hydrophilicity of the plasma treated fabric was due to these structural and physical changes. Copyright © 2016 Elsevier Ltd. All rights reserved.
Stability of dietary polyphenols under the cell culture conditions: avoiding erroneous conclusions.

PubMed

Xiao, Jianbo; Högger, Petra

2015-02-11

Most data of bioactivity from dietary polyphenols have been derived from in vitro cell culture experiments. In this context, little attention is paid to potential artifacts due to chemical instability of these natural antioxidants. An early degradation time ((C)T10) and half-degradation time ((C)T50) were defined to characterize the stability of 53 natural antioxidants incubated in Dulbecco's modified Eagle's medium (DMEM) at 37 °C. The degree of hydroxylation of flavones and flavonols significantly influenced the stability in order resorcinol-type > catechol-type > pyrogallol-type, with the pyrogallol-type being least stable. In contrast, any glycosylation of polyphenols obviously enhanced their stability. However, the glycosylation was less important compared to the substitution pattern of the nucleus rings. Methoxylation of flavonoids with more than three hydroxyl groups typically improved their stability as did the hydrogenation of the C2═C3 double bond of flavonoids to corresponding flavanoids. There was no significant correlation between the antioxidant potential of polyphenols and their stability. Notably, the polyphenols were clearly more stable in human plasma than in DMEM, which may be caused by polyphenol-protein interactions. It is strongly suggested to carry out stability tests in parallel with cell culture experiments for dietary antioxidants with catechol or pyrogallol structures and pyrogallol-type glycosides in order to avoid artifacts.
A Novel Diterpene Glycoside with Nine Glucose Units from Stevia rebaudiana Bertoni

PubMed Central

Prakash, Indra; Ma, Gil; Bunders, Cynthia; Charan, Romila D.; Ramirez, Catherine; Devkota, Krishna P.; Snyder, Tara M.

2017-01-01

Following our interest in new diterpene glycosides with better taste profiles than that of Rebaudioside M, we have recently isolated and characterized Rebaudioside IX—a novel steviol glycoside—from a commercially-supplied extract of Stevia rebaudiana Bertoni. This molecule contains a hexasaccharide group attached at C-13 of the central diterpene core, and contains three additional glucose units when compared with Rebaudioside M. Here we report the complete structure elucidation—based on extensive Nuclear Magnetic Resonance (NMR) analysis (1H, 13C, Correlation Spectroscopy (COSY), Heteronuclear Single Quantum Coherence-Distortionless Enhancement Polarization Transfer (HSQC-DEPT), Heteronuclear Multiple Bond Correlation (HMBC), 1D Total Correlation Spectroscopy (TOCSY), Nuclear Overhauser Effect Spectroscopy (NOESY)) and mass spectral data—of this novel diterpene glycoside with nine sugar moieties and containing a relatively rare 1→6 α-linked glycoside. A steviol glycoside bearing nine glucose units is unprecedented in the literature, and could have an impact on the natural sweetener catalog. PMID:28146121
Morning glory resin glycosides as α-glucosidase inhibitors: In vitro and in silico analysis.

PubMed

Rosas-Ramírez, Daniel; Escandón-Rivera, Sonia; Pereda-Miranda, Rogelio

2018-04-01

Twenty-seven individual resin glycosides from the morning glory family (Convolvulaceae) were evaluated for their α-glucosidase inhibitory potential. Four of these compounds displayed an inhibitory activity comparable to acarbose, which was used as a positive control. Molecular modeling studies performed by docking analysis were accomplished to predict that the active compounds and acarbose bind to the α-1,4-glucosidase enzyme catalytic site of MAL12 from the yeast Saccharomyces cerevisiae through stable hydrogen bonds primarily with the amino acid residues HIS279 and GLN322. Docking studies with the human maltase-glucoamylase (MGAM) also identified binding modes for resin glycosides inside the catalytic site in the proximity of TYR1251. These results postulate that resin glycosides may be a source of phytotherapeutic agents with antihyperglycemic properties for the prophylaxis and treatment of non-insulin-dependent type 2 diabetes mellitus. Copyright © 2018 Elsevier Ltd. All rights reserved.
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyler, Ludmila; Bragg, Jennifer; Wu, Jiajie

2010-01-01

Background Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolasemore » genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, both at the whole-genome level and at the level of individual glycoside hydrolase families. Results We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. Examination of individual glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51) revealed both similarities and distinctions between monocots and dicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. Conclusions This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a monocot model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.« less
Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.
A general synthetic strategy and the anti-proliferation properties on prostate cancer cell lines for natural phenylethanoid glycosides.

PubMed

Mulani, Shaheen K; Guh, Jih-Hwa; Mong, Kwok-Kong Tony

2014-05-14

A general strategy for the synthesis of phenylethanoid glycosides (PhG) including echinacoside 1, acteoside 2, calceolarioside-A 3 and calceolarioside-B 4 is reported. The strategy features the application of low substrate concentration glycosylation and N-formyl morpholine modulated glycosylation methods for the construction of 1,2-trans β- and α-glycosidic bonds. The reported strategy does not invoke the use of the participatory acyl protecting function, which is incompatible with the ester function present in target PhG compounds. A preliminary study of the anti-proliferation properties of the PhG compounds 1–4 was performed; the acteoside 2 exhibited the best inhibition on the prostatic cancer cell proliferation.
Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Brady D.; Apel, William A.; Sheridan, Peter P.

Background Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Results Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolasesmore » were down-regulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell. Conclusions Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases was not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than represented by the glycoside hydrolase family in which the enzymes were categorized.« less
Studies on the Selectivity Between Nickel-Catalyzed 1,2-Cis-2-Amino Glycosylation of Hydroxyl Groups of Thioglycoside Acceptors with C(2)-Substituted Benzylidene N-Phenyl Trifluoroacetimidates and Intermolecular Aglycon Transfer of the Sulfide Group

PubMed Central

Yu, Fei; Nguyen, Hien M.

2012-01-01

The stereoselective synthesis of saccharide thioglycosides containing 1,2-cis-2-amino glycosidic linkages is challenging. In addition to the difficulties associated with achieving high α-selectivity in the formation of 1,2-cis-2-amino glycosidic bonds, the glycosylation reaction is hampered by undesired transfer of the anomeric sulfide group from the glycosyl acceptor to the glycosyl donor. Overcoming these obstacles will pave the way for the preparation of oligosaccharides and glycoconjugates bearing the 1,2-cis-2-amino glycosidic linkages because the saccharide thioglycosides obtained can serve as donors for another coupling iteration. This approach streamlines selective deprotection and anomeric derivatization steps prior to the subsequent coupling event. We have developed an efficient approach for the synthesis of highly yielding and α-selective saccharide thioglycosides containing 1,2-cis-2-amino glycosidic bonds, via cationic nickel-catalyzed glycosylation of thioglycoside acceptors bearing the 2-trifluoromethylphenyl aglycon with N-phenyl trifluoroacetimidate donors. The 2-trifluoromethylphenyl group effectively blocks transfer of the anomeric sulfide group from the glycosyl acceptor to the C(2)-benzylidene donor and can be easily installed and activated. The current method also highlights the efficacy of the nickel catalyst selectively activating the C(2)-benzylidene imidate group in the presence of the anomeric sulfide group on the glycosyl acceptors. PMID:22838405
Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger.

PubMed

van der Kaaij, R M; Yuan, X-L; Franken, A; Ram, A F J; Punt, P J; van der Maarel, M J E C; Dijkhuizen, L

2007-07-01

In the genome sequence of Aspergillus niger CBS 513.88, three genes were identified with high similarity to fungal alpha-amylases. The protein sequences derived from these genes were different in two ways from all described fungal alpha-amylases: they were predicted to be glycosylphosphatidylinositol anchored, and some highly conserved amino acids of enzymes in the alpha-amylase family were absent. We expressed two of these enzymes in a suitable A. niger strain and characterized the purified proteins. Both enzymes showed transglycosylation activity on donor substrates with alpha-(1,4)-glycosidic bonds and at least five anhydroglucose units. The enzymes, designated AgtA and AgtB, produced new alpha-(1,4)-glycosidic bonds and therefore belong to the group of the 4-alpha-glucanotransferases (EC 2.4.1.25). Their reaction products reached a degree of polymerization of at least 30. Maltose and larger maltooligosaccharides were the most efficient acceptor substrates, although AgtA also used small nigerooligosaccharides containing alpha-(1,3)-glycosidic bonds as acceptor substrate. An agtA knockout of A. niger showed an increased susceptibility towards the cell wall-disrupting compound calcofluor white, indicating a cell wall integrity defect in this strain. Homologues of AgtA and AgtB are present in other fungal species with alpha-glucans in their cell walls, but not in yeast species lacking cell wall alpha-glucan. Possible roles for these enzymes in the synthesis and/or maintenance of the fungal cell wall are discussed.
Methyl 3-O-α-l-fucopyranosyl β-d-glucopyranoside tetrahydrate

PubMed Central

Eriksson, Lars; Widmalm, Göran

2012-01-01

The title compound, C13H24O10·4H2O, is the methyl glycoside of a disaccharide structural element present in the backbone of the capsular polysaccharide from Klebsiella K1, which contains only three sugars and a substituent in the polysaccharide repeating unit. The conformation of the title disaccharide is described by the glycosidic torsion angles ϕH = 51.1 (1)° and ψH = 25.8 (1)°. In the crystal, a number of O—H⋯O hydrogen bonds link the methyl glycoside and water molecules, forming a three-dimensional network. One water molecule is disordered over two positions with occupancies of 0.748 (4) and 0.252 (4). PMID:23284493
Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.

PubMed

Millen, Andrea L; Churchill, Cassandra D M; Manderville, Richard A; Wetmore, Stacey D

2010-10-14

Bulky DNA addition products (adducts) formed through attack at the C8 site of guanine can adopt the syn orientation about the glycosidic bond due to changes in conformational stability or hydrogen-bonding preferences directly arising from the bulky group. Indeed, the bulky substituent may improve the stability of (non-native) Hoogsteen pairs. Therefore, such adducts often result in mutations upon DNA replication. This work examines the hydrogen-bonded pairs between the Watson-Crick and Hoogsteen faces of the ortho or para C8-phenoxyl-2'-deoxyguanosine adduct and each natural (undamaged) nucleobase with the goal to clarify the conformational preference of this type of damage, as well as provide insight into the likelihood of subsequent mutation events. B3LYP/6-311+G(2df,p)//B3LYP/6-31G(d) hydrogen-bond strengths were determined using both nucleobase and nucleoside models for adduct pairs, as well as the corresponding complexes involving natural 2'-deoxyguanosine. In addition to the magnitude of the binding strengths, the R(C1'···C1') distances and ∠(N9C1'C1') angles, as well as the degree of propeller-twist and buckle distortions, were carefully compared to the values observed in natural DNA strands. Due to structural changes in the adduct monomer upon inclusion of the sugar moiety, the monomer deformation energy significantly affects the relative hydrogen-bond strengths calculated with the nucleobase and nucleoside models. Therefore, we recommend the use of at least a nucleoside model to accurately evaluate hydrogen-bond strengths of base pairs involving flexible, bulky nucleobase adducts. Our results also emphasize the importance of considering both the magnitude of the hydrogen-bond strength and the structure of the base pair when predicting the preferential binding patterns of nucleobases. Using our best models, we conclude that the Watson-Crick face of the ortho phenoxyl adduct forms significantly more stable complexes than the Hoogsteen face, which implies that the anti orientation of the damaged base will be favored by hydrogen bonding in DNA helices. Additionally, regardless of the hydrogen-bonding face involved, cytosine forms the most stable base pair with the ortho adduct, which implies that misincorporation due to this type of damage is unlikely. Similarly, cytosine is the preferred binding partner for the Watson-Crick face of the para adduct. However, Hoogsteen interactions with the para adduct are stronger than those with natural 2'-deoxyguanosine or the ortho adduct, and this form of damage binds with nearly equal stability to both cytosine and guanine in the Hoogsteen orientation. Therefore, the para adduct may adopt multiple orientations in DNA helices and potentially cause mutations by forming pairs with different natural bases. Models of oligonucleotide duplexes must be used in future work to further evaluate other factors (stacking, major groove contacts) that may influence the conformation and binding preference of these adducts in DNA helices.
Characterization of Hyaluronan-Degrading Enzymes from Yeasts.

PubMed

Smirnou, Dzianis; Krčmář, Martin; Kulhánek, Jaromír; Hermannová, Martina; Bobková, Lenka; Franke, Lukáš; Pepeliaev, Stanislav; Velebný, Vladimír

2015-10-01

Hyaluronidases (HAases) from yeasts were characterized for the first time. The study elucidated that hyaluronate 4-glycanohydrolase and hyaluronan (HA) lyase can be produced by yeasts. Six yeasts producing HAases were found through express screening of activities. The extracellular HAases from two of the yeast isolates, Pseudozyma aphidis and Cryptococcus laurentii, were characterized among them. P. aphidis HAase hydrolyzed β-1,4 glycosidic bonds of HA, yielding even-numbered oligosaccharides with N-acetyl-D-glucosamine at the reducing end. C. laurentii produced hyaluronan lyase, which cleaved β-1,4 glycosidic bonds of HA in β-elimination reaction, and the products of HA degradation were different-sized even-numbered oligosaccharides. The shortest detected HA oligomer was dimer. The enzymes' pH and temperature optima were pH 3.0 and 37-45 °C (P. aphidis) and pH 6.0 and 37 °C (C. laurentii), respectively. Both HAases showed good thermostability.
The long underestimated carbonyl function of carbohydrates – an organocatalyzed shot into carbohydrate chemistry.

PubMed

Mahrwald, R

2015-09-21

The aggressive and strong development of organocatalysis provides several protocols for the convenient utilization of the carbonyl function of unprotected carbohydrates in C-C-bond formation processes. These amine-catalyzed mechanisms enable multiple cascade-protocols for the synthesis of a wide range of carbohydrate-derived compound classes. Several, only slightly different protocols, have been developed for the application of 1,3-dicarbonyl compounds in the stereoselective chain-elongation of unprotected carbohydrates and the synthesis of highly functionalized C-glycosides of defined configuration. In addition, C-glycosides can also be accessed by amine-catalyzed reactions with methyl ketones. By a one-pot cascade reaction of isocyanides with unprotected aldoses and amino acids access to defined configured glycopeptide mimetics is achieved. Depending on the reaction conditions different origins to control the installation of configuration during the bond-formation process were observed.
A debranching enzyme IsoM of Corallococcus sp. strain EGB with potential in starch processing.

PubMed

Li, Zhoukun; Ji, Kai; Zhou, Jie; Ye, Xianfeng; Wang, Ting; Luo, Xue; Huang, Yan; Cao, Hui; Cui, Zhongli; Kong, Yi

2017-12-01

Interest in use of resistant starch and maltooligosaccharides as functional foods and biopreservatives has grown in recent years. In this research, a novel debranching enzyme IsoM from Corallococcus sp. strain EGB was identified and expressed in P. pastoris GS115. Sequence alignments showed that IsoM was typical isoamylase with the specific activity up to 70,600U/mg, which belongs to glycoside hydrolase family 13 (GH 13). Enzymatic reaction pattern demonstrated that IsoM has high debranching efficiency against α-1,6-glycosidic bond of branched starch, and exhibited no activity towards α-1,4-glycosidic bond. The potential application of IsoM in starch processing was determined. IsoM was a potential candidate for the production of RS (70.9%) from raw starch, which was comparable with the commercial pullulanase (Promozyme ® D2). IsoM also improved the maltohexaose yield in combination with maltohexaose-producing α-amylase AmyM (KM114206), the maltohexaose yield was improved by 63.3% compared with 21.9% improvement of Promozyme ® D2. The results of RS production and combination with other amylases suggesting that IsoM is a potential candidate for the efficient conversion of starch. Copyright © 2017. Published by Elsevier B.V.
Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism.

PubMed

Gregg, Katie J; Suits, Michael D L; Deng, Lehua; Vocadlo, David J; Boraston, Alisdair B

2015-10-16

O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-10-25

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65.
The Synthesis and Biological Characterization of Acetal-Free Mimics of the Tumor-Associated Carbohydrate Antigens.

PubMed

Sadraei, Seyed I; Reynolds, Michael R; Trant, John F

2017-01-01

Carcinomas express unique carbohydrates, known as tumor-associated carbohydrate antigens (TACAs), on their surface. These are potential targets for anticancer vaccines; however, to date, no such vaccine has reached the clinic. One factor that may complicate the success of this effort is the lability of the glycosidic bond. Acetal-free carbohydrates are analogues that lack the glycosidic linkage by replacing either the endo or exo oxygen with a methylene. This chapter summarizes the seminal syntheses of the mucin TACAs, provides an overview of common techniques for the synthesis of carbasugars and C-glycosides, reviews the syntheses published to date of acetal-free TACA analogues, and provides an overview of their observed biological activity. We conclude by offering a summation of the challenges remaining to the field biologically and the potential that acetal-free TACAs have of answering several basic questions in carbohydrate immunology. © 2017 Elsevier Inc. All rights reserved.

On the mechanism of peptidoglycan binding and cleavage by the endo-specific lytic transglycosylase MltE from Escherichia coli.

PubMed

Fibriansah, Guntur; Gliubich, Francesca I; Thunnissen, Andy-Mark W H

2012-11-13

The lytic transglycosylase MltE from Escherichia coli is a periplasmic, outer membrane-attached enzyme that cleaves the β-1,4-glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in the cell wall peptidoglycan, producing 1,6-anhydromuropeptides. Here we report three crystal structures of MltE: in a substrate-free state, in a binary complex with chitopentaose, and in a ternary complex with the glycopeptide inhibitor bulgecin A and the murodipeptide N-acetylglucosaminyl-N-acetylmuramyl-l-Ala-d-Glu. The substrate-bound structures allowed a detailed analysis of the saccharide-binding interactions in six subsites of the peptidoglycan-binding groove (subsites -4 to +2) and, combined with site-directed mutagenesis analysis, confirmed the role of Glu64 as catalytic acid/base. The structures permitted the precise modeling of a short glycan strand of eight saccharide residues, providing evidence for two additional subsites (+3 and +4) and revealing the productive conformational state of the substrate at subsites -1 and +1, where the glycosidic bond is cleaved. Full accessibility of the peptidoglycan-binding groove and preferential binding of an N-acetylmuramic acid residue in a (4)C(1) chair conformation at subsite +2 explain why MltE shows only endo- and no exo-specific activity toward glycan strands. The results further indicate that catalysis of glycosidic bond cleavage by MltE proceeds via distortion toward a sofa-like conformation of the N-acetylmuramic acid sugar ring at subsite -1 and by anchimeric assistance of the sugar's N-acetyl group, as shown previously for the lytic transglycosylases Slt70 and MltB.
Computational Insights into the Stability and Folding Pathways of Human Telomeric DNA G-Quadruplexes.

PubMed

Luo, Di; Mu, Yuguang

2016-06-09

G-quadruplex is a noncanonical yet crucial secondary structure of nucleic acids, which has proven its importance in cell aging, anticancer therapies, gene expression, and genome stability. In this study, the stability and folding dynamics of human telomeric DNA G-quadruplexes were investigated via enhanced sampling techniques. First, temperature-replica exchange MD (REMD) simulations were employed to compare the thermal stabilities among the five established folding topologies. The hybrid-2 type adopted by extended human telomeric sequence is revealed to be the most stable conformation in our simulations. Next, the free energy landscapes and folding intermediates of the hybrid-1 and -2 types were investigated with parallel tempering metadynamics simulations in the well-tempered ensemble. It was observed that the N-glycosidic conformations of guanines can flip over to accommodate into the cyclic Hoogsteen H-bonding on G-tetrads in which they were not originally involved. Furthermore, a hairpin and a triplex intermediate were identified for the folding of the hybrid-1 type conformation, whereas for the hybrid-2 type, there were no folding intermediates observed from its free energy surface. However, the energy barrier from its native topology to the transition structure is found to be extremely high compared to that of the hybrid-1 type, which is consistent with our stability predictions from the REMD simulations. We hope the insights presented in this work can help to complement current understanding on the stability and dynamics of G-quadruplexes, which is necessary not only to stabilize the structures but also to intervene their formation in genome.
An OFF-ON Two-Photon Fluorescent Probe for Tracking Cell Senescence in Vivo.

PubMed

Lozano-Torres, Beatriz; Galiana, Irene; Rovira, Miguel; Garrido, Eva; Chaib, Selim; Bernardos, Andrea; Muñoz-Espín, Daniel; Serrano, Manuel; Martínez-Máñez, Ramón; Sancenón, Félix

2017-07-05

A naphthalimide-based two-photon probe (AHGa) for the detection of cell senescence is designed. The probe contains a naphthalimide core, an l-histidine methyl ester linker, and an acetylated galactose bonded to one of the aromatic nitrogen atoms of the l-histidine through a hydrolyzable N-glycosidic bond. Probe AHGa is transformed into AH in senescent cells resulting in an enhanced fluorescent emission intensity. In vivo detection of senescence is validated in mice bearing tumor xenografts treated with senescence-inducing chemotherapy.
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay.

PubMed

Bashir, Sajid; Giannakopulos, Anastassios E; Derrick, Peter J; Critchley, Peter; Bottrill, Andrew; Padley, Henry J

2004-01-01

In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.
Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed Central

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-01-01

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65. PMID:2235481
Dielectric studies on mobility of the glycosidic linkage in seven disaccharides.

PubMed

Kaminski, K; Kaminska, E; Wlodarczyk, P; Pawlus, S; Kimla, D; Kasprzycka, A; Paluch, M; Ziolo, J; Szeja, W; Ngai, K L

2008-10-09

Isobaric dielectric relaxation measurements were performed on seven chosen disaccharides. For five of them, i.e., sucrose, maltose, trehalose, lactulose, and leucrose, we were able to observe the temperature evolution of the structural relaxation process. In the case of the other disaccharides studied (lactose and cellobiose), it was impossible to obtain such information because of the large contribution of the dc conductivity and polarization of the capacitor plates to the imaginary and real part of the complex permittivity, respectively. On the other hand, in the glassy state, two secondary relaxations have been identified in the dielectric spectra of all investigated carbohydrates. The faster one (gamma) is a common characteristic feature of the entire sugar family (mono-, di-, oligo-, and polysaccharide). The molecular origin of this process is still not unambiguously identified but is expected to involve intramolecular degrees of freedom as inferred from insensitivity of its relaxation time to pressure found in some monosaccharides (fructose and ribose). The slower one (labeled beta) was recently identified to be intermolecular in origin (i.e., a Johari-Goldstein (JG) beta-relaxation), involving twisting motion of the monosugar rings around the glycosidic bond. The activation energies and dielectric strengths for the beta-relaxation determined herein provide us valuable information about the flexibility of the glycosidic bond and the mobility of this particular linkage in the disaccharides studied. In turn, this information is essential for the control of the diffusivity of drugs or water entrapped in the sugar matrix.
Aroma Release in Wine Using Co-Immobilized Enzyme Aggregates.

PubMed

Ahumada, Katherine; Martínez-Gil, Ana; Moreno-Simunovic, Yerko; Illanes, Andrés; Wilson, Lorena

2016-11-08

Aroma is a remarkable factor of quality and consumer preference in wine, representing a distinctive feature of the product. Most aromatic compounds in varietals are in the form of glycosidic precursors, which are constituted by a volatile aglycone moiety linked to a glucose residue by an O -glycosidic bond; glucose is often linked to another sugar (arabinose, rhamnose or apiose). The use of soluble β-glycosidases for aroma liberation implies the addition of a precipitating agent to remove it from the product and precludes its reuse after one batch. An attractive option from a technological perspective that will aid in removing such constraints is the use of immobilized glycosidases. Immobilization by aggregation and crosslinking is a simple strategy producing enzyme catalysts of very high specific activity, being an attractive option to conventional immobilization to solid inert supports. The purpose of this work was the evaluation of co-immobilized β-glycosidases crosslinked aggregates produced from the commercial preparation AR2000, which contains the enzymes involved in the release of aromatic terpenes in Muscat wine (α-l-arabinofuranosidase and β-d-glucopyranosidase). To do so, experiments were conducted with co-immobilized crosslinked enzyme aggregates (combi-CLEAs), and with the soluble enzymes, using an experiment without enzyme addition as control. Stability of the enzymes at the conditions of winemaking was assessed and the volatiles composition of wine was determined by SPE-GC-MS. Stability of enzymes in combi-CLEAs was much higher than in soluble form, 80% of the initial activity remaining after 60 days in contact with the wine; at the same conditions, the soluble enzymes had lost 80% of their initial activities after 20 days. Such higher stabilities will allow prolonged use of the enzyme catalyst reducing its impact in the cost of winemaking. Wine treated with combi-CLEAs was the one exhibiting the highest concentration of total terpenes (18% higher than the control) and the highest concentrations of linalool (20% higher), nerol (20% higher) and geraniol (100% higher), which are the most important terpenes in determining Muscat typicity. Co-immobilized enzymes were highly stable at winemaking conditions, so their reutilization is possible and technologically attractive by reducing the impact of enzyme cost on winemaking cost.
Effect of dimer dissociation on activity and thermostability of the alpha-glucuronidase from Geobacillus stearothermophilus: dissecting the different oligomeric forms of family 67 glycoside hydrolases.

PubMed

Shallom, Dalia; Golan, Gali; Shoham, Gil; Shoham, Yuval

2004-10-01

The oligomeric organization of enzymes plays an important role in many biological processes, such as allosteric regulation, conformational stability and thermal stability. alpha-Glucuronidases are family 67 glycosidases that cleave the alpha-1,2-glycosidic bond between 4-O-methyl-D-glucuronic acid and xylose units as part of an array of hemicellulose-hydrolyzing enzymes. Currently, two crystal structures of alpha-glucuronidases are available, those from Geobacillus stearothermophilus (AguA) and from Cellvibrio japonicus (GlcA67A). Both enzymes are homodimeric, but surprisingly their dimeric organization is different, raising questions regarding the significance of dimerization for the enzymes' activity and stability. Structural comparison of the two enzymes suggests several elements that are responsible for the different dimerization organization. Phylogenetic analysis shows that the alpha-glucuronidases AguA and GlcA67A can be classified into two distinct subfamilies of bacterial alpha-glucuronidases, where the dimer-forming residues of each enzyme are conserved only within its own subfamily. It seems that the different dimeric forms of AguA and GlcA67A represent the two alternative dimeric organizations of these subfamilies. To study the biological significance of the dimerization in alpha-glucuronidases, we have constructed a monomeric form of AguA by mutating three of its interface residues (W328E, R329T, and R665N). The activity of the monomer was significantly lower than the activity of the wild-type dimeric AguA, and the optimal temperature for activity of the monomer was around 35 degrees C, compared to 65 degrees C of the wild-type enzyme. Nevertheless, the melting temperature of the monomeric protein, 72.9 degrees C, was almost identical to that of the wild-type, 73.4 degrees C. It appears that the dimerization of AguA is essential for efficient catalysis and that the dissociation into monomers results in subtle conformational changes in the structure which indirectly influence the active site region and reduce the activity. Structural and mechanistic explanations for these effects are discussed.
Effect of Dimer Dissociation on Activity and Thermostability of the α-Glucuronidase from Geobacillus stearothermophilus: Dissecting the Different Oligomeric Forms of Family 67 Glycoside Hydrolases

PubMed Central

Shallom, Dalia; Golan, Gali; Shoham, Gil; Shoham, Yuval

2004-01-01

The oligomeric organization of enzymes plays an important role in many biological processes, such as allosteric regulation, conformational stability and thermal stability. α-Glucuronidases are family 67 glycosidases that cleave the α-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and xylose units as part of an array of hemicellulose-hydrolyzing enzymes. Currently, two crystal structures of α-glucuronidases are available, those from Geobacillus stearothermophilus (AguA) and from Cellvibrio japonicus (GlcA67A). Both enzymes are homodimeric, but surprisingly their dimeric organization is different, raising questions regarding the significance of dimerization for the enzymes' activity and stability. Structural comparison of the two enzymes suggests several elements that are responsible for the different dimerization organization. Phylogenetic analysis shows that the α-glucuronidases AguA and GlcA67A can be classified into two distinct subfamilies of bacterial α-glucuronidases, where the dimer-forming residues of each enzyme are conserved only within its own subfamily. It seems that the different dimeric forms of AguA and GlcA67A represent the two alternative dimeric organizations of these subfamilies. To study the biological significance of the dimerization in α-glucuronidases, we have constructed a monomeric form of AguA by mutating three of its interface residues (W328E, R329T, and R665N). The activity of the monomer was significantly lower than the activity of the wild-type dimeric AguA, and the optimal temperature for activity of the monomer was around 35°C, compared to 65°C of the wild-type enzyme. Nevertheless, the melting temperature of the monomeric protein, 72.9°C, was almost identical to that of the wild-type, 73.4°C. It appears that the dimerization of AguA is essential for efficient catalysis and that the dissociation into monomers results in subtle conformational changes in the structure which indirectly influence the active site region and reduce the activity. Structural and mechanistic explanations for these effects are discussed. PMID:15466046
Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

2015-06-01

To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.
Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

USDA-ARS?s Scientific Manuscript database

New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...
Pyrolytic sugars from cellulosic biomass.

PubMed

Kuzhiyil, Najeeb; Dalluge, Dustin; Bai, Xianglan; Kim, Kwang Ho; Brown, Robert C

2012-11-01

Depolymerization of cellulose offers the prospect of inexpensive sugars from biomass. Breaking the glycosidic bonds of cellulose to liberate glucose has usually been pursued by acid or enzymatic hydrolysis although a purely thermal depolymerization route to sugars is also possible. Fast pyrolysis of pure cellulose yields primarily the anhydrosugar levoglucosan (LG) whereas the presence of naturally occurring alkali and alkaline earth metals (AAEMs) in biomass strongly catalyzes ring-breaking reactions that favor formation of light oxygenates. Here, we show a method of significantly increasing the yield of sugars from biomass by purely thermal means through infusion of certain mineral acids (phosphoric and sulfuric acid) into the biomass to convert the AAEMs into thermally stable salts (particularly potassium sulfates and phosphates). These salts not only passivate AAEMs that normally catalyze fragmentation of pyranose rings, but also buffer the system at pH levels that favor glycosidic bond breakage. It appears that AAEM passivation contributes to 80 % of the enhancement in LG yield while the buffering effect of the acid salts contributes to the balance of the enhancement. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
D-glucans from edible mushrooms: a review on the extraction, purification and chemical characterization approaches.

PubMed

Ruthes, Andrea Caroline; Smiderle, Fhernanda Ribeiro; Iacomini, Marcello

2015-03-06

D-Glucans from edible mushrooms present diversified chemical structures. The most common type consists of a backbone of β-D-glucose (1→3)-linked frequently branched at O-6 by β-D-glucose residues as side chains. However it is possible to distinguish α-, β- and mixed D-glucans. Further discrimination could be made on the basis of glycosidic bond position in a pyranoid ring, distribution of specific glycosidic bonds along the chain, branching and molecular weight. The present manuscript reviews the processes of extraction, purification and chemical characterization of D-glucans, such as NMR studies, methylation analysis, Smith degradation, and some other methodologies employed in carbohydrate chemistry characterization. In addition, these polysaccharides are important because they can provide many therapeutic benefits related to their biological activity in animals and humans, either immunostimulatory activity, inhibiting tumor growth, as well as exerting antinociceptive and anti-inflammatory action, among others, which are usually attached to their structure, molecular weight and degree of branching. Copyright © 2014 Elsevier Ltd. All rights reserved.
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.

PubMed

Wan, Qun; Parks, Jerry M; Hanson, B Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E; Graham, David E; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

2015-10-06

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.
Acetylated Triterpene Glycosides and Their Biological Activity from Holothuroidea Reported in the Past Six Decades

PubMed Central

Bahrami, Yadollah; Franco, Christopher M. M.

2016-01-01

Sea cucumbers have been valued for many centuries as a tonic and functional food, dietary delicacies and important ingredients of traditional medicine in many Asian countries. An assortment of bioactive compounds has been described in sea cucumbers. The most important and abundant secondary metabolites from sea cucumbers are triterpene glycosides (saponins). Due to the wide range of their potential biological activities, these natural compounds have gained attention and this has led to their emergence as high value compounds with extended application in nutraceutical, cosmeceutical, medicinal and pharmaceutical products. They are characterized by bearing a wide spectrum of structures, such as sulfated, non-sulfated and acetylated glycosides. Over 700 triterpene glycosides have been reported from the Holothuroidea in which more than 145 are decorated with an acetoxy group having 38 different aglycones. The majority of sea cucumber triterpene glycosides are of the holostane type containing a C18 (20) lactone group and either Δ7(8) or Δ9(11) double bond in their genins. The acetoxy group is mainly connected to the C-16, C-22, C-23 and/or C-25 of their aglycone. Apparently, the presence of an acetoxy group, particularly at C-16 of the aglycone, plays a significant role in the bioactivity; including induction of caspase, apoptosis, cytotoxicity, anticancer, antifungal and antibacterial activities of these compounds. This manuscript highlights the structure of acetylated saponins, their biological activity, and their structure-activity relationships. PMID:27527190
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

PubMed Central

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

2015-01-01

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen. PMID:26392527
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pK a values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. Themore » general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pK a values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pK a of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.« less
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

DOE PAGES

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; ...

2015-09-21

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pK a values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. Themore » general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pK a values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pK a of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.« less
Conformational study of the hydroxyproline-O-glycosidic linkage: sugar-peptide orientation and prolyl amide isomerization in (α/β)-galactosylated 4(R/S)-hydroxyproline.

PubMed

Naziga, Emmanuel B; Schweizer, Frank; Wetmore, Stacey D

2012-01-19

Glycosylation is a frequent post-translational modification of proteins that has been shown to influence protein structure and function. Glycosylation of hydroxyproline occurs widely in plants, but is absent in humans and animals. Previous experimental studies on model amides have indicated that α/β-galactosylation of 4R-hydroxyproline (Hyp) has no measurable effect on prolyl amide isomerization, while a 7% increase in the trans isomer population, as well as a 25-50% increase in the isomerization rate, was observed for the 4S stereoisomer (hyp). In this work, molecular dynamics simulations in explicit water and implicit solvent DFT optimizations are used to examine the structure of the hydroxyproline-O-galactosyl linkage and the effect of glycosylation on the structure and cis/trans isomerization of the peptide backbone. The calculations show two major minima with respect to the glycosidic linkage in all compounds. The C(γ)-exo puckering observed in 4R compounds projects the sugar away from the peptide backbone, while a twisted C(γ)-endo/C(β)-exo pucker in the 4S compounds brings the peptide and sugar rings together and leads to an intramolecular hydrogen-bonding interaction that is sometimes bridged by a water molecule. This hydrogen bond changes the conformation of the peptide backbone, inducing a favorable n → π* interaction between the oxygen lone pair from the prolyl N-terminal amide and the C═O, which explains the observed increase in trans isomer population in α/β-galactosylated 4S-hydroxyproline. Our results provide the first molecular level information about this important glycosidic linkage, as well as provide an explanation for the previously observed increase in trans isomer population in 4S-hyp compounds. Moreover, this study provides evidence that sugar-mediated long-range hydrogen bonding between hydroxyl groups and the carbonyl peptide backbone can modify the properties of N-terminal prolyl cis/trans isomerization in peptides.
Structures, chemotaxonomic significance, cytotoxic and Na(+),K(+)-ATPase inhibitory activities of new cardenolides from Asclepias curassavica.

PubMed

Zhang, Rong-Rong; Tian, Hai-Yan; Tan, Ya-Fang; Chung, Tse-Yu; Sun, Xiao-Hui; Xia, Xue; Ye, Wen-Cai; Middleton, David A; Fedosova, Natalya; Esmann, Mikael; Tzen, Jason T C; Jiang, Ren-Wang

2014-11-28

Five new cardenolide lactates (1–5) and one new dioxane double linked cardenolide glycoside (17) along with 15 known compounds (6–16 and 18–21) were isolated from the ornamental milkweed Asclepias curassavica. Their structures were elucidated by extensive spectroscopic methods (IR, UV, MS, 1D- and 2D-NMR). The molecular structures and absolute configurations of 1–3 and 17 were further confirmed by single-crystal X-ray diffraction analysis. Simultaneous isolation of dioxane double linked cardenolide glycosides (17–21) and cardenolide lactates (1–5) provided unique chemotaxonomic markers for this genus. Compounds 1–21 were evaluated for the inhibitory activities against DU145 prostate cancer cells. The dioxane double linked cardenolide glycosides showed the most potent cytotoxic effect followed by normal cardenolides and cardenolide lactates, while the C21 steroids were non-cytotoxic. Enzymatic assay established a correlation between the cytotoxic effects in DU145 cancer cells and the Ki for the inhibition of Na(+),K(+)-ATPase. Molecular docking analysis revealed relatively strong H-bond interactions between the bottom of the binding cavity and compounds 18 or 20, and explained why the dioxane double linked cardenolide glycosides possessed higher inhibitory potency on Na(+),K(+)-ATPase than the cardenolide lactate.

Synthesis of oxocarbon-encapsulated gold nanoparticles with blue-shifted localized surface plasmon resonance by pulsed laser ablation in water with CO2 absorbers

NASA Astrophysics Data System (ADS)

Del Rosso, T.; Rey, N. A.; Rosado, T.; Landi, S.; Larrude, D. G.; Romani, E. C.; Freire Junior, F. L.; Quinteiro, S. M.; Cremona, M.; Aucelio, R. Q.; Margheri, G.; Pandoli, O.

2016-06-01

Colloidal suspensions of oxocarbon-encapsulated gold nanoparticles have been synthesized in a one-step procedure by pulsed-laser ablation (PLA) at 532 nm of a solid gold target placed in aqueous solution containing CO2 absorbers, but without any stabilizing agent. Multi-wavelength surface enhanced Raman spectroscopy allows the identification of adsorbed amorphous carbon and graphite, Au-carbonyl, Au coordinated CO2-derived bicarbonates/carbonates and hydroxyl groups around the AuNPs core. Scanning electron microscopy, energy dispersive x-ray analysis and high resolution transmission electron microscopy highlight the organic shell structure around the crystalline metal core. The stability of the colloidal solution of nanocomposites (NCs) seems to be driven by solvation forces and is achieved only in neutral or basic pH using monovalent hydroxide counter-ions (NaOH, KOH). The NCs are characterized by a blue shift of the localized surface plasmon resonance (LSPR) band typical of metal-ligand stabilization by terminal π-back bonding, attributed to a core charging effect caused by Au-carbonyls. Total organic carbon measurements detect the final content of organic carbon in the colloidal solution of NCs that is about six times higher than the value of the water solution used to perform PLA. The colloidal dispersions of NCs are stable for months and are applied as analytical probes in amino glycoside antibiotic LSPR based sensing.
Synthesis of oxocarbon-encapsulated gold nanoparticles with blue-shifted localized surface plasmon resonance by pulsed laser ablation in water with CO2 absorbers.

PubMed

Del Rosso, T; Rey, N A; Rosado, T; Landi, S; Larrude, D G; Romani, E C; Junior, F L Freire; Quinteiro, S M; Cremona, M; Aucelio, R Q; Margheri, G; Pandoli, O

2016-06-24

Colloidal suspensions of oxocarbon-encapsulated gold nanoparticles have been synthesized in a one-step procedure by pulsed-laser ablation (PLA) at 532 nm of a solid gold target placed in aqueous solution containing CO2 absorbers, but without any stabilizing agent. Multi-wavelength surface enhanced Raman spectroscopy allows the identification of adsorbed amorphous carbon and graphite, Au-carbonyl, Au coordinated CO2-derived bicarbonates/carbonates and hydroxyl groups around the AuNPs core. Scanning electron microscopy, energy dispersive x-ray analysis and high resolution transmission electron microscopy highlight the organic shell structure around the crystalline metal core. The stability of the colloidal solution of nanocomposites (NCs) seems to be driven by solvation forces and is achieved only in neutral or basic pH using monovalent hydroxide counter-ions (NaOH, KOH). The NCs are characterized by a blue shift of the localized surface plasmon resonance (LSPR) band typical of metal-ligand stabilization by terminal π-back bonding, attributed to a core charging effect caused by Au-carbonyls. Total organic carbon measurements detect the final content of organic carbon in the colloidal solution of NCs that is about six times higher than the value of the water solution used to perform PLA. The colloidal dispersions of NCs are stable for months and are applied as analytical probes in amino glycoside antibiotic LSPR based sensing.
Cholesterol accelerates the binding of Alzheimer's β-amyloid peptide to ganglioside GM1 through a universal hydrogen-bond-dependent sterol tuning of glycolipid conformation

PubMed Central

Fantini, Jacques; Yahi, Nouara; Garmy, Nicolas

2013-01-01

Age-related alterations of membrane lipids in brain cell membranes together with high blood cholesterol are considered as major risk factors for Alzheimer's disease. Yet the molecular mechanisms by which these factors increase Alzheimer's risk are mostly unknown. In lipid raft domains of the plasma membrane, neurotoxic Alzheimer's beta-amyloid (Abeta) peptides interact with both cholesterol and ganglioside GM1. Recent data also suggested that cholesterol could stimulate the binding of Abeta to GM1 through conformational modulation of the ganglioside headgroup. Here we used a combination of physicochemical and molecular modeling approaches to decipher the mechanisms of cholesterol-assisted binding of Abeta to GM1. With the aim of decoupling the effect of cholesterol on GM1 from direct Abeta-cholesterol interactions, we designed a minimal peptide (Abeta5-16) containing the GM1-binding domain but lacking the amino acid residues involved in cholesterol recognition. Using the Langmuir technique, we showed that cholesterol (but not phosphatidylcholine or sphingomyelin) significantly accelerates the interaction of Abeta5-16 with GM1. Molecular dynamics simulations suggested that Abeta5-16 interacts with a cholesterol-stabilized dimer of GM1. The main structural effect of cholesterol is to establish a hydrogen-bond between its own OH group and the glycosidic-bond linking ceramide to the glycone part of GM1, thereby inducing a tilt in the glycolipid headgroup. This fine conformational tuning stabilizes the active conformation of the GM1 dimer whose headgroups, oriented in two opposite directions, form a chalice-shaped receptacle for Abeta. These data give new mechanistic insights into the stimulatory effect of cholesterol on Abeta/GM1 interactions. They also support the emerging concept that cholesterol is a universal modulator of protein-glycolipid interactions in the broader context of membrane recognition processes. PMID:23772214
The use of neutron scattering to determine the functional structure of glycoside hydrolase.

PubMed

Nakamura, Akihiko; Ishida, Takuya; Samejima, Masahiro; Igarashi, Kiyohiko

2016-10-01

Neutron diffraction provides different information from X-ray diffraction, because neutrons are scattered by atomic nuclei, whereas X-rays are scattered by electrons. One of the key advantages of neutron crystallography is the ability to visualize hydrogen and deuterium atoms, making it possible to observe the protonation state of amino acid residues, hydrogen bonds, networks of water molecules and proton relay pathways in enzymes. But, because of technical difficulties, less than 100 enzyme structures have been evaluated by neutron crystallography to date. In this review, we discuss the advantages and disadvantages of neutron crystallography as a tool to investigate the functional structure of glycoside hydrolases, with some examples. Copyright © 2016 Elsevier Ltd. All rights reserved.
Alkylpurine glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases.

PubMed

Kossmann, Bradley; Ivanov, Ivaylo

2014-07-01

Alkylpurine glycosylase D (AlkD) exhibits a unique base excision strategy. Instead of interacting directly with the lesion, the enzyme engages the non-lesion DNA strand. AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression. Since this strategy leaves the alkylated base solvent exposed, the means to achieve enzymatic cleavage had remained unclear. We determined a minimum energy path for flipping out a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the energetics of base extrusion. We show that AlkD acts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state. These states are almost equivalent in free energy and separated by low barriers. Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA. N-glycosidic bond scission is then facilitated by a backbone phosphate group proximal to the alkylated base.
Lead Optimization Studies on FimH Antagonists: Discovery of Potent and Orally Bioavailable Ortho-substituted Biphenyl Mannosides

PubMed Central

Han, Zhenfu; Pinkner, Jerome S.; Ford, Bradley; Chorell, Erik; Crowley, Jan M.; Cusumano, Corinne K.; Campbell, Scott; Henderson, Jeffrey P.; Hultgren, Scott J.; Janetka, James W.

2012-01-01

Herein, we describe the X-ray structure-based design and optimization of biaryl mannoside FimH inhibitors. Diverse modifications to the biaryl ring to improve drug-like physical and pharmacokinetic properties of mannosides were assessed for FimH binding affinity based on their effects on hemagglutination and biofilm formation along with direct FimH binding assays. Substitution on the mannoside phenyl ring ortho to the glycosidic bond results in large potency enhancements of several-fold higher than corresponding unsubstituted matched pairs and can be rationalized from increased hydrophobic interactions with the FimH hydrophobic ridge (Ile13) or “tyrosine gate” (Tyr137 and Tyr48) also lined by Ile52. The lead mannosides have increased metabolic stability and oral bioavailability as determined from in vitro PAMPA predictive model of cellular permeability and in vivo pharmacokinetic studies in mice, thereby representing advanced preclinical candidates with promising potential as novel therapeutics for the clinical treatment and prevention of recurring urinary tract infections. PMID:22449031
[superscript 1]H NMR Spectroscopy-Based Configurational Analysis of Mono- and Disaccharides and Detection of ß-Glucosidase Activity: An Undergraduate Biochemistry Laboratory

ERIC Educational Resources Information Center

Periyannan, Gopal R.; Lawrence, Barbara A.; Egan, Annie E.

2015-01-01

A [superscript 1]H NMR spectroscopy-based laboratory experiment explores mono- and disaccharide structural chemistry, and the enzyme-substrate specificity of glycosidic bond cleavage by ß-glucosidase towards cellobiose (ß-linked gluco-disaccharide) and maltose (a-linked gluco-disaccharide). Structural differences between cellobiose, maltose, and…
Utilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals

USDA-ARS?s Scientific Manuscript database

Inulins are polysaccharides that belong to an important class of carbohydrates known as fructans and are used by many plants as a means of storing energy. Inulins contain 20 to several thousand fructose units joined by ß-2,1 glycosidic bonds, typically with a terminal glucose unit. Plants with high ...
Fast characterization of C-glycoside acetophenones in Medemia argun male racemes (an Ancient Egyptian palm) using LC-MS analyses and computational study with their antioxidant effect

NASA Astrophysics Data System (ADS)

Ben Said, Ridha; Hamed, Arafa I.; Essalah, Khaled; Al-Ayed, Abdullah S.; Boughdiri, Salima; Tangour, Bahoueddine; Kowalczyk, Mariusz; Moldoch, Jaroslaw; Mahalel, Usama A.; Olezek, Wolesow; Stochmal, Anna

2017-10-01

Medemia argun is an ancient endemic palm growing in Nubian Desert of Egypt and Sudan. Liquid chromatography coupled with mass spectrometry in negative ion mode (LC/ESI-MS) has proved to be a potent tool for rapid identification and characterization of complex phytochemicals in male racemes of M. argun. A total of seven compounds were tentatively identified comprising of two C-glycoside acetophenones, along with the known compounds one stilbene derivative and four known flavonol derivatives from 40% methanolic portion. The product ions of acetophenone derivatives [M-H]- were shown to be cross-ring cleavages of the hexoside moiety [M-(90/120)-H]- characteristic for C-glycoside linkage. The position of Csbnd C-linkage was elucidated by DFT study using the Fukui functions and descriptors. The results revealed that hexose was conjugated with aglycones at C3 or C5. In addition, the theoretical antioxidant activity of compounds 6 and 7 was evaluated by using Bond Dissociation Enthalpy (BDE).
The physicochemical characterization and in vitro/in vivo evaluation of natural surfactants-based emulsions as vehicles for diclofenac diethylamine.

PubMed

Vucinić-Milanković, Nada; Savić, Snezana; Vuleta, Gordana; Vucinić, Slavica

2007-03-01

Two sugar-based emulsifiers, cetearyl alcohol & cetearyl glycoside and sorbitan stearate & sucrose cocoate, known as potential promoters of lamellar liquid crystals/gel phases, were investigated in order to formulate an optimal vehicle for amphiphilic drug - diclofenac diethylamine (DDA). Physico-chemical characterization and study of vehicle's physical stability were performed. Then, the in vitro DDA liberation profile, dependent on the mode of drug incorporation to the system, and the in vivo, short-term effects of chosen samples on skin parameters were examined. Droplets size distribution and rheological behavior indicated satisfying physical stability of both types of vehicles. Unexpectedly, the manner of DDA incorporation to the system had no significant influence on DDA release. In vivo study pointed to emulsion's favorable potential for skin hydration and barrier improvement, particularly in cetearyl glycoside-based vehicle.
Metabolic fate of cardiac glycosides and flavonoids upon fermentation of aqueous sea squill (Drimia maritima L.) extracts.

PubMed

Knittel, Diana N; Stintzing, Florian C; Kammerer, Dietmar R

2015-06-10

Sea squill (Drimia maritima L.) extracts have been used for centuries for the medical treatment of heart diseases. A procedure for the preparation of Drimia extracts applied for such purposes comprising a fermentation step is described in the German Homoeopathic Pharmacopoeia (GHP). However, little is known about the secondary metabolite profile of such extracts and the fate of these components upon processing and storage. Thus, in the present study sea squill extracts were monitored during fermentation and storage by HPLC-DAD-MS(n) and GC-MS to characterise and quantitate individual cardiac glycosides and phenolic compounds. For this purpose, a previously established HPLC method for the separation and quantitation of pharmacologically relevant cardiac glycosides (bufadienolides) was validated. Within 12 months of storage, total bufadienolide contents decreased by about 50%, which was attributed to microbial and plant enzyme activities. The metabolisation and degradation rates of individual bufadienolide glycosides significantly differed, which was attributed to differing structures of the aglycones. Further degradation of bufadienolide aglycones was also observed. Besides reactions well known from human metabolism studies, dehydration of individual compounds was monitored. Quantitatively predominating flavonoids were also metabolised throughout the fermentation process. The present study provides valuable information about the profile and stability of individual cardiac glycosides and phenolic compounds in fermented Drimia extracts prepared for medical applications, and expands the knowledge of cardiac glycoside conversion upon microbial fermentation. Copyright © 2015 Elsevier B.V. All rights reserved.
Utilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals.

PubMed

Hughes, Stephen R; Qureshi, Nasib; López-Núñez, Juan Carlos; Jones, Marjorie A; Jarodsky, Joshua M; Galindo-Leva, Luz Ángela; Lindquist, Mitchell R

2017-04-01

Inulins are polysaccharides that belong to an important class of carbohydrates known as fructans and are used by many plants as a means of storing energy. Inulins contain 20 to several thousand fructose units joined by β-2,1 glycosidic bonds, typically with a terminal glucose unit. Plants with high concentrations of inulin include: agave, asparagus, coffee, chicory, dahlia, dandelion, garlic, globe artichoke, Jerusalem artichoke, jicama, onion, wild yam, and yacón. To utilize inulin as its carbon and energy source directly, a microorganism requires an extracellular inulinase to hydrolyze the glycosidic bonds to release fermentable monosaccharides. Inulinase is produced by many microorganisms, including species of Aspergillus, Kluyveromyces, Penicillium, and Pseudomonas. We review various inulinase-producing microorganisms and inulin feedstocks with potential for industrial application as well as biotechnological efforts underway to develop sustainable practices for the disposal of residues from processing inulin-containing crops. A multi-stage biorefinery concept is proposed to convert cellulosic and inulin-containing waste produced at crop processing operations to valuable biofuels and bioproducts using Kluyveromyces marxianus, Yarrowia lipolytica, Rhodotorula glutinis, and Saccharomyces cerevisiae as well as thermochemical treatments.
Lactosylamidine-based affinity purification for cellulolytic enzymes EG I and CBH I from Hypocrea jecorina and their properties.

PubMed

Ogata, Makoto; Kameshima, Yumiko; Hattori, Takeshi; Michishita, Kousuke; Suzuki, Tomohiro; Kawagishi, Hirokazu; Totani, Kazuhide; Hiratake, Jun; Usui, Taichi

2010-12-10

Selective adsorption and separation of β-glucosidase, endo-acting endo-β-(1→4)-glucanase I (EG I), and exo-acting cellobiohydrolase I (CBH I) were achieved by affinity chromatography with β-lactosylamidine as ligand. A crude cellulase preparation from Hypocrea jecorina served as the source of enzyme. When crude cellulase was applied to the lactosylamidine-based affinity column, β-glucosidase appeared in the unbound fraction. By contrast, EG I and CBH I were retained on the column and then separated from each other by appropriately adjusting the elution conditions. The relative affinities of the enzymes, based on their column elution conditions, were strongly dependent on the ligand. The highly purified EG I and CBH I, obtained by affinity chromatography, were further purified by Mono P and DEAE chromatography, respectively. EG I and CBH I cleave only at the phenolic bond in p-nitrophenyl glycosides with lactose and N-acetyllactosamine (LacNAc). By contrast, both scissile bonds in p-nitrophenyl glycosides with cellobiose were subject to hydrolysis although with important differences in their kinetic parameters. Copyright © 2010 Elsevier Ltd. All rights reserved.
Microwave-assisted ionic liquid-mediated rapid catalytic conversion of non-edible lignocellulosic Sunn hemp fibres to biofuels.

PubMed

Paul, Souvik Kumar; Chakraborty, Saikat

2018-04-01

Sunn hemp fibre - a cellulose-rich crystalline non-food energy crop, containing 75.6% cellulose, 10.05% hemicellulose, 10.32% lignin, with high crystallinity (80.17%) and degree of polymerization (650) - is identified as a new non-food substrate for lignocellulosic biofuel production. Microwave irradiation is employed to rapidly rupture the cellulose's glycosidic bonds and enhance glucose yield to 78.7% at 160 °C in only 46 min. The reactants - long-chain cellulose, ionic liquid, transition metal catalyst, and water - form a polar supramolecular complex that rotates under the microwave's alternating polarity and rapidly dissipates the electromagnetic energy through molecular collisions, thus accelerating glycosidic bond breakage. In 46 min, 1 kg of Sunn hemp fibres containing 756 g of cellulose produces 595 g of glucose at 160 °C, and 203 g of hydroxymethyl furfural (furanic biofuel precursor) at 180 °C. Yeast mediated glucose fermentation produces 75.6% bioethanol yield at 30 °C, and the ionic liquid is recycled for cost-effectiveness. Copyright © 2018 Elsevier Ltd. All rights reserved.
Preliminary X-ray diffraction analysis of a thermophilic β-1,3-1,4-glucanase from Clostridium thermocellum.

PubMed

Zhang, Lilan; Zhao, Puya; Chen, Chun-Chi; Huang, Chun-Hsiang; Ko, Tzu-Ping; Zheng, Yingying; Guo, Rey-Ting

2014-07-01

β-1,3-1,4-Glucanases catalyze the specific hydrolysis of internal β-1,4-glycosidic bonds adjacent to the 3-O-substituted glucose residues in mixed-linked β-glucans. The thermophilic glycoside hydrolase CtGlu16A from Clostridium thermocellum exhibits superior thermal profiles, high specific activity and broad pH adaptability. Here, the catalytic domain of CtGlu16A was expressed in Escherichia coli, purified and crystallized in the trigonal space group P3121, with unit-cell parameters a=b=74.5, c=182.9 Å, by the sitting-drop vapour-diffusion method and diffracted to 1.95 Å resolution. The crystal contains two protein molecules in an asymmetric unit. Further structural determination and refinement are in progress.
Investigation of an "alternate water supply system" in enzymatic hydrolysis in the processive endocellulase Cel7A from Rasamsonia emersonii by molecular dynamics simulation.

PubMed

Sun, Xun; Qian, Meng-Dan; Guan, Shan-Shan; Shan, Ya-Ming; Dong, Ying; Zhang, Hao; Wang, Song; Han, Wei-Wei

2017-02-01

Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation. In addition, four strong hydrophobic interactions are also determined. The domain cross-correlation map analysis shows movement correlation of protein including autocorrelation between residues. The root mean square fluctuations analysis represents the various flexibilities of different fragment in the two conformations. Comparing the two conformations reveals the water-supply mechanism of selective hydrolysis of cellulose in Cel7A. The mechanism can be described as follow. When the reducing end of substrate slides from the unhydrolyzing site (sliding conformation) to the hydrolyzing site (hydrolyzing conformation), His225 is pushed down and rotated, the rotation leads to the movement of Glu209 with the interstrand hydrogen bonding in β-sheet. It further makes Asp211 close to the hydrolysis center and provides a water molecule bounding on its carboxyl in the previous unhydrolyzing site. After the hydrolysis takes place and the product is excluded from the enzyme, the Asp211 comes back to its initial position. In summary, Asp211 acts as an elevator to transport outer water molecules into the hydrolysis site for every other glycosidic bond. © 2016 Wiley Periodicals, Inc.
X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

NASA Astrophysics Data System (ADS)

Prokofev, I. I.; Lashkov, A. A.; Gabdulkhakov, A. G.; Balaev, V. V.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

2016-11-01

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2'-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation
X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prokofev, I. I.; Lashkov, A. A., E-mail: alashkov83@gmail.com; Gabdulkhakov, A. G.

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data,more » supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2′-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation.« less
Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayes, Heather B.; Knott, Brandon C.; Crowley, Michael F.

In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase ( TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleavingmore » the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2S O ring configuration as it reaches its binding site. Lastly, this work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.« less
Blackbody infrared radiative dissociation of protonated oligosaccharides.

PubMed

Fentabil, Messele A; Daneshfar, Rambod; Kitova, Elena N; Klassen, John S

2011-12-01

The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel(6)), which is composed of β-(1→4)-linked glucopyranose rings, and five malto-oligosaccharides (Mal(x), where x=4-8), which are composed of α-(1→4)-linked glucopyranose units. At the temperatures investigated (85-160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B(1) and B(2)) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (E(a) and A) were determined. The E(a) and A-factors measured for protonated Mal(x) (x>4) are indistinguishable within error (~19 kcal mol(-1), 10(10) s(-1)), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel(6) (24 kcal mol(-1), 10(12) s(-1)) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage. © American Society for Mass Spectrometry, 2011

Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Bing; Kognole, Abhishek A.; Wu, Miao

Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for bothmore » aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.« less
The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases.

PubMed

Iglesias-Fernández, Javier; Raich, Lluís; Ardèvol, Albert; Rovira, Carme

2015-02-01

Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer-Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2 S O → [ 2,5 B] ǂ → 5 S 1 and 1 S 3 → [ 4 H 3 ] ǂ → 4 C 1 , which clearly appear in low energy regions of the FEL. Consistently, 2 S O and 1 S 3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the O E → [ O S 2 ] ǂ → B 2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed O E conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.
Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases

DOE PAGES

Mayes, Heather B.; Knott, Brandon C.; Crowley, Michael F.; ...

2016-06-01

In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase ( TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleavingmore » the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2S O ring configuration as it reaches its binding site. Lastly, this work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.« less
The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4sc02240h Click here for additional data file.

PubMed Central

Iglesias-Fernández, Javier; Raich, Lluís; Ardèvol, Albert

2015-01-01

Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer–Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2SO → [2,5B]ǂ → 5S1 and 1S3 → [4H3]ǂ → 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE → [OS2]ǂ → B2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed OE conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases. PMID:29560204
Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi

PubMed Central

2011-01-01

Background Lignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production. Results The study herein shows comprehensive functional characterization of crude body extracts from Coptotermes gestroi along with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract from C. gestroi was enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in the C. gestroi digestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in the C. gestroi digestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis. Conclusions Here we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termite C. gestroi. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29). PMID:22081966
Carbohydrate Analysis Experiment Involving Mono- and Disaccharides with a Twist of Glycobiology: Two New Tests for Distinguishing Pentoses and Glycosidic Bonds

ERIC Educational Resources Information Center

Herdman, Chelsea; Diop, Lamine; Dickman, Michael

2013-01-01

Carbohydrate analysis is an excellent way to expose second-year biochemistry majors to the subtlety and nuance of sugar chemistry. In one, 3-h practical period, students must identify an unknown mono- or disaccharide from a collection of three hexoses (glucose, galactose, and mannose), two pentoses (ribose and arabinose), and three disaccharides…
A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad

PubMed Central

Sarian, Fean D.; Janeček, Štefan; Pijning, Tjaard; Ihsanawati; Nurachman, Zeily; Radjasa, Ocky K.; Dijkhuizen, Lubbert; Natalia, Dessy; van der Maarel, Marc J. E. C.

2017-01-01

α-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia. In BmaN1 the third residue, the aspartic acid that acts as the transition state stabilizer, was replaced by a histidine. Three-dimensional structure modeling of the BmaN1 amino acid sequence confirmed the aberrant catalytic triad. Glucose and maltose were found as products of the action of the novel α-amylase on soluble starch, demonstrating that it is active in spite of the peculiar catalytic triad. This novel BmaN1 α-amylase is part of a group of α-amylases that all have this atypical catalytic triad, consisting of aspartic acid, glutamic acid and histidine. Phylogenetic analysis showed that this group of α-amylases comprises a new subfamily of the glycoside hydrolase family 13. PMID:28287181
Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

PubMed Central

Zhang, Liangyi; Reilly, James P.

2009-01-01

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v- and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds. PMID:19113943
Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

NASA Astrophysics Data System (ADS)

Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

2017-04-01

We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms . Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.
The preparation of Cistanche phenylethanoid glycosides liquid proliposomes: Optimized formulation, characterization and proliposome dripping pills in vitro and in vivo evaluation.

PubMed

Li, Meng; Li, Yunjing; Liu, Weiwei; Li, Rongli; Qin, Cuiying; Liu, Nan; Han, Jing

2016-10-10

Water-soluble Cistanche phenylethanoid glycosides (CPhGs) have poor permeability and low bioavailability. However, liposomes can improve the permeability of such drugs and their poor stability, and proliposomes have been used to overcome these problems. Based on this, Cistanche phenylethanoid glycoside liquid proliposomes (CPhGsP) and dripping(?) pills were prepared and optimized using response surface methodology. The properties of CPhGsP were evaluated in terms of their encapsulation efficiency, particle size, zeta potential, and morphology. The results obtained showed that the optimal formulation was drug/soybean phospholipid/poloxamer-188/sodium deoxycholate/propylene glycol 1:22.38:3.52:0.84:80 (w/w/w/w/v). This resulted in an encapsulation efficiency, particle size, and zeta potential of hydrated proliposomes with phosphate buffer solution (pH7.4) of 51.97%, 671.7nm, and -25.49mV, respectively. Stability testing of CPhGsP and CPhGs ordinary liposomes was carried out for 3months at 4±2°C, 25±2°C, 40±2°C, 75±5% RH. The results obtained showed that the stability of the proliposomes was better than that of ordinary liposomes at the same temperature, while a lower temperature of 4°C is ideal for storage. Cistanche phenylethanoid glycoside liquid proliposomes dripping pills (CPhGsPD) are efficiently released in gastrointestinal solution as shown by in vitro release experiments and the structure of the liposomes does not destroy the proliposome dripping pills by hydration. In vivo experiments showed that the areas under the plasma level-time curves and peak concentrations of CPhGsPD and hydrated proliposomes were higher than those of CPhGs. Moreover, with CPhGsPD, the pharmacokinetic parameters were similar to those with hydrated proliposomes. These results showed that CPhGsPD offer a good way to improve the oral delivery of CPhGs. Copyright © 2016 Elsevier B.V. All rights reserved.
A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation

PubMed Central

Sattelle, Benedict M.; Shakeri, Javad; Roberts, Ian S.; Almond, Andrew

2010-01-01

The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-strucutre at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without 15N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the β(1→3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the β(1→3) ψ dihedral (as previously predicted by simulation), while the β(1→4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties. PMID:20022001
Putative identification of new p-coumaroyl glycoside flavonoids in grape by ultra-high performance liquid chromatography/high-resolution mass spectrometry.

PubMed

Panighel, Annarita; De Rosso, Mirko; Dalla Vedova, Antonio; Flamini, Riccardo

2015-02-28

Grape polyphenols are antioxidant compounds, markers in vine chemotaxonomy, and involved in color stabilization of red wines. Sugar acylation usually confers higher stability on glycoside derivatives and this effect is enhanced by an aromatic substituent such as p-coumaric acid. Until now, only p-coumaroyl anthocyanins have been found in grape. A method of 'suspect screening analysis' by ultra-high-performance liquid chromatography/high-resolution mass spectrometry (UHPLC/QTOFMS) has recently been developed to study grape metabolomics. In the present study, this approach was used to identify new polyphenols in grape by accurate mass measurement, MS/MS fragmentation, and study of correlations between fragments observed and putative structures. Three putative p-coumaroyl flavonoids were identified in Raboso Piave grape extract: a dihydrokaempferide-3-O-p-coumaroylhexoside-like flavanone, isorhamnetin-3-O-p-coumaroylglucoside, and a chrysoeriol-p-coumaroylhexoside-like flavone. Accurate MS provided structural characterization of functional groups, and literature data indicates their probable position in the molecule. A fragmentation scheme is proposed for each compound. Compounds were identified by overlapping various analytical methods according to recommendations in the MS-based metabolomics literature. Stereochemistry and the definitive position of substituents in the molecule can only be confirmed by isolation and characterization or synthesis of each compound. These findings suggest addressing research of acylated polyphenol glycosides to other grape varieties. Copyright © 2015 John Wiley & Sons, Ltd.
Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, A. E., E-mail: schmidt@omrb.pnpi.spb.ru; Shvetsov, A. V.; Kuklin, A. I.

2016-01-15

Glucoamylase from fungus Aspergillus awamori is glycoside hydrolase that catalyzes the hydrolysis of α-1,4- and α-1,6-glucosidic bonds in glucose polymers and oligomers. This glycoprotein consists of a catalytic domain and a starch-binding domain connected by an O-glycosylated polypeptide chain. The conformation of the linker, the relative arrangement of the domains, and the structure of the full-length enzyme are unknown. The structure of the recombinant glucoamylase GA1 was studied by molecular modelling and small-angle neutron scattering (SANS) methods. The experimental SANS data provide evidence that glucoamylase exists as a monomer in solution and contains a glycoside component, which makes a substantialmore » contribution to the scattering. The model of full-length glucoamylase, which was calculated without taking into account the effect of glycosylation, is consistent with the experimental data and has a radius of gyration of 33.4 ± 0.6 Å.« less
Natural macromolecules with protective and antitumor activity.

PubMed

Cioanca, Oana; Trifan, Adriana; Mircea, Cornelia; Dragos, Scripcariu; Hancianu, Monica

2018-04-24

This review summarizes the literature data regarding plant lectins and as novel drug sources in prevention or treatment of cancer. Moreover, such compounds have been described as natural toxins that possess different biological activities (cytotoxic, antitumor, antimutagenic and anticarcinogenic properties). This activity depends greatly on their structure and affinity. Most of the mushroom heterosides are known as β-glucans with β-(1→3)-glycosidic bonds. It is thought that their conformation, bonds, molecular size can modulate the immune response by triggering different receptors. The mechanism on normal and tumor cells of various plant and mushroom polysaccharides and lectins is briefly presented in this paper. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
[Sugar Chain Construction of Functional Natural Products Using Plant Glucosyltransferases].

PubMed

Mizukami, Hajime

2015-01-01

Plant secondary product glycosyltransferases belong to family 1 of the glycosyltransferase superfamily and mediate the transfer of a glycosyl residue from activated nucleotide sugars to lipophilic small molecules, thus affecting the solubility, stability and pharmacological activities of the sugar-accepting compounds. The biotechnological application of plant glycosyltransferases in glycoside synthesis has attracted attention because enzymatic glycosylation offers several advantages over chemical methods, including (1) avoiding the use of harsh conditions and toxic catalysts, (2) providing strict control of regio-and stereo-selectivity and (3) high efficiency. This review describes the in vivo and in vitro glycosylation of natural organic compounds using glycosyltransferases, focusing on our investigation of enzymatic synthesis of curcumin glycosides. Our current efforts toward functional characterization of some glycosyltransferases involved in the biosynthesis of iridoids and crocin, as well as in the sugar chain elongation of quercetin glucosides, are described. Finally, I describe the relationship of the structure of sugar chains and the intestinal absorption which was investigated using chemoenzymatically synthesized quercetin glycosides.
Asymmetric Synthesis of Apratoxin E.

PubMed

Mao, Zhuo-Ya; Si, Chang-Mei; Liu, Yi-Wen; Dong, Han-Qing; Wei, Bang-Guo; Lin, Guo-Qiang

2016-10-21

An efficient method for asymmetric synthesis of apratoxin E 2 is described in this report. The chiral lactone 8, recycled from the degradation of saponin glycosides, was utilized to prepare the non-peptide fragment 6. In addition to this "from nature to nature" strategy, olefin cross-metathesis (CM) was applied as an alternative approach for the formation of the double bond. Moreover, pentafluorophenyl diphenylphosphinate was found to be an efficient condensation reagent for the macrocyclization.
Amylases and Their Importance during Glycan Degradation: Genome Sequence Release of Salmonella Amylase Knockout Strains.

PubMed

Arabyan, Narine; Huang, Bihua C; Weimer, Bart C

2017-05-18

Amylases catalyze the cleavage of α-d-1,4 and α-d-1,6-glycosidic bonds in starch and related carbohydrates. Amylases are widely distributed in nature and are important in carbohydrate metabolism. This is the release of four single and two double deletions in Salmonella enterica serovar Typhimurium LT2 that are important for glycan degradation during infection. Copyright © 2017 Arabyan et al.
Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ito, Tasuku; Saikawa, Kyo; Kim, Seonah

2014-04-25

Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - Abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-L-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-L-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system ofmore » hydroxyproline-linked β-L-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-L-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn{sup 2+} coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-L-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.« less
Carbohydrate binding specificity of pea lectin studied by NMR spectroscopy and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Cheong, Youngjoo; Shim, Gyuchang; Kang, Dongil; Kim, Yangmee

1999-02-01

The conformational details of Man( α1,6)Man( α)OMe are investigated through NMR spectroscopy in conjunction with molecular modeling. The lowest energy structure (M1) in the adiabatic energy map calculated with a dielectric constant of 50 has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=180°. The other low energy structure (M2) has glycosidic dihedral angles of φ=-60°, ψ=180° and ω=-60°. Molecular dynamics simulations and NMR experiments prove that Man( α1,6)Man( α)OMe in the free form exists with conformational averaging of M1 and M2 conformers predominantly. Molecular dynamics simulations of the pea lectin-carbohydrate complex with explicit water molecules starting from the X-ray crystallographic structure of pea lectin show that the protein-carbohydrate interaction centers mainly on the hydrogen bonds and van der Waals interactions between protein and carbohydrate. From the molecular dynamics simulation, it is found that the M1 structure can bind to pea lectin better than the M2 structure. The origin of this selectivity is the water- mediated hydrogen bond interactions between the remote mannose and the binding site of pea lectin as well as the direct hydrogen bond interaction between the terminal mannose and pea lectin. Extensive networks of interactions in the carbohydrate binding site and the metal binding site are important in maintaining the carbohydrate binding properties of pea lectin. Especially, the predominant factors of mannose binding specificity of pea lectin are the hydrogen bond interactions between the 4th hydroxyl groups of the terminal sugar ring and the side chains of Asp-81 and Asn-125 in the carbohydrate binding site, and the additional interactions between these side chains of Asp-81 and Asn-125 and the calcium ion in the metal binding site of pea lectin.
A coarse-grained model for synergistic action of multiple enzymes on cellulose

DOE PAGES

Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; ...

2012-08-01

In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose,more » several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.« less

Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight into the Degradation (of a Polysaccharide from) Red Seaweeds*

PubMed Central

Hehemann, Jan-Hendrik; Smyth, Leo; Yadav, Anuj; Vocadlo, David J.; Boraston, Alisdair B.

2012-01-01

Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating d-galactose and 3,6-anhydro-l-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-l-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-l-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds. PMID:22393053
All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.
Structural characterization and identification of iridoid glycosides, saponins, phenolic acids and flavonoids in Flos Lonicerae Japonicae by a fast liquid chromatography method with diode-array detection and time-of-flight mass spectrometry.

PubMed

Qi, Lian-Wen; Chen, Chun-Yun; Li, Ping

2009-10-01

A fast liquid chromatography method with diode-array detection (DAD) and time-of-flight mass spectrometry (TOF-MS) has been developed for analysis of constituents in Flos Lonicerae Japonicae (FLJ), a traditional Chinese medicine derived from the flower bud of Lonicera japonica. The chromatographic analytical time decreased to 25 min without sacrificing resolution using a column packed with 1.8-microm porous particles (4.6 x 50 mm), three times faster than the performance of conventional 5.0-microm columns (4.6 x 150 mm). Four major groups of compounds previously isolated from FLJ were structurally characterized by DAD-TOF-MS: iridoid glycosides showed maximum UV absorption at 240 nm; phenolic acids at 217, 242, and 326 nm; flavonoids at 255 and 355 nm; while saponins had no absorption. In electrospray ionization (ESI)-TOF-MS experiments, elimination of a glucose unit (162 Da), and successive losses of H(2)O, CH(3)OH and CO, were generally observed in iridoid glycosides; saponins were characterized by a series of identical aglycone ions; phenolic acids typically generated a base peak at [M-H-caffeoyl](-) by loss of a caffeic acid unit (162 Da) and several marked quinic acid moiety ions; cleavage of the glycosidic bond (loss of 162 or 308 Da), subsequent losses of H(2)O, CO, RDA and C-ring fragmentation were the most possible fragmentation pathways for flavonoids. By accurate mass measurements within 4 ppm error for each molecular ion and subsequent fragment ions, as well as the 'full mass spectral' information of TOF-MS, a total of 41 compounds including 13 iridoid glycosides, 11 phenolic acids, 7 saponins, and 10 flavonoids were identified in a methanolic extract of FLJ. Copyright (c) 2009 John Wiley & Sons, Ltd.
"Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.

PubMed

Nakamura, Akihiko; Ishida, Takuya; Kusaka, Katsuhiro; Yamada, Taro; Fushinobu, Shinya; Tanaka, Ichiro; Kaneko, Satoshi; Ohta, Kazunori; Tanaka, Hiroaki; Inaka, Koji; Higuchi, Yoshiki; Niimura, Nobuo; Samejima, Masahiro; Igarashi, Kiyohiko

2015-08-01

Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.
Comparative studies on the chemical and enzymatic stability of alpa-and beta-arbutin

USDA-ARS?s Scientific Manuscript database

Alpha and beta arbutin are glycoside derivatives used as skin whitening agents. Both compounds interfere with tyrosinases activity in a fashion similar to their aglycone hydroquinone. Hydroquinone has been associated with ochronosis and possible carcinogenic effect. Due to their structural similarit...
Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.

PubMed

Frandsen, Kristian E H; Poulsen, Jens Christian Navarro; Tovborg, Morten; Johansen, Katja S; Lo Leggio, Leila

2017-01-01

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.
Complete structure of the polysaccharide from Streptococcus sanguis J22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1990-01-09

The cell wall polysaccharides of certain oral streptococci such as Streptococcus sanguis strains 34 and J22, although immunologically distinct, act as receptors for the fimbrial lectins of Actinomyces viscosus T14V. The authors report the complete covalent structure of the polysaccharide from S. sanguis J22 which is composed of a heptasaccharide subunit linked by phosphodiester bonds. The repeating subunit, which contains {alpha}-GalNAc, {alpha}-rhamnose, {beta}-rhamnose, {beta}-glucose, and {beta}-galactose all in the pyranoside form and {beta}-galactofuranose, is compared with the previously published structure of the polysaccharide from strain 34. The structure has been determined almost exclusively by high-resolution nuclear magnetic resonance methods. Themore » {sup 1}H and {sup 13}C NMR spectra of the polysaccharides from both strains 34 and J22 have been completely assigned. The stereochemistry of pyranosides was assigned from J{sub H-H} values determined from phase-sensitive COSY spectra, and acetamido sugars were assigned by correlation of the resonances of the amide {sup 1}H with the sugar ring protons. The {sup 13}C spectra were assigned by {sup 1}H-detected multiple-quantum correlation (HMQC) spectra, and the assignments were confirmed by {sup 1}H-detected multiple-bond correlation (HMBC) spectra. The positions of the glycosidic linkages were assigned by detection of three-bond {sup 1}H-{sup 13}C correlation across the glycosidic linkage in the HMBC spectra. The positions of the phosphodiester linkages were determined by splittings observed in the {sup 13}C resonances due to {sup 31}P coupling and also by {sup 1}H-detected {sup 31}P correlation spectroscopy.« less
Synthesis of Chrysogeside B from Halotolerant Fungus Penicillium and Its Antimicrobial Activities Evaluation

NASA Astrophysics Data System (ADS)

Liu, Ruiquan; Wang, Lei; Li, Qibo; Liao, Min; Yang, Zhikun; Huang, Yun; Lv, Cong; Zheng, Bing; Zhong, Jiangchun; Bian, Qinghua; Wang, Min; Liu, Shangzhong

2017-04-01

Chrysogeside B, a natural cerebroside, was efficiently synthesized from commercial feedstocks. The bioassays showed that compounds 4, 5 and 6 exhibited enhanced biological activities compared Chrysogeside B. Further studies revealed that free hydroxyl groups and glycosidic bond have significant impact on the antimicrobial activities. The synthesis of Chrysogeside B and analogues designed to allow identification of the features of this glycolipid required for recognition by tested bacteria and Hela cells is described.
Dissociation reactions of protonated anthracycline antibiotics following electrospray ionization-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Sleno, Lekha; Campagna-Slater, Valerie; Volmer, Dietrich A.

2006-09-01

Fragmentation pathways of doxorubicin, a common cancer therapy agent, and three closely related analogs (epirubicin, daunorubicin, idarubicin) were compared using electrospray ionization with tandem mass spectrometry. This class of antibiotics with anti-tumour activity has important structural features, with a tetracyclic aromatic, polyketide portion, which is glycosylated with an amino sugar in order to exhibit its biological activity. Collision-induced dissociation spectra revealed very similar product ions for each analog, however, important differences were seen in the relative abundances and the ease at which certain fragments were formed. Fragment ions observed included those from cleavage of the glycosidic bond, loss of the side chain from the aglycone moiety, water losses and loss of a methyl radical. Following cleavage of the glycosidic bond, the charge can either reside on the aglycone portion or the sugar moiety, and each of these primary fragments undergoes several secondary dissociation pathways, depending on the collision energy. By ramping the collision voltage, we were able to correlate the changes in fragmentation behavior with small alterations in the structure of the precursor ion. The detailed study of the fragmentation behavior of doxorubicin was supported by accurate mass measurements, using an electrospray-time of flight instrument, as well as MS3 data from a quadrupole-linear ion trap mass spectrometer. Computational studies were also performed to help explain the role of certain functional groups in the fragmentation reactions.
The conformational free-energy landscape of β-D-mannopyranose: evidence for a (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary in β-mannosidases.

PubMed

Ardèvol, Albert; Biarnés, Xevi; Planas, Antoni; Rovira, Carme

2010-11-17

The mechanism of glycosidic bond cleavage by glycosidases involves substrate ring distortions in the Michaelis complex that favor catalysis. Retaining β-mannosidases bind the substrate in a (1)S(5) conformation, and recent experiments have proposed an unusual substrate conformational pathway ((1)S(5) → B(2,5) → (O)S(2)) for the hydrolysis reaction. By means of Car-Parrinello metadynamics simulations, we have obtained the conformational free-energy surface (FES) of a β-d-mannopyranose molecule associated with the ideal Stoddart conformational diagram. We have found that (1)S(5) is among the most stable conformers and simultaneously is the most preactivated conformation in terms of elongation/shortening of the C1-O1/C1-O5 bonds, C1-O1 orientation, and charge development at the anomeric carbon. Analysis of the computed FES gives support to the proposed (1)S(5) → B(2,5) → (O)S(2) catalytic itinerary, showing that the degree of preactivation of the substrate in glycoside hydrolases (GHs) is related to the properties of an isolated sugar ring. We introduce a simple preactivation index integrating several structural, electronic, and energetic properties that can be used to predict the conformation of the substrate in the Michaelis complex of any GH.
Hydrogen bonding in the neutron structure of the mononucleotide 5'-UMP disodium salt

NASA Astrophysics Data System (ADS)

Chitra, R.; Ranjan-Choudhury, R.; Ramanadham, M.

Disodium uridine 5'-monophosphate heptahydrate (5'-UMPNa2), Na2[C9H11N2O9P].7H2O, crystallises in space group C2221 with a=22.985, b=8.911 and c=19.494Å. A neutron beam of λ=1.216Å was used; Z=8 and V=3992.75Å3. Data consisted of 1785 unique reflections. Na ions were connected to the main molecule through water molecules and sugar oxygens. One of the Na ions occupied a special position, and the other at a general position was partially disordered. The uracil base was planar, and had anti conformation about the glycosidic bond. The sugar had C(2') endo conformation and was gauche-gauche.
Effects of Chemical Cross-linkers on Caries-affected Dentin Bonding

PubMed Central

Macedo, G.V.; Yamauchi, M.; Bedran-Russo, A.K.

2009-01-01

The achievement of a strong and stable bond between composite resin and dentin remains a challenge in restorative dentistry. Over the past two decades, dental materials have been substantially improved, with better handling and bonding characteristics. However, little attention has been paid to the contribution of collagen structure/stability to bond strength. We hypothesized that the induction of cross-linking in dentin collagen improves dentin collagen stability and bond strength. This study investigated the effects of glutaraldehyde- and grape seed extract-induced cross-linking on the dentin bond strengths of sound and caries-affected dentin, and on the stability of dentin collagen. Our results demonstrated that the application of chemical cross-linking agents to etched dentin prior to bonding procedures significantly enhanced the dentin bond strengths of caries-affected and sound dentin. Glutaraldehyde and grape seed extract significantly increased dentin collagen stability in sound and caries-affected dentin, likely via distinct mechanisms. PMID:19892915
Hyaluronidase Inhibitory Activity of Pentacylic Triterpenoids from Prismatomeris tetrandra (Roxb.) K. Schum: Isolation, Synthesis and QSAR Study

PubMed Central

Abdullah, Nor Hayati; Thomas, Noel Francis; Sivasothy, Yasodha; Lee, Vannajan Sanghiran; Liew, Sook Yee; Noorbatcha, Ibrahim Ali; Awang, Khalijah

2016-01-01

The mammalian hyaluronidase degrades hyaluronic acid by the cleavage of the β-1,4-glycosidic bond furnishing a tetrasaccharide molecule as the main product which is a highly angiogenic and potent inducer of inflammatory cytokines. Ursolic acid 1, isolated from Prismatomeris tetrandra, was identified as having the potential to develop inhibitors of hyaluronidase. A series of ursolic acid analogues were either synthesized via structure modification of ursolic acid 1 or commercially obtained. The evaluation of the inhibitory activity of these compounds on the hyaluronidase enzyme was conducted. Several structural, topological and quantum chemical descriptors for these compounds were calculated using semi empirical quantum chemical methods. A quantitative structure activity relationship study (QSAR) was performed to correlate these descriptors with the hyaluronidase inhibitory activity. The statistical characteristics provided by the best multi linear model (BML) (R2 = 0.9717, R2cv = 0.9506) indicated satisfactory stability and predictive ability of the developed model. The in silico molecular docking study which was used to determine the binding interactions revealed that the ursolic acid analog 22 had a strong affinity towards human hyaluronidase. PMID:26907251
Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vordtriede, Paul B.; Yoder, Marilyn D., E-mail: yoderm@umkc.edu

2008-07-01

The acidic polygalacturonase PehA from A. vitis has been crystallized. A molecular-replacement solution indicated a right-handed parallel β-helix fold. Polygalacturonases are pectate-degrading enzymes that belong to glycoside hydrolase family 28 and hydrolyze the α-1,4 glycosidic bond between neighboring galacturonasyl residues of the homogalacturonan substrate. The acidic polygalacturonase PehA from Agrobacterium vitis was overexpressed in Escherichia coli, where it accumulated in the periplasmic fraction. It was purified to homogeneity via a two-step chromatography procedure and crystallized using the hanging-drop vapour-diffusion technique. PehA crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 52.387, b = 62.738, c = 149.165more » Å, β = 89.98°. Crystals diffracted to 1.59 Å resolution and contained two molecules per asymmetric unit. An initial structure determination by molecular replacement indicated a right-handed parallel β-helix fold.« less
Characterization of in Vitro Pharmacokinetic Properties of Hoodigogenin A from Hoodia gordonii

USDA-ARS?s Scientific Manuscript database

This study was aimed to determine ADME properties of Hoodigogenin A, which is aglycone of oxypregnane steroidal glycoside P57AS3 (P57) isolated from Hoodia gordonii. A series of in vitro assays were used to predict its gastric, intestinal and metabolic stability, intestinal and blood brain barrier (...
Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

PubMed

Jarzembska, Katarzyna N; Řlepokura, Katarzyna; Kamiński, Radosław; Gutmann, Matthias J; Dominiak, Paulina M; Woźniak, Krzysztof

2017-08-01

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH - anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.
[Induction of polygalacturonases important in pathogenicity of Pseudomonas solanacearum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-01-01

Recent studies on the importance of hydroxyproline-rich glycoproteins (HPRG's) in the nature and function of plant cell walls have led to the question as to whether proteolytic enzymes are also involved in tissue maceration and act in concert with other cell wall degrading enzymes in the process. The primary objective of this research was to determine whether proteolytic enzymes, in combination with other enzymes, are involved in the degradation of plant cell walls and thus may be essential for pathogenesis by certain soft rot bacteria. The proteolytic enzymes of Erwinia carotovora subsp.carotovora (Ecc) grown on various media were examined bymore » isoelectrofocusing in polyacrylamide gels over a pH range of 3-10. In addition to the main protease present in culture filtrates, low concentrations of several other proteases were present in extracts from potato tubers infected by Ecc. These enzymes degraded gelatin, soluble collagen, and Hide Powder Azure, and showed weak activity on casein, but did not degrade insoluble collagen or elastin. Ecc proteases appear capable of degrading at least one type of cell wall protein in vitro, but we were unable to obtain evidence that these proteases can attack cell wall proteins in muro. The results indicate that some glycosidic alkali- labile bonds have to be broken befor Ecc proteases can degrade cell wall proteins. Thus, these proteases may play a role in cell wall degradation only when acting in concert with other enzymes that split glycosidic bonds.« less
[Induction of polygalacturonases important in pathogenicity of Pseudomonas solanacearum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-12-31

Recent studies on the importance of hydroxyproline-rich glycoproteins (HPRG`s) in the nature and function of plant cell walls have led to the question as to whether proteolytic enzymes are also involved in tissue maceration and act in concert with other cell wall degrading enzymes in the process. The primary objective of this research was to determine whether proteolytic enzymes, in combination with other enzymes, are involved in the degradation of plant cell walls and thus may be essential for pathogenesis by certain soft rot bacteria. The proteolytic enzymes of Erwinia carotovora subsp.carotovora (Ecc) grown on various media were examined bymore » isoelectrofocusing in polyacrylamide gels over a pH range of 3-10. In addition to the main protease present in culture filtrates, low concentrations of several other proteases were present in extracts from potato tubers infected by Ecc. These enzymes degraded gelatin, soluble collagen, and Hide Powder Azure, and showed weak activity on casein, but did not degrade insoluble collagen or elastin. Ecc proteases appear capable of degrading at least one type of cell wall protein in vitro, but we were unable to obtain evidence that these proteases can attack cell wall proteins in muro. The results indicate that some glycosidic alkali- labile bonds have to be broken befor Ecc proteases can degrade cell wall proteins. Thus, these proteases may play a role in cell wall degradation only when acting in concert with other enzymes that split glycosidic bonds.« less
Analysis of the 3H8 antigen of Candida albicans reveals new aspects of the organization of fungal cell wall proteins.

PubMed

Sentandreu, Rafael; Caminero, Antonio; Rentería, Itzel; León-Ramirez, Claudia; González-de-la-Vara, Luis; Valentin-Gomez, Eulogio; Ruiz-Herrera, José

2018-06-01

The walls of both, yeast and mycelial cells of Candida albicans possess a species-specific antigen that is recognized by a monoclonal antibody (MAb 3H8). This antigen can be extracted in the form of a very high Mr complex, close or over 106 Da, by treatment, with β-1,3-glucanase, β mercaptoethanol or dithothreitol, or mild alkali, but not by saturated hydrogen fluoride (HF) in pyridine, suggesting that the complex is bound to wall β-1,3 glucans, and to proteins by disulfide bonds, but not to β-1,6 glucans. Through its sensitivity to trypsin and different deglycosylation procedures, it was concluded that the epitope is associated to a glycoprotein containing N-glycosidic, but not O-glycosidic mannan moieties. By means of electrophoresis in polycrylamide gradient gels, followed by mass spectrometric analysis, the epitope was pinpointed to a very high MW complex containing Agglutinin-Like Sequence (ALS) family proteins, and other cytoplasmic, membrane and secreted proteins. The components of this complex are bound by unknown covalent bonds. The material extracted with β mercaptoethanol or dilute alkali appeared under the electron microscope as large aggregates in the form of spheroidal and mostly web-like structures of large sizes. These, and additional data, suggest that this protein complex may constitute an important part of the basic glycoprotein structure of C. albicans. The possibility that similar complexes exist in the wall of other fungi is an attractive, although yet untested possibility.
Transcriptional Regulation and Characterization of a Novel β-Fructofuranosidase-Encoding Gene from Bifidobacterium breve UCC2003

PubMed Central

Ryan, Sinéad M.; Fitzgerald, Gerald F.; van Sinderen, Douwe

2005-01-01

An operon involved in fructooligosaccharide breakdown was identified in the genome of Bifidobacterium breve UCC2003. This 2.6-kb transcriptional unit was comprised of three genes that encoded a putative permease, a conserved hypothetical protein, and a β-fructofuranosidase. Active transcription of the operon was observed when B. breve UCC2003 was grown on sucrose or Actilight, while transcription appeared to be repressed when the organism was grown on glucose, fructose, a combination of glucose and sucrose, or a combination of fructose and sucrose. The β-fructofuranosidase encoded by this operon was purified and biochemically characterized. The optimum pH and temperature for catalytic activity were determined to be pH 6.0 and 37°C, respectively, and there was a dependence on bivalent cations, particularly manganese. The Km and Vmax values for sucrose hydrolysis were determined to be 25 ± 2 mM and 24 ± 3 μmol min−1 mg−1, respectively. Interestingly, the enzyme was shown to specifically catalyze cleavage of the β(2-1) glycosidic bond between glucose and its neighboring fructose moiety in sucrose and other fructooligosaccharides with a relatively low degree of polymerization, and there was no detectable activity towards the β(2-1) glycosidic bond between two fructose moieties within the same substrate. To our knowledge, such an enzymatic activity has not previously been described in bifidobacteria or other gram-positive bacteria. PMID:16000751

In vitro biosynthesis, isolation, and identification of predominant metabolites of 2-(4-(2-hydroxyethoxy)-3,5-dimethylphenyl)-5,7-dimethoxyquinazolin-4(3H)-one (RVX-208).

PubMed

Khmelnitsky, Yuri L; Mozhaev, Vadim V; Cotterill, Ian C; Michels, Peter C; Boudjabi, Sihem; Khlebnikov, Vladimir; Madhava Reddy, M; Wagner, Gregory S; Hansen, Henrik C

2013-06-01

The structures of the two predominant metabolites (M4 and M5) of RVX-208, observed both in in vitro human and animal liver microsomal incubations, as well as in plasma from animal in vivo studies, were determined. A panel of biocatalytic systems was tested to identify biocatalysts suitable for milligram scale production of metabolite M4 from RVX-208. Rabbit liver S9 fraction was selected as the most suitable system, primarily based on pragmatic metrics such as catalyst cost and estimated yield of M4 (∼55%). Glucuronidation of RVX-208 catalyzed by rabbit liver S9 fraction was optimized to produce M4 in amounts sufficient for structural characterization. Structural studies using LC/MS/MS analysis and (1)H NMR spectroscopy showed the formation of a glycosidic bond between the primary hydroxyl group of RVX-208 and glucuronic acid. NMR results suggested that the glycosidic bond has the β-anomeric configuration. A synthetic sample of M4 confirmed the proposed structure. Metabolite M5, hypothesized to be the carboxylate of RVX-208, was prepared using human liver microsomes, purified by HPLC, and characterized by LC/MS/MS and (1)H NMR. The structure was confirmed by comparison to a synthetic sample. Both samples confirmed M5 as a product of oxidation of primary hydroxyl group of RVX-208 to carboxylic acid. Copyright © 2013 Elsevier Masson SAS. All rights reserved.
Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories.

PubMed

Chikalov, Igor; Yao, Peggy; Moshkov, Mikhail; Latombe, Jean-Claude

2011-02-15

Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration Δ. We model dependence of the output variable on the predictors by a regression tree. Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings. We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone.
Receptor protein of Lysinibacillus sphaericus mosquito-larvicidal toxin displays amylomaltase activity.

PubMed

Sharma, Mahima; Gupta, Gagan D; Kumar, Vinay

2018-02-01

The activated binary toxin (BinAB) from Lysinibacillus sphaericus binds to surface receptor protein (Cqm1) on the midgut cell membrane and kills Culex quinquefasciatus larvae on internalization. Cqm1 is attached to cells via a glycosyl-phosphatidylinositol (GPI) anchor. It has been classified as a member of glycoside hydrolase family 13 of the CAZy database. Here, we report characterization of the ordered domain (residues 23-560) of Cqm1. Gene expressing Cqm1 of BinAB susceptible mosquito was chemically synthesized and the protein was purified using E. coli expression system. Values for the Michaelis-Menten kinetics parameters towards 4-nitrophenyl α-D-glucopyranoside (α-pNPG) substrate were estimated to be 0.44 mM (Km) and 1.9 s -1 (kcat). Thin layer chromatography experiments established Cqm1 as α-glucosidase competent to cleave α-1,4-glycosidic bonds of maltose and maltotriose with high glycosyltransferase activity to form glucose-oligomers. The observed hydrolysis and synthesis of glucose-oligomers is consistent with open and accessible active-site in the structural model. The protein also hydrolyses glycogen and sucrose. These activities suggest that Cqm1 may be involved in carbohydrate metabolism in mosquitoes. Further, toxic BinA component does not inhibit α-glucosidase activity of Cqm1, while BinB reduced the activity by nearly 50%. The surface plasmon resonance study reveals strong binding of BinB with Cqm1 (Kd, 9.8 nM). BinA interaction with Cqm1 however, is 1000-fold weaker. Notably the estimated Kd values match well with dissociation constants reported earlier with larvae brush border membrane fractions. The Cqm1 protein forms a stable dimer that is consistent with its apical localization in lipid rafts. Its melting temperature (T m ) as observed by thermofluor-shift assay is 51.5 °C and Ca 2+ provides structural stability to the protein. Copyright © 2017 Elsevier Ltd. All rights reserved.
[Intermolecular hydrogen bond between protein and flavonoid and its contribution to the stability of the flavonoids].

PubMed

Fang, Ru; Leng, Xiao-jing; Wu, Xia; Li, Qi; Hao, Rui-fang; Ren, Fa-zheng; Jing, Hao

2012-01-01

The interactions between three proteins (BSA, lysozyme and myoglobin) and three flavonoids (quercetin, kaempferol and rutin) were analyzed, using three-dimensional fluorescence spectrometry in combination with UV-Vis spectrometry and Fourier transform infrared (FTIR) spectroscopy. The stabilities of unbound flavonoids and protein-bound flavonoids were compared. The correlation between the interaction and stability was analyzed. The results showed that the hydrophobic interaction was the main binding code in all proteins and flavonoids systems. However, the hydrogen bond has been involved merely in the BSA system. The stability of all three flavonoids (quercetin, kaempferol and rutin) was improved by BSA. There was a great correlation between the hydrogen bonding and the stability of the flavonoids in the presence of BSA. It suggested that the protection of BSA on the flavonoids was due to the intermolecular hydrogen bonding between BSA and flavonoid, and the stronger hydrogen bonding resulted in more protection.
Quantitative Analysis and Comparison of Four Major Flavonol Glycosides in the Leaves of Toona sinensis (A. Juss.) Roemer (Chinese Toon) from Various Origins by High-Performance Liquid Chromatography-Diode Array Detector and Hierarchical Clustering Analysis

PubMed Central

Sun, Xiaoxiang; Zhang, Liting; Cao, Yaqi; Gu, Qinying; Yang, Huan; Tam, James P.

2016-01-01

Background: Toona sinensis (A. Juss.) Roemer is an endemic species of Toona genus native to Asian area. Its dried leaves are applied in the treatment of many diseases; however, few investigations have been reported for the quantitative analysis and comparison of major bioactive flavonol glycosides in the leaves harvested from various origins. Objective: To quantitatively analyze four major flavonol glycosides including rutinoside, quercetin-3-O-β-D-glucoside, quercetin-3-O-α-L-rhamnoside, and kaempferol-3-O-α-L-rhamnoside in the leaves from different production sites and classify them according to the content of these glycosides. Materials and Methods: A high-performance liquid chromatography-diode array detector (HPLC-DAD) method for their simultaneous determination was developed and validated for linearity, precision, accuracy, stability, and repeatability. Moreover, the method established was then employed to explore the difference in the content of these four glycosides in raw materials. Finally, a hierarchical clustering analysis was performed to classify 11 voucher specimens. Results: The separation was performed on a Waters XBridge Shield RP18 column (150 mm × 4.6 mm, 3.5 μm) kept at 35°C, and acetonitrile and H2O containing 0.30% trifluoroacetic acid as mobile phase was driven at 1.0 mL/min during the analysis. Ten microliters of solution were injected and 254 nm was selected to monitor the separation. A strong linear relationship between the peak area and concentration of four analytes was observed. And, the method was also validated to be repeatable, stable, precise, and accurate. Conclusion: An efficient and reliable HPLC-DAD method was established and applied in the assays for the samples from 11 origins successfully. Moreover, the content of those flavonol glycosides varied much among different batches, and the flavonoids could be considered as biomarkers to control the quality of Chinese Toon. SUMMARY Four major flavonol glycosides in the leaves of Toona sinensis were determined by HPLC-DAD and their contents were compared among various origins by HCA. Abbreviations used: HPLC-DAD: High-performance liquid chromatography-diode array detector, HCA: Hierarchical clustering analysis, MS: Mass spectrometry, RSD: Relative standard deviation. PMID:27279719
Dimensional Stability of Hexoloy SA® Silicon Carbide and Zerodur™ Materials for the LISA Mission

NASA Astrophysics Data System (ADS)

Preston, Alix; Cruz, Rachel J.; Thorpe, J. Ira; Mueller, Guido; Boothe, G. Trask; Delgadillo, Rodrigo; Guntaka, Sridhar R.

2006-11-01

In the LISA mission, incoming gravitational waves will modulate the distance between proof masses while laser beams monitor the optical path length changes with 20 pm/√Hz accuracy. Optical path length changes between bench components or the relative motion between the primary and secondary mirrors of the telescope need to be well below this level to result in a successful operation of LISA. The reference cavity for frequency stabilization must have a dimensional stability of a few fm/√Hz. While the effects of temperature fluctuations are well characterized in most materials at the macroscopic level (i.e. coefficients of thermal expansion), microscopic material internal processes and long term processes in the bonds between different components can dominate the dimensional stability at the pm or fm levels. Zerodur and ULE have been well studied, but the ultimate stabilities of other materials like silicon carbide or CFRP are virtually unknown. Chemical bonding techniques, like hydroxide bonding, provide significantly stronger bonds than the standard optical contacts. However, the noise levels of these bonds are also unknown. In this paper we present our latest results on the stability of silicon carbide and hydroxide bonds on Zerodur.
The influence of disulfide bonds on the mechanical stability of proteins is context dependent.

PubMed

Manteca, Aitor; Alonso-Caballero, Álvaro; Fertin, Marie; Poly, Simon; De Sancho, David; Perez-Jimenez, Raul

2017-08-11

Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces. For this purpose, we chose the pilus protein FimG from Gram-negative bacteria and a disulfide-bonded variant of the I91 human cardiac titin polyprotein. Our results show that disulfide bonds can alter the mechanical stability of proteins in different ways depending on the properties of the system. Specifically, disulfide-bonded FimG undergoes a 30% increase in its mechanical stability compared with its reduced counterpart, whereas the unfolding force of I91 domains experiences a decrease of 15% relative to the WT form. Using a coarse-grained simulation model, we rationalized that the increase in mechanical stability of FimG is due to a shift in the mechanical unfolding pathway. The simple topology-based explanation suggests a neutral effect in the case of titin. In summary, our results indicate that disulfide bonds in proteins act in a context-dependent manner rather than simply as mechanical lockers, underscoring the importance of considering disulfide bonds both computationally and experimentally when studying the mechanical properties of proteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Evaluation of enzymatic reactors for large-scale panose production.

PubMed

Fernandes, Fabiano A N; Rodrigues, Sueli

2007-07-01

Panose is a trisaccharide constituted by a maltose molecule bonded to a glucose molecule by an alpha-1,6-glycosidic bond. This trisaccharide has potential to be used in the food industry as a noncariogenic sweetener, as the oral flora does not ferment it. Panose can also be considered prebiotic for stimulating the growth of benefic microorganisms, such as lactobacillus and bifidobacteria, and for inhibiting the growth of undesired microorganisms such as E. coli and Salmonella. In this paper, the production of panose by enzymatic synthesis in a batch and a fed-batch reactor was optimized using a mathematical model developed to simulate the process. Results show that optimum production is obtained in a fed-batch process with an optimum production of 11.23 g/l h of panose, which is 51.5% higher than production with batch reactor.
Advantages of a distant cellulase catalytic base.

PubMed

Burgin, Tucker; Ståhlberg, Jerry; Mayes, Heather B

2018-03-30

The inverting glycoside hydrolase Trichoderma reesei ( Hypocrea jecorina ) Cel6A is a promising candidate for protein engineering for more economical production of biofuels. Until recently, its catalytic mechanism had been uncertain: The best candidate residue to serve as a catalytic base, Asp-175, is farther from the glycosidic cleavage site than in other glycoside hydrolase enzymes. Recent unbiased transition path sampling simulations revealed the hydrolytic mechanism for this more distant base, employing a water wire; however, it is not clear why the enzyme employs a more distant catalytic base, a highly conserved feature among homologs across different kingdoms. In this work, we describe molecular dynamics simulations designed to uncover how a base with a longer side chain, as in a D175E mutant, affects procession and active site alignment in the Michaelis complex. We show that the hydrogen bond network is tuned to the shorter aspartate side chain, and that a longer glutamate side chain inhibits procession as well as being less likely to adopt a catalytically productive conformation. Furthermore, we draw comparisons between the active site in Trichoderma reesei Cel6A and another inverting, processive cellulase to deduce the contribution of the water wire to the overall enzyme function, revealing that the more distant catalytic base enhances product release. Our results can inform efforts in the study and design of enzymes by demonstrating how counterintuitive sacrifices in chemical reactivity can have worthwhile benefits for other steps in the catalytic cycle. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
The effects of disulfide bonds on the denatured state of barnase.

PubMed Central

Clarke, J.; Hounslow, A. M.; Bond, C. J.; Fersht, A. R.; Daggett, V.

2000-01-01

The effects of engineered disulfide bonds on protein stability are poorly understood because they can influence the structure, dynamics, and energetics of both the native and denatured states. To explore the effects of two engineered disulfide bonds on the stability of barnase, we have conducted a combined molecular dynamics and NMR study of the denatured state of the two mutants. As expected, the disulfide bonds constrain the denatured state. However, specific extended beta-sheet structure can also be detected in one of the mutant proteins. This mutant is also more stable than would be predicted. Our study suggests a possible cause of the very high stability conferred by this disulfide bond: the wild-type denatured ensemble is stabilized by a nonnative hydrophobic cluster, which is constrained from occurring in the mutant due to the formation of secondary structure. PMID:11206061
Engineering glycoside hydrolase stability by the introduction of zinc binding

DOE PAGES

Ellinghaus, Thomas L.; Pereira, Jose H.; McAndrew, Ryan P.; ...

2018-06-27

The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activitymore » with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn 2+ site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.« less
Engineering glycoside hydrolase stability by the introduction of zinc binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ellinghaus, Thomas L.; Pereira, Jose H.; McAndrew, Ryan P.

The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance. The amino-acid sequence of J30 shows comparably low identity to those of previously analyzed enzymes. As an enzyme that combines a well measurable activitymore » with a relatively low optimal temperature (50°C) and a modest thermal tolerance, it offers the potential for structural optimization aimed at increased stability. Here, the crystal structure of wild-type J30 is presented along with that of a designed triple-mutant variant with improved characteristics for industrial applications. Through the introduction of a structural Zn 2+ site, the thermal tolerance was increased by more than 10°C and was paralleled by an increase in the catalytic optimum temperature by more than 5°C.« less
The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks.

PubMed

Shen, Tongye; Gnanakaran, S

2009-04-22

A critical roadblock to the production of biofuels from lignocellulosic biomass is the efficient degradation of crystalline microfibrils of cellulose to glucose. A microscopic understanding of how different physical conditions affect the overall stability of the crystalline structure of microfibrils could facilitate the design of more effective protocols for their degradation. One of the essential physical interactions that stabilizes microfibrils is a network of hydrogen (H) bonds: both intrachain H-bonds between neighboring monomers of a single cellulose polymer chain and interchain H-bonds between adjacent chains. We construct a statistical mechanical model of cellulose assembly at the resolution of explicit hydrogen-bond networks. Using the transfer matrix method, the partition function and the subsequent statistical properties are evaluated. With the help of this lattice-based model, we capture the plasticity of the H-bond network in cellulose due to frustration and redundancy in the placement of H-bonds. This plasticity is responsible for the stability of cellulose over a wide range of temperatures. Stable intrachain and interchain H-bonds are identified as a function of temperature that could possibly be manipulated toward rational destruction of crystalline cellulose.
Crystal structure and genetic modifications of FI-CMCase from Aspergillus aculeatus F-50.

PubMed

Huang, Jian-Wen; Liu, Weidong; Lai, Hui-Lin; Cheng, Ya-Shan; Zheng, Yingying; Li, Qian; Sun, Hong; Kuo, Chih-Jung; Guo, Rey-Ting; Chen, Chun-Chi

2016-09-16

Cellulose is the major component of the plant cell wall and the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in many commercial applications. Endo-1,4-β-d-glucanase (EC 3.2.1.4; endoglucanase), which catalyzes the random hydrolysis of 1,4-β-glycosidic bonds of the cellulose main chain to cleave cellulose into smaller fragments, is the key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase), which is classified into the glycoside hydrolase (GH) family 12, was demonstrated to be effectively expressed in the industrial strain Pichia pastoris. Here, the crystal structure and complex structures of P. pastoris-expressed FI-CMCase were solved to high resolution. The overall structure is analyzed and compared to other GH12 members. In addition, the substrate-surrounding residues were engineered to search for variants with improved enzymatic activity. Among 14 mutants constructed, one with two-fold increase in protein expression was identified, which possesses a potential to be further developed as a commercial enzyme product. Copyright © 2016 Elsevier Inc. All rights reserved.
Crystallization and preliminary X-ray diffraction analysis of an endo-1,4-β-D-glucanase from Aspergillus aculeatus F-50.

PubMed

Chen, Yun; Huang, Jian Wen; Chen, Chun Chi; Lai, Hui Lin; Jin, Jian; Guo, Rey Ting

2015-04-01

Cellulose is the most abundant renewable biomass on earth, and its decomposition has proven to be very useful in a wide variety of industries. Endo-1,4-β-D-glucanase (EC 3.2.1.4; endoglucanase), which can catalyze the random hydrolysis of β-1,4-glycosidic bonds to cleave cellulose into smaller fragments, is a key cellulolytic enzyme. An endoglucanase isolated from Aspergillus aculeatus F-50 (FI-CMCase) that was classified into glycoside hydrolase family 12 has been found to be effectively expressed in the industrial strain Pichia pastoris. Here, recombinant FI-CMCase was crystallized. Crystals belonging to the orthorhombic space group C222₁, with unit-cell parameters a = 74.2, b = 75.1, c = 188.4 Å, were obtained by the sitting-drop vapour-diffusion method and diffracted to 1.6 Å resolution. Initial phase determination by molecular replacement clearly shows that the crystal contains two protein molecules in the asymmetric unit. Further model building and structure refinement are in progress.
Investigations of Scope and Mechanism of Nickel-Catalyzed Transformations of Glycosyl Trichloroacetimidates to Glycosyl Trichloroacetamides and Subsequent, Atom-Economical, One-Step Conversion to α-Urea-Glycosides

PubMed Central

McKay, Matthew J.; Park, Nathaniel H.; Nguyen, Hien M.

2014-01-01

The development and mechanistic investigation of a highly stereoselective methodology for preparing α-linked-urea neo-glycoconjugates and pseudo-oligosaccharides is described. This two-step procedure begins with the selective nickel-catalyzed conversion of glycosyl trichloroacetimidates to the corresponding α-trichloroacetamides. The α-selective nature of the conversion is controlled with a cationic nickel(II) catalyst, Ni(dppe)(OTf)2. Mechanistic studies have identified the coordination of the nickel catalyst with the equatorial C2-ether functionality of the α-glycosyl trichloroacetimidate to be paramount for achieving an α-stereoselective transformation. A cross-over experiment has indicated that the reaction does not proceed in an exclusively-intramolecular fashion. The second step in this sequence is the direct conversion of α-glycosyl trichloroacetamide products into the corresponding α-urea glycosides by reacting them with a wide variety of amine nucleophiles in presence of cesium carbonate. Only α-urea-product formation is observed, as the reaction proceeds with complete retention of stereochemical integrity at the anomeric C-N bond. PMID:24905328
Analyzing Activities of Lytic Polysaccharide Monooxygenases by Liquid Chromatography and Mass Spectrometry.

PubMed

Westereng, Bjørge; Arntzen, Magnus Ø; Agger, Jane Wittrup; Vaaje-Kolstad, Gustav; Eijsink, Vincent G H

2017-01-01

Lytic polysaccharide monooxygenases perform oxidative cleavage of glycosidic bonds in various polysaccharides. The majority of LMPOs studied so far possess activity on either cellulose or chitin and analysis of these activities is therefore the main focus of this review. Notably, however, the number of LPMOs that are active on other polysaccharides is increasing. The products generated by LPMOs from cellulose are either oxidized in the downstream end (at C1) or upstream end (at C4), or at both ends. These modifications only result in small structural changes, which makes both chromatographic separation and product identification by mass spectrometry challenging. The changes in physicochemical properties that are associated with oxidation need to be considered when choosing analytical approaches. C1 oxidation leads to a sugar that is no longer reducing but instead has an acidic functionality, whereas C4 oxidation leads to products that are inherently labile at high and low pH and that exist in a keto-gemdiol equilibrium that is strongly shifted toward the gemdiol in aqueous solutions. Partial degradation of C4-oxidized products leads to the formation of native products, which could explain why some authors claim to have observed glycoside hydrolase activity for LPMOs. Notably, apparent glycoside hydrolase activity may also be due to small amounts of contaminating glycoside hydrolases since these normally have much higher catalytic rates than LPMOs. The low catalytic turnover rates of LPMOs necessitate the use of sensitive product detection methods, which limits the analytical possibilities considerably. Modern liquid chromatography and mass spectrometry have become essential tools for evaluating LPMO activity, and this chapter provides an overview of available methods together with a few novel tools. The methods described constitute a suite of techniques for analyzing oxidized carbohydrate products, which can be applied to LPMOs as well as other carbohydrate-active redox enzymes.
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-Assisted Catalysis in Family 85 Glycoside Hydrolases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abbott, D.; Macauley, M; Vocadlo, D

2009-01-01

Endo-?-d-glucosaminidases from family 85 of glycoside hydrolases (GH85 endohexosaminidases) act to cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. Endohexosaminidase D (Endo-D), produced by Streptococcus pneumoniae, is believed to contribute to the virulence of this organism by playing a role in the deglycosylation of IgG antibodies. Endohexosaminidases have received significant attention for this reason and, moreover, because they are powerful tools for chemoenzymatic synthesis of proteins having defined glycoforms. Here we describe mechanistic and structural studies of the catalytic domain (SpGH85) of Endo-D that provide compelling support for GH85 enzymes usingmore » a catalytic mechanism involving substrate-assisted catalysis. Furthermore, the structure of SpGH85 in complex with the mechanism-based competitive inhibitor NAG-thiazoline (Kd = 28 ?m) provides a coherent rationale for previous mutagenesis studies of Endo-D and other related GH85 enzymes. We also find GH85, GH56, and GH18 enzymes have a similar configuration of catalytic residues. Notably, GH85 enzymes have an asparagine in place of the aspartate residue found in these other families of glycosidases. We propose that this residue, as the imidic acid tautomer, acts analogously to the key catalytic aspartate of GH56 and GH18 enzymes. This topographically conserved arrangement of the asparagine residue and a conserved glutamic acid, coupled with previous kinetic studies, suggests these enzymes may use an unusual proton shuttle to coordinate effective general acid and base catalysis to aid cleavage of the glycosidic bond. These results collectively provide a blueprint that may be used to facilitate protein engineering of these enzymes to improve their function as biocatalysts for synthesizing glycoproteins having defined glycoforms and also may serve as a guide for generating inhibitors of GH85 enzymes.« less
Simultaneous estimation of phenolic acids in sea buckthorn (Hippophaë rhamnoides) using RP-HPLC with DAD.

PubMed

Arimboor, Ranjith; Kumar, K Sarin; Arumughan, C

2008-05-12

A RP-HPLC-DAD method was developed and validated for the simultaneous analysis of nine phenolic acids including gallic acid, protocatechuic acid, p-hydroxybenzoic acid, vanillic acid, salicylic acid, p-coumaric acid, cinnamic acid, caffiec acid and ferulic acid in sea buckthorn (SB) (Hippophaë rhamnoides) berries and leaves. The method was validated in terms of linearity, LOD, precision, accuracy and recovery and found to be satisfactory. Phenolic acid derivatives in anatomical parts of SB berries and leaves were separated into free phenolic acids, phenolic acids bound as esters and phenolic acids bound as glycosides and profiled in HPLC. Berry pulp contained a total of 1068 mg/kg phenolic acids, of which 58.8% was derived from phenolic glycosides. Free phenolic acids and phenolic acid esters constituted 20.0% and 21.2%, respectively, of total phenolic acids in SB berry pulp. The total phenolic acid content in seed kernel (5741 mg/kg) was higher than that in berry pulp and seed coat (Table 2). Phenolic acids liberated from soluble esters constituted the major fraction of phenolic acids (57.3% of total phenolic acids) in seed kernel. 8.4% and 34.3% of total phenolic acids in seed kernel were, respectively contributed by free and phenolic acids liberated from glycosidic bonds. The total soluble phenolic acids content in seed coat (448 mg/kg) was lower than that in seed kernel and pulp (Table 2). Proportion of free phenolic acids in total phenolic acids in seed coat was higher than that in seed kernel and pulp. Phenolic acids bound as esters and glycosides, respectively contributed 49.1% and 20.3% of total phenolic acids in seed coat. The major fraction (approximately 70%) of phenolic acids in SB berries was found to be concentrated in the seeds. Gallic acid was the predominant phenolic acid both in free and bound forms in SB berry parts and leaves.
Assignment of the Stereochemistry and Anomeric Configuration of Sugars within Oligosaccharides Via Overlapping Disaccharide Ladders Using MSn

NASA Astrophysics Data System (ADS)

Konda, Chiharu; Londry, Frank A.; Bendiak, Brad; Xia, Yu

2014-08-01

A systematic approach is described that can pinpoint the stereo-structures (sugar identity, anomeric configuration, and location) of individual sugar units within linear oligosaccharides. Using a highly modified mass spectrometer, dissociation of linear oligosaccharides in the gas phase was optimized along multiple-stage tandem dissociation pathways (MSn, n = 4 or 5). The instrument was a hybrid triple quadrupole/linear ion trap mass spectrometer capable of high-efficiency bidirectional ion transfer between quadrupole arrays. Different types of collision-induced dissociation (CID), either on-resonance ion trap or beam-type CID could be utilized at any given stage of dissociation, enabling either glycosidic bond cleavages or cross-ring cleavages to be maximized when wanted. The approach first involves optimizing the isolation of disaccharide units as an ordered set of overlapping substructures via glycosidic bond cleavages during early stages of MSn, with explicit intent to minimize cross-ring cleavages. Subsequently, cross-ring cleavages were optimized for individual disaccharides to yield key diagnostic product ions ( m/ z 221). Finally, fingerprint patterns that establish stereochemistry and anomeric configuration were obtained from the diagnostic ions via CID. Model linear oligosaccharides were derivatized at the reducing end, allowing overlapping ladders of disaccharides to be isolated from MSn. High confidence stereo-structural determination was achieved by matching MSn CID of the diagnostic ions to synthetic standards via a spectral matching algorithm. Using this MSn ( n = 4 or 5) approach, the stereo-structures, anomeric configurations, and locations of three individual sugar units within two pentasaccharides were successfully determined.

Improvement of single domain antibody stability by disulfide bond introduction.

PubMed

Hagihara, Yoshihisa; Saerens, Dirk

2012-01-01

The successful medical application of single domain antibodies largely depends on their functionality. This feature is partly determined by the intrinsic stability of the single domain. Therefore a lot of research has gone into the elucidation of rules to uniformly increase stability of antibodies. Recently, a novel intra-domain disulfide bond was independently discovered by two research groups, after either rational design or careful investigation of the naturally occurring camelid antibody repertoire. By introducing this particular disulfide bond within a single domain antibody, the conformational stability can be increased in general. In this chapter it is described how to introduce this extra intra-domain disulfide bond and how to estimate the biophysical and biochemical impact of this cystine on the domain.
Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.
BCB Bonding Technology of Back-Side Illuminated COMS Device

NASA Astrophysics Data System (ADS)

Wu, Y.; Jiang, G. Q.; Jia, S. X.; Shi, Y. M.

2018-03-01

Back-side illuminated CMOS(BSI) sensor is a key device in spaceborne hyperspectral imaging technology. Compared with traditional devices, the path of incident light is simplified and the spectral response is planarized by BSI sensors, which meets the requirements of quantitative hyperspectral imaging applications. Wafer bonding is the basic technology and key process of the fabrication of BSI sensors. 6 inch bonding of CMOS wafer and glass wafer was fabricated based on the low bonding temperature and high stability of BCB. The influence of different thickness of BCB on bonding strength was studied. Wafer bonding with high strength, high stability and no bubbles was fabricated by changing bonding conditions.
Stability of peptides in high-temperature aqueous solutions

NASA Astrophysics Data System (ADS)

Shock, Everett L.

1992-09-01

Estimated standard molal thermodynamic properties of aqueous dipeptides and their constituent amino acids indicate that temperature increases correspond to increased stability of peptide bonds relative to hydrolysis reactions. Pressure increases cause slight decreases in peptide bond stability, which are generally offset by greater stability caused by temperature increases along geothermal gradients. These calculations suggest that peptides, polypeptides, and proteins may survive hydrothermal alteration of organic matter depending on the rates of the hydrolysis reactions. Extremely thermophilic organisms may be able to take advantage of the decreased energy required to form peptide bonds in order to maintain structural proteins and enzymes at elevated temperatures and pressures. As the rates of hydrolysis reactions increase with increasing temperature, formation of peptide bonds may become a facile process in hydrothermal systems and deep in sedimentary basins.
Extraction, characterisation and antioxidant activity of Allium sativum polysaccharide.

PubMed

Cheng, Hao; Huang, Gangliang

2018-07-15

Extraction and antioxidant activity of polysaccharide from Allium sativum were investigated. The crude polysaccharide was obtained by the hot-water extraction method. The molecular weight of polysaccharide deproteinized with CaCl 2 was 7.35×10 3 . It indicated that polysaccharide from Allium sativum consisted of three monosaccharides, namely fructose, glucose, and galactose by HPLC. The polysaccharide had the β-glycosidic bond. Moreover, it was proved that the polysaccharide had the potential scavenging ability to superoxide anions and hydroxyl radicals. So, it should be a potential antioxidant. Copyright © 2018 Elsevier B.V. All rights reserved.
Cellulase activities in biomass conversion: measurement methods and comparison.

PubMed

Dashtban, Mehdi; Maki, Miranda; Leung, Kam Tin; Mao, Canquan; Qin, Wensheng

2010-12-01

Cellulose, the major constituent of all plant materials and the most abundant organic molecule on the Earth, is a linear biopolymer of glucose molecules, connected by β-1,4-glycosidic bonds. Enzymatic hydrolysis of cellulose requires mixtures of hydrolytic enzymes including endoglucanases, exoglucanases (cellobiohydrolases), and β-glucosidases acting in a synergistic manner. In biopolymer hydrolysis studies, enzyme assay is an indispensable part. The most commonly used assays for the individual enzymes as well as total cellulase activity measurements, including their advantages and limitations, are summarized in this review article. In addition, some novel approaches recently used for enzyme assays are summarized.
Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli

PubMed Central

Pilipczuk, Justyna; Zalewska-Piątek, Beata; Bruździak, Piotr; Czub, Jacek; Wieczór, Miłosz; Olszewski, Marcin; Wanarska, Marta; Nowicki, Bogdan; Augustin-Nowacka, Danuta; Piątek, Rafał

2017-01-01

Dr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond that joins their A and B strands. Here, we investigated how this disulfide bond affects the stability and folding/unfolding pathway of DraE. We found that the disulfide bond stabilizes self-complemented DraE (DraE-sc) by ∼50 kJ mol−1 in an exclusively thermodynamic manner, i.e. by lowering the free energy of the native state and with almost no effect on the free energy of the transition state. This finding was confirmed by experimentally determined folding and unfolding rate constants of DraE-sc and a disulfide bond-lacking DraE-sc variant. Although the folding of both proteins exhibited similar kinetics, the unfolding rate constant changed upon deletion of the disulfide bond by 10 orders of magnitude, from ∼10−17 s−1 to 10−7 s−1. Molecular simulations revealed that unfolding of the disulfide bond-lacking variant is initiated by strands A or G and that disulfide bond-mediated joining of strand A to the core strand B cooperatively stabilizes the whole protein. We also show that the disulfide bond in DraE is recognized by the DraB chaperone, indicating a mechanism that precludes the incorporation of less stable, non-oxidized DraE forms into the fimbriae. PMID:28739804
A Novel Method to Quantify Soil Aggregate Stability by Measuring Aggregate Bond Energies

NASA Astrophysics Data System (ADS)

Efrat, Rachel; Rawlins, Barry G.; Quinton, John N.; Watts, Chris W.; Whitmore, Andy P.

2016-04-01

Soil aggregate stability is a key indicator of soil quality because it controls physical, biological and chemical functions important in cultivated soils. Micro-aggregates are responsible for the long term sequestration of carbon in soil, therefore determine soils role in the carbon cycle. It is thus vital that techniques to measure aggregate stability are accurate, consistent and reliable, in order to appropriately manage and monitor soil quality, and to develop our understanding and estimates of soil as a carbon store to appropriately incorporate in carbon cycle models. Practices used to assess the stability of aggregates vary in sample preparation, operational technique and unit of results. They use proxies and lack quantification. Conflicting results are therefore drawn between projects that do not provide methodological or resultant comparability. Typical modern stability tests suspend aggregates in water and monitor fragmentation upon exposure to an un-quantified amount of ultrasonic energy, utilising a laser granulometer to measure the change in mean weight diameter. In this project a novel approach has been developed based on that of Zhu et al., (2009), to accurately quantify the stability of aggregates by specifically measuring their bond energies. The bond energies are measured operating a combination of calorimetry and a high powered ultrasonic probe, with computable output function. Temperature change during sonication is monitored by an array of probes which enables calculation of the energy spent heating the system (Ph). Our novel technique suspends aggregates in heavy liquid lithium heteropolytungstate, as opposed to water, to avoid exposing aggregates to an immeasurable disruptive energy source, due to cavitation, collisions and clay swelling. Mean weight diameter is measured by a laser granulometer to monitor aggregate breakdown after successive periods of calculated ultrasonic energy input (Pi), until complete dispersion is achieved and bond energy (Pb; input energy used in aggregate breakdown) can be calculated by the following equation: ΣPi - Ph = Pb The novel technique was tested by comparing the bond energies measured from a series of soil aggregates sampled from different land management histories, to the samples corresponding stability measurement obtained from standard modern stability tests. The effectiveness of the heavy liquid as a suspension (as opposed to water) was evaluated by comparing the bond energies of samples measured in both suspensions. Our results determine i) how disruptive water is in aggregate stability tests, ii) how accurate and representative standard aggregate stability tests are, and iii) how bond strength varies depending on land use. Keywords: Aggregate; Bond; Fragmentation; Soil; Sonication; Stability References: Zhu, Z. L., Minasny, B. & Field D. J. 2009. Measurement of aggregate bond energy using ultrasonic dispersion. European Journal of Soil Science, 60, 695-705
Theoretical Studies of the Glycosidation of 2-O-Substituted 5-Fluorouracil: N-Regioselective Synthesis with the Phase-Transfer-Catalysis Method.

PubMed

Wang, Yi-Gui; Barnes, Ericka C

2017-11-22

The observed N-regioselective glycosidation of 2-O-substituted 5-fluorouracil (5-FU) via the phase-transfer-catalysis (PTC) method was investigated computationally. The Gibbs free energy reaction barrier of the N-reaction between the 5-FU anion and 1-bromo-1-deoxy-2,3,4,6-tetra-O-acetyl-α-d-glucopyranose was computed at the MP2/6-311++G(2d,p)//B3LYP/6-31+G* level. The calculated transition states were, in general, quite "loose", with the ambident reaction sites at the N3- or O4-positions on 5-FU located approximately 2.0 Å from the anomeric carbon. With the S N 2 mechanism, the formation of β-glycosides was explained by the characteristics of transition states, and the N-regioselectivity was explained by three considerations: (1) the conformations of initial complexes and the structural requirement of the reactions; (2) the formation of an ionic pair between nBu 4 N + and 2-O-substituted 5-FU anions; and (3) the thermodynamic conversion of O-glycosides to N-glycosides. The reactions between the oxocarbenium ion and the 2-O-substituted 5-FU anions (the fast step of S N 1 mechanism) were also examined at the same level of theory. Because there were no "promoters" to extract Br in the PTC method, the S N 1 mechanism might have an unfavorably high barrier to produce oxocarbenium ion. However, both the formation of β-glycosides and the experimentally observed N-regioselectivity could also be explained by the S N 1 mechanism: The former was explained by the neighboring group participation, and the latter was explained by the formation of ionic pairs between nBu 4 N + and 2-O-substituted 5-FU anions. The formation of ionic pairs possibly changed the diffusion-controlled mechanism into an activation-controlled mechanism. Two factors were demonstrated by Marcus theory to play an important role for the experimentally observed N-resioselectivity in the PTC method: (1) the thermodynamic stability of N-products over O-products; (2) the formation of ionic pair between nBu 4 N + and 2-O-substituted 5-FU anions.
Biological activity of natural flavonoids as impacted by protein flexibility: an example of flavanones.

PubMed

Ding, Fei; Peng, Wei

2015-04-01

Naturally multifunctional Rutaceae hesperidin and its aglycone hesperetin have a great variety of biopharmaceutical activities, e.g. anti-cancer, anti-inflammatory, antioxidant and antitumor; however, the influence of the molecular structures of hesperidin and hesperetin, and in particular, the structural properties such as flexibility and dynamic features of protein on the biological activities of these bioactive compounds remains ambiguous. In the present study, the biomolecular recognition of crucial biopolymer - albumin from human serum (HSA) with Rutaceae, the recognition differences between HSA-hesperidin and HSA-hesperetin, the key elements that lead to the discrepancies as well as the structural characters of protein to the recognition processes were comparatively examined by employing biophysical approaches at the molecular scale. The results illustrated distinctly that (1) aglycone hesperetin can form stronger noncovalent bonds with HSA and possess higher recognition stability as compared with hesperidin. This phenomenon suggest that the introduction of glycoside structure into flavanone may possibly not be able to increase the noncovalent recognition of flavanone by a biopolymer, and conversely, this event will probably decrease the recognition capacity. (2) Although hesperidin and hesperetin can be located within subdomains IIA and IIIA, respectively, the conformational stability of flavanones in subdomain IIA is greater than subdomain IIIA; as a result, the recognition ability of subdomain IIIA with flavanones is patently lesser than subdomain IIA. These discrepancies likely originate from the unique characteristics of the respective cavity, or more specifically, subdomain IIA is basically a closed space, whereas subdomain IIIA is a semi-open region. Meanwhile, the detailed analyses of root-mean-square fluctuation interpreted the recognition of flavanones by subdomain IIA on HSA, which would evoke larger conformational alterations in several amino acid residues, and the similar phenomenon also resides in subdomain IIIA, which signifies that the flexible characteristics of different binding patches in protein may possess fairly notable effects on the HSA-flavanones recognition. Moreover, the integral structural changes of HSA exhibit some disparities on account of the dissimilarities of recognition capability to the protein-flavanone biointeractions, and all these conclusions received further forceful supports from fluorescence and circular dichroism experiments in solution. Perhaps the work emerged herein could not only help us to better evaluate the bioavailability of natural flavanones with or without glycoside, but to understand the sketches of the three-dimensional structure trait of certain biomacromolecules for the medicinal properties of flavonoids in the human body.
The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach.

PubMed

Hleap, Jose Sergio; Blouin, Christian

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape.
The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

PubMed Central

2018-01-01

The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates and members of the family have been bioengineered to improve catalytic function under industrial environments. We introduce a framework to analyze the response to selection of GH13 protein structures given some phylogenetic and simulated dynamic information. We find that the TIM-barrel (a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone, common to all amylases) is not selectable since it is under purifying selection. We also show a method to rank important residues with higher inferred response to selection. These residues can be altered to effect change in properties. In this work, we define fitness as inferred thermodynamic stability. We show that under the developed framework, residues 112Y, 122K, 124D, 125W, and 126P are good candidates to increase the stability of the truncated α-amylase protein from Geobacillus thermoleovorans (PDB code: 4E2O; α-1,4-glucan-4-glucanohydrolase; EC 3.2.1.1). Overall, this paper demonstrates the feasibility of a framework for the analysis of protein structures for any other fitness landscape. PMID:29698417
Steviol glycosides in purified stevia leaf extract sharing the same metabolic fate.

PubMed

Purkayastha, Sidd; Markosyan, Avetik; Prakash, Indra; Bhusari, Sachin; Pugh, George; Lynch, Barry; Roberts, Ashley

2016-06-01

The safety of steviol glycosides is based on data available on several individual steviol glycosides and on the terminal absorbed metabolite, steviol. Many more steviol glycosides have been identified, but are not yet included in regulatory assessments. Demonstration that these glycosides share the same metabolic fate would indicate applicability of the same regulatory paradigm. In vitro incubation assays with pooled human fecal homogenates, using rebaudiosides A, B, C, D, E, F and M, as well as steviolbioside and dulcoside A, at two concentrations over 24-48 h, were conducted to assess the metabolic fate of various steviol glycoside classes and to demonstrate that likely all steviol glycosides are metabolized to steviol. The data show that glycosidic side chains containing glucose, rhamnose, xylose, fructose and deoxy-glucose, including combinations of α(1-2), β-1, β(1-2), β(1-3), and β(1-6) linkages, were degraded to steviol mostly within 24 h. Given a common metabolite structure and a shared metabolic fate, safety data available for individual steviol glycosides can be used to support safety of purified steviol glycosides in general. Therefore, steviol glycosides specifications adopted by the regulatory authorities should include all steviol glycosides belonging to the five groups of steviol glycosides and a group acceptable daily intake established. Copyright © 2016 Elsevier Inc. All rights reserved.
Engineering an improved IgG4 molecule with reduced disulfide bond heterogeneity and increased Fab domain thermal stability.

PubMed

Peters, Shirley J; Smales, C Mark; Henry, Alistair J; Stephens, Paul E; West, Shauna; Humphreys, David P

2012-07-13

The integrity of antibody structure, stability, and biophysical characterization are becoming increasingly important as antibodies receive increasing scrutiny from regulatory authorities. We altered the disulfide bond arrangement of an IgG4 molecule by mutation of the Cys at the N terminus of the heavy chain constant domain 1 (C(H)1) (Kabat position 127) to a Ser and introduction of a Cys at a variety of positions (positions 227-230) at the C terminus of C(H)1. An inter-LC-C(H)1 disulfide bond is thus formed, which mimics the disulfide bond arrangement found in an IgG1 molecule. The antibody species present in the supernatant following transient expression in Chinese hamster ovary cells were analyzed by immunoblot to investigate product homogeneity, and purified product was analyzed by a thermofluor assay to determine thermal stability. We show that the light chain can form an inter-LC-C(H)1 disulfide bond with a Cys when present at several positions on the upper hinge (positions 227-230) and that such engineered disulfide bonds can consequently increase the Fab domain thermal stability between 3 and 6.8 °C. The IgG4 disulfide mutants displaying the greatest increase in Fab thermal stability were also the most homogeneous in terms of disulfide bond arrangement and antibody species present. Importantly, mutations did not affect the affinity for antigen of the resultant molecules. In combination with the previously described S241P mutation, we present an IgG4 molecule with increased Fab thermal stability and reduced product heterogeneity that potentially offers advantages for the production of IgG4 molecules.
Advance on the Flavonoid C-glycosides and Health Benefits.

PubMed

Xiao, Jianbo; Capanoglu, Esra; Jassbi, Amir Reza; Miron, Anca

2016-07-29

The dietary flavonoids, especially their glycosides, are the most vital phytochemicals in diets and are of great general interest due to their diverse bioactivity. Almost all natural flavonoids exist as their O-glycoside or C-glycoside forms in plants. The dietary flavonoid C-glycosides have received less attention than their corresponding O-glycosides. This review summarizes current knowledge regarding flavonoid C-glycosides and their influence on human health. Among the flavonoid C-glycosides, flavone C-glycosides, especially vitexin, isoorientin, orientin, isovitexin and their multiglycosides are more frequently mentioned than others. Flavonoid C-monoglycosides are poorly absorbed in human beings with very few metabolites in urine and blood and are deglycosylated and degraded by human intestinal bacteria in colon. However, flavonoid C-multiglycosides are absorbed unchanged in the intestine and distributed to other tissues. Flavonoid C-glycosides showed significant antioxidant activity, anticancer and antitumor activity, hepatoprotective activity, anti-inflammatory activity, anti-diabetes activity, antiviral activity, antibacterial and antifungal activity, and other biological effects. It looks like that the C-glycosylflavonoids in most cases showed higher antioxidant and anti-diabetes potential than their corresponding O-glycosylflavonoids and aglycones. However, there is a lack of in vivo data on the biological benefits of flavonoid C-glycosides. It is necessary to investigate more on how flavonoid C-glycosides prevent and handle the diseases.
San Francisquito Creek Stabilization at Bonde Weir Project

EPA Pesticide Factsheets

Information about the SFBWQP San Francisquito Creek Stabilization at Bonde Weir Project, part of an EPA competitive grant program to improve SF Bay water quality focused on restoring impaired waters and enhancing aquatic resources.
Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli*

PubMed Central

Weiss, Simon C.; Skerra, Arne; Schiefner, André

2015-01-01

Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1–4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli. PMID:26139606
Steroid-like compounds in Chinese medicines promote blood circulation via inhibition of Na+/K+-ATPase

PubMed Central

Chen, Ronald JY; Chung, Tse-yu; Li, Feng-yin; Yang, Wei-hung; Jinn, Tzyy-rong; Tzen, Jason TC

2010-01-01

Aim: To examine if steroid-like compounds found in many Chinese medicinal products conventionally used for the promotion of blood circulation may act as active components via the same molecular mechanism triggered by cardiac glycosides, such as ouabain. Methods: The inhibitory potency of ouabain and the identified steroid-like compounds on Na+/K+-ATPase activity was examined and compared. Molecular modeling was exhibited for the docking of these compounds to Na+/K+-ATPase. Results: All the examined steroid-like compounds displayed more or less inhibition on Na+/K+-ATPase, with bufalin (structurally almost equivalent to ouabain) exhibiting significantly higher inhibitory potency than the others. In the pentacyclic triterpenoids examined, ursolic acid and oleanolic acid were moderate inhibitors of Na+/K+-ATPase, and their inhibitory potency was comparable to that of ginsenoside Rh2. The relatively high inhibitory potency of ursolic acid or oleanolic acid was due to the formation of a hydrogen bond between its carboxyl group and the Ile322 residue in the deep cavity close to two K+ binding sites of Na+/K+-ATPase. Moreover, the drastic difference observed in the inhibitory potency of ouabain, bufalin, ginsenoside Rh2, and pentacyclic triterpenoids is ascribed mainly to the number of hydrogen bonds and partially to the strength of hydrophobic interaction between the compounds and residues around the deep cavity of Na+/K+-ATPase. Conclusion: Steroid-like compounds seem to contribute to therapeutic effects of many cardioactive Chinese medicinal products. Chinese herbs, such as Prunella vulgaris L, rich in ursolic acid, oleanolic acid and their glycoside derivatives may be adequate sources for cardiac therapy via effective inhibition on Na+/K+-ATPase. PMID:20523340
Benchmark studies on the building blocks of DNA. 2. Effect of biological environment on the electronic excitation spectrum of nucleobases.

PubMed

Szalay, Péter G; Watson, Thomas; Perera, Ajith; Lotrich, Victor; Fogarasi, Géza; Bartlett, Rodney J

2012-09-06

In the first paper of this series (Szalay; et al. J. Phys. Chem. A, 2012, 116, 6702) we have investigated the excited states of nucleobases. It was shown that it is only the equation of motion excitation energy coupled-cluster (EOMEE-CC) methods, which can give a balanced description for all type of the transitions of these molecules; if the goal is to obtain accurate results with uncertainty of about 0.1 eV only, triples corrections in the form of, e.g., the EOMEE-CCSD(T) method need to be included. In this second paper we extend this study to nucleobases in their biological environment, considering hydration, glycoside bond, and base pairing. EOMEE-CCSD and EOMEE-CCSD(T) methods are used with aug-cc-pVDZ basis. The effect of surrounding water was systematically investigated by considering one to five water molecules at different positions. It was found that hydration can modify the order of the excited states: in particular, nπ* states get shifted above the neighboring ππ* ones. The glycoside bond's effect is smaller, as shown by our calculations on cytidine and guanosine. Here the loss of planarity causes some intensity shift from ππ* to nπ* states. Finally, the guanine-cytosine (GC) Watson-Crick pair was studied; most of the states could be identified as local excitations on one of the bases, but there is also a low-lying charge-transfer state. Significant discrepancy with earlier CASPT2 and TDDFT studies was found for the GC pair and triples effects seem to be essential for all of these systems.
Stabilization of an immunoglobulin fold domain by an engineered disulfide bond at the buried hydrophobic region.

PubMed

Hagihara, Yoshihisa; Mine, Shouhei; Uegaki, Koichi

2007-12-14

We report for the first time the stabilization of an immunoglobulin fold domain by an engineered disulfide bond. In the llama single-domain antibody, which has human chorionic gonadotropin as its specific antigen, Ala49 and Ile70 are buried in the structure. A mutant with an artificial disulfide bond at this position showed a 10 degrees C higher midpoint temperature of thermal unfolding than that without the extra disulfide bond. The modified domains exhibited an antigen binding affinity comparable with that of the wild-type domain. Ala49 and Ile70 are conserved in camel and llama single-domain antibody frameworks. Therefore, domains against different antigens are expected to be stabilized by the engineered disulfide bond examined here. In addition to the effect of the loop constraints in the unfolded state, thermodynamic analysis indicated that internal interaction and hydration also control the stability of domains with disulfide bonds. The change in physical properties resulting from mutation often causes unpredictable and destabilizing effects on these interactions. The introduction of a hydrophobic cystine into the hydrophobic region maintains the hydrophobicity of the protein and is expected to minimize the unfavorable mutational effects.

Discrete and polymeric self-assembled dendrimers: Hydrogen bond-mediated assembly with high stability and high fidelity

PubMed Central

Corbin, Perry S.; Lawless, Laurence J.; Li, Zhanting; Ma, Yuguo; Witmer, Melissa J.; Zimmerman, Steven C.

2002-01-01

Hydrogen bond-mediated self-assembly is a powerful strategy for creating nanoscale structures. However, little is known about the fidelity of assembly processes that must occur when similar and potentially competing hydrogen-bonding motifs are present. Furthermore, there is a continuing need for new modules and strategies that can amplify the relatively weak strength of a hydrogen bond to give more stable assemblies. Herein we report quantitative complexation studies on a ureidodeazapterin-based module revealing an unprecedented stability for dimers of its self-complementary acceptoracceptor-donor-donor (AADD) array. Linking two such units together with a semirigid spacer that carries a first-, second-, or third-generation Fréchet-type dendron affords a ditopic structure programmed to self assemble. The specific structure that is formed depends both on the size of the dendron and the solvent, but all of the assemblies have exceptionally high stability. The largest discrete nanoscale assembly is a hexamer with a molecular mass of about 17.8 kDa. It is stabilized by 30 hydrogen bonds, including six AADD⋅DDAA contacts. The hexamer forms and is indefinitely stable in the presence of a hexamer containing six ADD⋅DAA hydrogen-bonding arrays. PMID:11917113
Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.
Super-pnicogen bonding in the radical anion of the fluorophosphine dimer

NASA Astrophysics Data System (ADS)

Setiawan, Dani; Cremer, Dieter

2016-10-01

The LUMO of the pnicogen-bonded fluoro-phosphine dimer has PP bonding character. Radical anion and dianion form relatively strong pnicogen bonds with some covalent character where however the dianion turns out to be a second order transition state. The binding energy of (FPH 2)2- is 30.4 kcal/mol (CCSD(T)/aug-cc-pVTZ; CASPT2(5,8): 30.7 kcal/mol) and the bond strength order measured with the local PP bond stretching force constant increases from 0.055 for the neutral dimer to 0.187 thus revealing that the stabilization of the radical anion is to a large extend a result of one-electron six-center delocalization. Pnicogen-bonded complexes have a stabilizing electron affinity.
Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules.

PubMed

Ayoub, Ahmed T; Craddock, Travis J A; Klobukowski, Mariusz; Tuszynski, Jack

2014-08-05

Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the β-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Dissecting the conformational determinants of chitosan and chitlac oligomers.

PubMed

Esteban, Carmen; Donati, Ivan; Pantano, Sergio; Villegas, Myriam; Benegas, Julio; Paoletti, Sergio

2018-06-01

Chitosan and its highly hydrophilic 1-deoxy-lactit-1-yl derivative (Chitlac) are polysaccharides with increasing biomedical applications. Aimed to unravel their conformational properties we have performed a series of molecular dynamics simulations of Chitosan/Chitlac decamers, exploring different degrees of substitution (DS) of lactitol side chains. At low DS, two conformational regions with different populations are visited, while for DS ≥ 20% the oligomers remain mostly linear and only one main region of the glycosidic angles is sampled. These conformers are (locally) characterized by extended helical "propensities". Helical conformations 3 2 and 2 1, by far the most abundant, only develop in the main region. The accessible conformational space is clearly enlarged at high ionic strength, evidencing also a new region accessible to the glycosidic angles, with short and frequent interchange between regions. Simulations of neutral decamers share these features, pointing to a central role of electrostatic repulsion between charged moieties. These interactions seem to determine the conformational behavior of the chitosan backbone, with no evident influence of H-bond interactions. Finally, it is also shown that increasing temperature only slightly enlarges the available conformational space, but certainly without signs of a temperature-induced conformational transition. © 2018 Wiley Periodicals, Inc.
High-resolution four-dimensional carbon-correlated 1H- 1H ROESY experiments employing isotags and the filter diagonalization method for effective assignment of glycosidic linkages in oligosaccharides

NASA Astrophysics Data System (ADS)

Armstrong, Geoffrey S.; Bendiak, Brad

2006-07-01

Four-dimensional nuclear magnetic resonance spectroscopy of oligosaccharides that correlates 1H-1H ROESY cross peaks to two additional 13C frequency dimensions is reported. The 13C frequencies were introduced by derivatization of all free hydroxyl groups with doubly 13C-labeled acetyl isotags. Pulse sequences were optimized for processing with the filter diagonalization method. The extensive overlap typically observed in 2D ROESY 1H-1H planes was alleviated by resolution of ROESY cross peaks in the two added dimensions associated with the carbon frequencies of the isotags. This enabled the interresidue 1H-1H ROESY cross peaks to be unambiguously assigned hence spatially proximate sugar spin systems across glycosidic bonds could be effectively ascertained. An experiment that selectively amplifies interresidue ROESY 1H-1H cross peaks is also reported. It moves the magnetization of an intraresidue proton normally correlated to a sugar H-1 signal orthogonally along the z axis prior to a Tr-ROESY mixing sequence. This virtually eliminates the incoherent intraresidue ROESY transfer, suppresses coherent TOCSY transfer, and markedly enhances the intensity of interresidue ROESY cross peaks.
High-resolution four-dimensional carbon-correlated 1H-1H ROESY experiments employing isotags and the filter diagonalization method for effective assignment of glycosidic linkages in oligosaccharides.

PubMed

Armstrong, Geoffrey S; Bendiak, Brad

2006-07-01

Four-dimensional nuclear magnetic resonance spectroscopy of oligosaccharides that correlates 1H-1H ROESY cross peaks to two additional 13C frequency dimensions is reported. The 13C frequencies were introduced by derivatization of all free hydroxyl groups with doubly 13C-labeled acetyl isotags. Pulse sequences were optimized for processing with the filter diagonalization method. The extensive overlap typically observed in 2D ROESY 1H-1H planes was alleviated by resolution of ROESY cross peaks in the two added dimensions associated with the carbon frequencies of the isotags. This enabled the interresidue 1H-1H ROESY cross peaks to be unambiguously assigned hence spatially proximate sugar spin systems across glycosidic bonds could be effectively ascertained. An experiment that selectively amplifies interresidue ROESY 1H-1H cross peaks is also reported. It moves the magnetization of an intraresidue proton normally correlated to a sugar H-1 signal orthogonally along the z axis prior to a Tr-ROESY mixing sequence. This virtually eliminates the incoherent intraresidue ROESY transfer, suppresses coherent TOCSY transfer, and markedly enhances the intensity of interresidue ROESY cross peaks.
Determination of acarbose by capillary zone electrophoresis.

PubMed

Lachmann, B; Noe, C R

2013-07-01

Acarbose (Glucobay, Bayer AG) acts as a potent alpha-glucosidase-inhibitor, which delays the intestinal starch digestion resulting in a reduction of postprandial blood glucose and insulin levels. Acarbose is a pseudo-tetrasaccharide, with two D-glucose units linked via an alpha 1-->4 glycosidic bond to acarviosin, which is a N-glycoside composed of an unsaturated cyclitol and 4-amino-4,6-dideoxy-alpha-D-glucopyranose. Several methods for the determination of acarbose by capillary electrophoresis can be found in literature. They are based either on the derivatisation with 7-aminonaphthalene-1,3-disulfonic acid (ANDS) or on the detection of the unsaturated cyclitol at wavelengths below 200 nm. The aim of our work was the determination of acarbose making use of a previously developed method based on reductive amination with S-phenylethylamine. The aminoalditols generated in the reaction formed differently charged borate-complexes depending on the configuration of the sugar. After successful method optimisation we were able to separate two potential impurities of acarbose, D-maltose und D-glucose. For the quantitation of acarbose in Glucobay tablets an additional borate-buffer system was established, reducing the total time of analysis to less than 10 min.
Purification and characterization of an antioxidant glycoprotein from the hydrolysate of Mustelus griseus.

PubMed

Li, Zhongrui; Wang, Bin; Chi, Changfeng; Gong, Yandan; Tang, Jiajia; Luo, Hongyu

2013-01-01

An antioxidant glycoprotein (Fraction AIV-2) with molecular weight of 27.2 kDa was purified from the ethanol-soluble protein hydrolysate of Mustelus griseus muscle. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity of Fraction AIV-2 reached up to 96.73±2.33% and was higher than that of ascorbic acid at the concentration of 5.0mg/mL. Total protein and carbohydrate contents of Fraction AIV-2 were 62.65±0.63% and 33.49±1.60%, respectively. Seventeen amino acids were identified in Fraction AIV-2, most of which are serine. GC-MS analysis showed that Fraction AIV-2 was composed of fucose, arabinose, galactose, glucose and mannose with the ratio of 1.00:1.53:7.27:9.07:2.09. The FT-IR spectrum of Fraction AIV-2 showed typical characteristics of polysaccharide and protein. For Fraction AIV-2, the changes of ultraviolet absorption curve, amino acid composition after the β-elimination reaction and its deglycosylation with the treatment of N-glycosidase F suggested that both O-glycosidic and N-glycosidic bonds were involved in the polysaccharide and protein moieties. Copyright © 2012 Elsevier B.V. All rights reserved.
Purine 3':5'-cyclic nucleotides with the nucleobase in a syn orientation: cAMP, cGMP and cIMP.

PubMed

Řlepokura, Katarzyna Anna

2016-06-01

Purine 3':5'-cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid-state conformational details still require investigation. Five crystals containing purine 3':5'-cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3':5'-cyclic phosphate dihydrate, C10H12N5O6P·2H2O or cAMP·2H2O, (I), adenosine 3':5'-cyclic phosphate 0.3-hydrate, C10H12N5O6P·0.3H2O or cAMP·0.3H2O, (II), guanosine 3':5'-cyclic phosphate pentahydrate, C10H12N5O7P·5H2O or cGMP·5H2O, (III), sodium guanosine 3':5'-cyclic phosphate tetrahydrate, Na(+)·C10H11N5O7P(-)·4H2O or Na(cGMP)·4H2O, (IV), and sodium inosine 3':5'-cyclic phosphate tetrahydrate, Na(+)·C10H10N4O7P(-)·4H2O or Na(cIMP)·4H2O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP(-) in (IV) and cIMP(-) in (V)] are syn conformers about the N-glycosidic bond, and this nucleobase arrangement is accompanied by Crib-H...Npur hydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context of syn-anti conformational preferences has revealed that among the syn conformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing the syn conformation have been indicated. The inter-nucleotide contacts in (I)-(V) have been systematized in terms of the chemical groups involved. All five structures display three-dimensional hydrogen-bonded networks.
Lipoxygenase-inhibiting phenolic glycosides and monoterpene glycosides from Paeonia lactiflora.

PubMed

Zou, Liang; Hu, Lin-Feng; Guo, Yi-Dong; Song, Yu; Fu, Qiang

2015-01-01

The EtOH extract of the roots of Paeonia lactiflora afforded a new phenolic glycoside paenoside A (1) and a new monoterpene glycoside paeonin D (2), and five known monoterpene glycosides. Their structures were elucidated on the basis of spectroscopic means and hydrolysis products. All compounds displayed inhibitory potential against enzyme lipoxygenase.
Energy decomposition analysis of single bonds within Kohn-Sham density functional theory.

PubMed

Levine, Daniel S; Head-Gordon, Martin

2017-11-28

An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.
Development of a novel niosomal system for oral delivery of Ginkgo biloba extract

PubMed Central

Jin, Ye; Wen, Jingyuan; Garg, Sanjay; Liu, Da; Zhou, Yulin; Teng, Lirong; Zhang, Weiyu

2013-01-01

Background The aim of this study was to develop an optimal niosomal system to deliver Ginkgo biloba extract (GbE) with improved oral bioavailability and to replace the conventional GbE tablets. Methods In this study, the film dispersion-homogenization method was used to prepare GbE niosomes. The resulting GbE niosome suspension was freeze-dried or spray-dried to improve the stability of the niosomes. GbE-loaded niosomes were formulated and characterized in terms of their morphology, particle size, zeta potential, entrapment efficiency, and angle of repose, and differential scanning calorimetry analysis was performed. In vitro release and in vivo distribution studies were also carried out. Results The particle size of the optimal delivery system prepared with Tween 80, Span 80, and cholesterol was about 141 nm. There was a significant difference (P < 0.05) in drug entrapment efficiency between the spray-drying method (about 77.5%) and the freeze-drying method (about 50.1%). The stability study revealed no significant change in drug entrapment efficiency for the GbE niosomes at 4°C and 25°C after 3 months. The in vitro release study suggested that GbE niosomes can prolong the release of flavonoid glycosides in phosphate-buffered solution (pH 6.8) for up to 48 hours. The in vivo distribution study showed that the flavonoid glycoside content in the heart, lung, kidney, brain, and blood of rats treated with the GbE niosome carrier system was greater than in the rats treated with the oral GbE tablet (P < 0.01). No flavonoid glycosides were detected in the brain tissue of rats given the oral GbE tablets, but they were detected in the brain tissue of rats given the GbE niosomes. Conclusion Niosomes are a promising oral system for delivery of GbE to the brain. PMID:23378764
Engineering of isoamylase: improvement of protein stability and catalytic efficiency through semi-rational design.

PubMed

Li, Youran; Zhang, Liang; Ding, Zhongyang; Gu, Zhenghua; Shi, Guiyang

2016-01-01

Isoamylase catalyzes the hydrolysis of α-1,6-glycosidic linkages in glycogen, amylopectin and α/β-limit dextrins. A semi-rational design strategy was performed to improve catalytic properties of isoamylase from Bacillus lentus. Three residues in vicinity of the essential residues, Arg505, Asn513, and Gly608, were chosen as the mutation sites and were substituted by Ala, Pro, Glu, and Lys, respectively. Thermal stability of the mutant R505P and acidic stability of the mutant R505E were enhanced. The k cat /K m values of the mutant G608V have been promoted by 49%, and the specific activity increased by 33%. This work provides an effective strategy for improving the catalytic activity and stability of isoamylase, and the results obtained here may be useful for the improvement of catalytic properties of other α/β barrel enzymes.
A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria.

PubMed

Javornik, Uroš; Plavec, Janez; Wang, Baifan; Graham, Steven M

2018-01-02

A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca 2+ -release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔH o , ΔS o ) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ + conformer, whereas the A-ring γ-bond was a mixture of the γ + and γ t conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ + conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond. Copyright © 2017 Elsevier Ltd. All rights reserved.
Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

PubMed

Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

1999-03-12

In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

PubMed Central

Sharma, Rita; Cao, Peijian; Jung, Ki-Hong; Sharma, Manoj K.; Ronald, Pamela C.

2013-01-01

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification. PMID:23986771
Novel Benzoxazine-Based Aglycones Block Glucose Uptake In Vivo by Inhibiting Glycosidases

PubMed Central

Jagadish, Swamy; Paricharak, Shardul; Hemshekhar, Mahadevappa; Mason, Daniel; Kemparaju, Kempaiah; Girish, Kesturu S.; Basappa; Bender, Andreas; Rangappa, Kanchugarakoppal S.

2014-01-01

Glycoside hydrolases catalyze the selective hydrolysis of glycosidic bonds in oligosaccharides, polysaccharides, and their conjugates. β-glucosidases occur in all domains of living organisms and constitute a major group among glycoside hydrolases. On the other hand, the benzoxazinoids occur in living systems and act as stable β-glucosides, such as 2-(2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one)-β-D-gluco-pyranose, which hydrolyse to an aglycone DIMBOA. Here, we synthesized the library of novel 1,3-benzoxazine scaffold based aglycones by using 2-aminobenzyl alcohols and aldehydes from one-pot reaction in a chloroacetic acid catalytic system via aerobic oxidative synthesis. Among the synthesized benzoxazines, 4-(7-chloro-2,4-dihydro-1H-benzo[d][1,3]oxazin-2-yl)phenol (compound 7) exhibit significant inhibition towards glucosidase compared to acarbose, with a IC50 value of 11.5 µM. Based upon results generated by in silico target prediction algorithms (Naïve Bayesian classifier), these aglycones potentially target the additional sodium/glucose cotransporter 1 (where a log likelihood score of 2.70 was observed). Furthermore, the in vitro glucosidase activity was correlated with the in silico docking results, with a high docking score for the aglycones towards the substrate binding site of glycosidase. Evidently, the in vitro and in vivo experiments clearly suggest an anti-hyperglycemic effect via glucose uptake inhibition by 4-(7-chloro-2,4-dihydro-1H-benzo[d][1,3]oxazin-2-yl)phenol in the starved rat model. These synthetic aglycones could constitute a novel pharmacological approach for the treatment, or re-enforcement of existing treatments, of type 2 diabetes and associated secondary complications. PMID:25047583
Structural characterization by both positive and negative electrospray ion trap mass spectrometry of oligogalacturonates purified by high-performance anion-exchange chromatography.

PubMed

Quéméner, Bernard; Désiré, Cédric; Debrauwer, Laurent; Rathahao, Estelle

2003-01-17

The off-line coupling of high-performance anion-exchange chromatography to electrospray ion trap mass spectrometry (ESI-IT-MS) is described. Two sets of isocratic conditions were optimised for the semi-preparative purification of oligogalacturonates of degree of polymerisation from 4 to 6 by monitoring eluates with either pulsed amperometric detection or evaporative light scattering detection in the presence of an online Dionex Carbohydrate Membrane Desalter (CMD). In these conditions, purified oligogalacturonate solutions were suitable, without further desalting steps, for infusion ESI-IT-MS experiments. This paper provides some interesting features of positive and negative ESI-IT-multiple MS (MSn) of these acidic oligosaccharides. The spectra acquired in both ion modes show characteristic fragments resulting from glycosidic bond and cross-ring cleavages. Under negative ionization conditions, the fragmentation of the singly-charged [M-H]- ions, as well as the Ci-, and Zi-, fragment ions through sequential MSn experiments, was always dominated by product ions from C- and Z-type glycosidic cleavages. All spectra also displayed 0.2 A-type cross-ring cleavage ions which carry linkage information. Collision-induced dissociation (CID) spectra of sodium-cationized species obtained under positive ionization conditions were more complex. Successive MSn experiments also led to the 0.2 A-type cross-ring cleavage ions observed together with B- and Y-type ions. The presence of the 0.2 A ion series was related to Mr 60 (C2H4O2) losses. Combined with the absence of the Mr 30 (CH2O) and the Mr 90 (C3H6O3) ions, these ions were indicative of 1-4 type glycosidic linkage.
Computational Investigation of the pH Dependence of Loop Flexibility and Catalytic Function in Glycoside Hydrolases*

PubMed Central

Bu, Lintao; Crowley, Michael F.; Himmel, Michael E.; Beckham, Gregg T.

2013-01-01

Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ∼5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pKa values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pKa values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pKa values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes. PMID:23504310

Liquid chromatography-tandem mass spectrometry analysis allows the simultaneous characterization of C-glycosyl and O-glycosyl flavonoids in stingless bee honeys.

PubMed

Truchado, Pilar; Vit, Patricia; Ferreres, Federico; Tomas-Barberan, Francisco

2011-10-21

The analysis of the phytochemicals present in stingless bee honey samples has been a difficult task due to the small amounts of samples available and to the complexity of the phytochemical composition that often combines flavonoid glycosides and aglycones. Honey samples produced in Venezuela from Melipona species were analyzed using a combination of solid-phase extraction and HPLC-DAD-MSn/ESI methodologies with specific study of the fragment ions produced from flavonoid glycosides. The analyses revealed that flavonoid glycosides were the main constituents. The honey samples analyzed contained a consistent flavonoid pattern composed of flavone-C-glycosides, flavonol-O-glycosides and flavonoid aglycones. The HPLC-DAD-MSn/ESI analysis and the study of the fragment ions obtained allowed the characterization and quantification for the first time of five apigenin-di-C-glycosides, and ten quercetin, kaempferol and isorhamnetin O-glycosides (di- and tri- glycosides), and the aglycones pinobanksin, quercetin, kaempferol and isorhamnetin in the different samples. This is the first report of flavonoid-C-glycosides in honey. The results show that the content of flavonoid-glycosides (mean values of 2712 μg/100 g) in stingless bee honeys is considerably higher than the content of flavonoid aglycones (mean values of 315 μg/100 g). This differs from previous studies on Apis mellifera honeys that consistently showed much higher aglycone content and smaller flavonoid glycoside content. The occurrence of relevant amounts of flavonoid glycosides, and particularly C-glycosides, in stingless bee honeys could be associated with their putative anticataract properties. Copyright © 2011 Elsevier B.V. All rights reserved.
Synthesis of the oligosaccharides related to branching sites of fucosylated chondroitin sulfates from sea cucumbers.

PubMed

Ustyuzhanina, Nadezhda E; Fomitskaya, Polina A; Gerbst, Alexey G; Dmitrenok, Andrey S; Nifantiev, Nikolay E

2015-02-02

Natural anionic polysaccharides fucosylated chondroitin sulfates (FCS) from sea cucumbers attract great attention nowadays due to their ability to influence various biological processes, such as blood coagulation, thrombosis, angiogenesis, inflammation, bacterial and viral adhesion. To determine pharmacophore fragments in FCS we have started systematic synthesis of oligosaccharides with well-defined structure related to various fragments of these polysaccharides. In this communication, the synthesis of non-sulfated and selectively O-sulfated di- and trisaccharides structurally related to branching sites of FCS is described. The target compounds are built up of propyl β-d-glucuronic acid residue bearing at O-3 α-l-fucosyl or α-l-fucosyl-(1→3)-α-l-fucosyl substituents. O-Sulfation pattern in the fucose units of the synthetic targets was selected according to the known to date holothurian FCS structures. Stereospecific α-glycoside bond formation was achieved using 2-O-benzyl-3,4-di-O-chloroacetyl-α-l-fucosyl trichloroacetimidate as a donor. Stereochemical outcome of the glycosylation was explained by the remote participation of the chloroacetyl groups with the formation of the stabilized glycosyl cations, which could be attacked by the glycosyl acceptor only from the α-side. The experimental results were in good agreement with the SCF/MP2 calculated energies of such participation. The synthesized oligosaccharides are regarded as model compounds for the determination of a structure-activity relationship in FCS.
Synthesis of the Oligosaccharides Related to Branching Sites of Fucosylated Chondroitin Sulfates from Sea Cucumbers

PubMed Central

Ustyuzhanina, Nadezhda E.; Fomitskaya, Polina A.; Gerbst, Alexey G.; Dmitrenok, Andrey S.; Nifantiev, Nikolay E.

2015-01-01

Natural anionic polysaccharides fucosylated chondroitin sulfates (FCS) from sea cucumbers attract great attention nowadays due to their ability to influence various biological processes, such as blood coagulation, thrombosis, angiogenesis, inflammation, bacterial and viral adhesion. To determine pharmacophore fragments in FCS we have started systematic synthesis of oligosaccharides with well-defined structure related to various fragments of these polysaccharides. In this communication, the synthesis of non-sulfated and selectively O-sulfated di- and trisaccharides structurally related to branching sites of FCS is described. The target compounds are built up of propyl β-d-glucuronic acid residue bearing at O-3 α-l-fucosyl or α-l-fucosyl-(1→3)-α-l-fucosyl substituents. O-Sulfation pattern in the fucose units of the synthetic targets was selected according to the known to date holothurian FCS structures. Stereospecific α-glycoside bond formation was achieved using 2-O-benzyl-3,4-di-O-chloroacetyl-α-l-fucosyl trichloroacetimidate as a donor. Stereochemical outcome of the glycosylation was explained by the remote participation of the chloroacetyl groups with the formation of the stabilized glycosyl cations, which could be attacked by the glycosyl acceptor only from the α-side. The experimental results were in good agreement with the SCF/MP2 calculated energies of such participation. The synthesized oligosaccharides are regarded as model compounds for the determination of a structure-activity relationship in FCS. PMID:25648510
Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics.

PubMed

Pinto-Junior, Vanir Reis; Santiago, Mayara Queiroz; Nobre, Camila Bezerra; Osterne, Vinicius Jose Silva; Leal, Rodrigo Bainy; Cajazeiras, Joao Batista; Lossio, Claudia Figueiredo; Rocha, Bruno Anderson Matias; Martins, Maria Gleiciane Queiroz; Nobre, Clareane Avelino Simplicio; Silva, Mayara Torquato Lima; Nascimento, Kyria Santiago; Cavada, Benildo Sousa

2017-09-15

The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P2 1 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 Å and was similar to that of other Vicieae lectins. The structure presented R factor and R free of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe. Copyright © 2017 Elsevier Inc. All rights reserved.
Detection and Quantitation of Afucosylated N-Linked Oligosaccharides in Recombinant Monoclonal Antibodies Using Enzymatic Digestion and LC-MS

NASA Astrophysics Data System (ADS)

Du, Yi; May, Kimberly; Xu, Wei; Liu, Hongcheng

2012-07-01

The presence of N-linked oligosaccharides in the CH2 domain has a significant impact on the structure, stability, and biological functions of recombinant monoclonal antibodies. The impact is also highly dependent on the specific oligosaccharide structures. The absence of core-fucose has been demonstrated to result in increased binding affinity to Fcγ receptors and, thus, enhanced antibody-dependent cellular cytotoxicity (ADCC). Therefore, a method that can specifically determine the level of oligosaccharides without the core-fucose (afucosylation) is highly desired. In the current study, recombinant monoclonal antibodies and tryptic peptides from the antibodies were digested using endoglycosidases F2 and H, which cleaves the glycosidic bond between the two primary GlcNAc residues. As a result, various oligosaccharides of either complex type or high mannose type that are commonly observed for recombinant monoclonal antibodies are converted to either GlcNAc residue only or GlcNAc with the core-fucose. The level of GlcNAc represents the sum of all afucosylated oligosaccharides, whereas the level of GlcNAc with the core-fucose represents the sum of all fucosylated oligosaccharides. LC-MS analysis of the enzymatically digested antibodies after reduction provided a quick estimate of the levels of afucosylation. An accurate determination of the level of afucosylation was obtained by LC-MS analysis of glycopeptides after trypsin digestion.
Structural insights into the catalytic mechanism of a family 18 exo-chitinase

PubMed Central

van Aalten, D. M. F.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. H.

2001-01-01

Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites −2 to +3) shows closure of the “roof” of the active site tunnel. It also shows that the sugar in the −1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle. PMID:11481469
Brachybacterium sp. CH-KOV3 isolated from an oil-polluted environment-a new producer of levan.

PubMed

Djurić, Aleksandra; Gojgić-Cvijović, Gordana; Jakovljević, Dragica; Kekez, Branka; Kojić, Jovana Stefanović; Mattinen, Maija-Liisa; Harju, Inka Elina; Vrvić, Miroslav M; Beškoski, Vladimir P

2017-11-01

Various microorganisms isolated from polluted environments, such as Pseudomonas sp. and Micrococcus sp. can synthesize exopolysaccharides (EPSs) which are natural, non-toxic and biodegradable polymers. EPSs play a key role in protection of microbial cells under various external influences. For humans, these substances have potential use in many industries. EPSs can be applied as a flavor or a fragrance carrier, an emulsifier, a stabilizer, a prebiotic, an antioxidant or an antitumor agent. In this study, we characterized an environmental microorganism that produces EPS, optimized EPS production by this strain and characterized the EPS produced. Isolate CH-KOV3 was identified as Brachybacterium paraconglomeratum. The sucrose level in the growth medium greatly influenced EPS production, and the highest yield was when the microorganism was incubated in media with 500g/L of sucrose. The optimal temperature and pH were 28°C and 7.0, respectively. The nuclear magnetic resonance (NMR) results and GC-MS analysis confirmed that the residues were d-fructofuranosyl residues with β-configuration, where fructose units are linked by β-2,6-glycosidic bonds, with β-2,1-linked branches. All these data indicate that the investigated EPS is a levan-type polysaccharide. Thus, it was concluded that Brachybacterium sp. CH-KOV3 could constitute a new source for production of the bioactive polysaccharide, levan. Copyright © 2017 Elsevier B.V. All rights reserved.
Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods.

PubMed

Shen, Liangliang; Xu, Hong; Huang, Fengwen; Li, Yi; Xiao, Huafeng; Yang, Zhen; Hu, Zhangli; He, Zhendan; Zeng, Zheling; Li, Yinong

2015-01-25

Ligupurpuroside A is one of the major glycoside in Ku-Din-Cha, a type of Chinese functional tea. In order to better understand its digestion and metabolism in humans, the interaction between Ligupurpuroside A and pepsin has been investigated by fluorescence spectra, UV-vis absorption spectra and synchronous fluorescence spectra along with molecular docking method. The fluorescence experiments indicate that Ligupurpuroside A can effectively quench the intrinsic fluorescence of pepsin through a combined quenching way at the low concentration of Ligupurpuroside A, and a static quenching procedure at the high concentration. The binding constant, binding sites of Ligupurpuroside A with pepsin have been calculated. The thermodynamic analysis suggests that non-covalent reactions, including electrostatic force, hydrophobic interaction and hydrogen bond are the main forces stabilizing the complex. According to the Förster's non-radiation energy transfer theory, the binding distance between pepsin and Ligupurpuroside A was calculated to be 3.15 nm, which implies that energy transfer occurs between pepsin and Ligupurpuroside A. Conformation change of pepsin was observed from UV-vis absorption spectra and synchronous fluorescence spectra under experimental conditions. In addition, all these experimental results have been validated by the protein-ligand docking studies which show that Ligupurpuroside A is located in the cleft between the domains of pepsin. Copyright © 2014 Elsevier B.V. All rights reserved.
EVALUATION OF CHEMICALLY BONDED PHOSPHATE CERAMICS FOR MERCURY STABILIZATION OF A MIXED SYNTHETIC WASTE

EPA Science Inventory

This experimental study was conducted to evaluate the stabilization and encapsulation technique developed by Argonne National Laboratory, called the Chemically Bonded Phosphate Ceramics technology for Hg- and HgCl₂-contaminated synthetic waste materials. Leachability ...
Structure-based approach to the prediction of disulfide bonds in proteins.

PubMed

Salam, Noeris K; Adzhigirey, Matvey; Sherman, Woody; Pearlman, David A

2014-10-01

Protein engineering remains an area of growing importance in pharmaceutical and biotechnology research. Stabilization of a folded protein conformation is a frequent goal in projects that deal with affinity optimization, enzyme design, protein construct design, and reducing the size of functional proteins. Indeed, it can be desirable to assess and improve protein stability in order to avoid liabilities such as aggregation, degradation, and immunogenic response that may arise during development. One way to stabilize a protein is through the introduction of disulfide bonds. Here, we describe a method to predict pairs of protein residues that can be mutated to form a disulfide bond. We combine a physics-based approach that incorporates implicit solvent molecular mechanics with a knowledge-based approach. We first assign relative weights to the terms that comprise our scoring function using a genetic algorithm applied to a set of 75 wild-type structures that each contains a disulfide bond. The method is then tested on a separate set of 13 engineered proteins comprising 15 artificial stabilizing disulfides introduced via site-directed mutagenesis. We find that the native disulfide in the wild-type proteins is scored well, on average (within the top 6% of the reasonable pairs of residues that could form a disulfide bond) while 6 out of the 15 artificial stabilizing disulfides scored within the top 13% of ranked predictions. Overall, this suggests that the physics-based approach presented here can be useful for triaging possible pairs of mutations for disulfide bond formation to improve protein stability. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Identification of complex, naturally occurring flavonoid glycosides in kale (Brassica oleracea var. sabellica) by high-performance liquid chromatography diode-array detection/electrospray ionization multi-stage mass spectrometry.

PubMed

Schmidt, Susanne; Zietz, Michaela; Schreiner, Monika; Rohn, Sascha; Kroh, Lothar W; Krumbein, Angelika

2010-07-30

Kale is a member of the Brassicaceae family and has a complex profile of flavonoid glycosides. Therefore, kale is a suitable matrix to discuss in a comprehensive study the different fragmentation patterns of flavonoid glycosides. The wide variety of glycosylation and acylation patterns determines the health-promoting effects of these glycosides. The aim of this study is to investigate the naturally occurring flavonoids in kale. A total of 71 flavonoid glycosides of quercetin, kaempferol and isorhamnetin were identified using a high-performance liquid chromatography diode-array detection/electrospray ionization multi-stage mass spectrometry (HPLC-DAD/ESI-MS(n)) method. Of these 71 flavonol glycosides, 27 were non-acylated, 30 were monoacylated and 14 were diacylated. Non-acylated flavonol glycosides were present as mono-, di-, tri- and tetraglycosides. This is the first time that the occurrence of four different fragmentation patterns of non-acylated flavonol triglycosides has been reported in one matrix simultaneously. In addition, 44 flavonol glycosides were acylated with p-coumaric, caffeic, ferulic, hydroxyferulic or sinapic acid. While monoacylated glycosides existed as di-, tri- and tetraglycosides, diacylated glycosides occurred as tetra- and pentaglycosides. To the best of our knowledge, 28 compounds in kale are reported here for the first time. These include three acylated isorhamnetin glycosides (isorhamnetin-3-O-sinapoyl-sophoroside-7-O-D-glucoside, isorhamnetin-3-O-feruloyl-sophoroside-7-O-diglucoside and isorhamnetin-3-O-disinapoyl-triglucoside-7-O-diglucoside) and seven non-acylated isorhamnetin glycosides. Copyright 2010 John Wiley & Sons, Ltd.
Electrostatics determine vibrational frequency shifts in hydrogen bonded complexes.

PubMed

Dey, Arghya; Mondal, Sohidul Islam; Sen, Saumik; Ghosh, Debashree; Patwari, G Naresh

2014-12-14

The red-shifts in the acetylenic C-H stretching vibration of C-H∙∙∙X (X = O, N) hydrogen-bonded complexes increase with an increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the dispersion modulates the stabilization energy.
Perspectives for the industrial enzymatic production of glycosides.

PubMed

de Roode, B Mattheus; Franssen, Maurice C R; van der Padt, Albert; Boom, Remko M

2003-01-01

Glycosides are of commercial interest for industry in general and specifically for the pharmaceutical and food industry. Currently chemical preparation of glycosides will not meet EC food regulations, and therefore chemical preparation of glycosides is not applicable in the food industry. Thus, enzyme-catalyzed reactions are a good alternative. However, until now the low yields obtained by enzymatic methods prevent the production of glycosides on a commercial scale. Therefore, high yields should be established by a combination of optimum reaction conditions and continuous removal of the product. Unfortunately, a bioreactor for the commercial scale production of glycosides is not available. The aim of this article is to discuss the literature with respect to enzymatic production of glycosides and the design of an industrially viable bioreactor system.
Design of SGLT2 Inhibitors for the Treatment of Type 2 Diabetes: A History Driven by Biology to Chemistry.

PubMed

Cai, Wenqing; Jiang, Linlin; Xie, Yafei; Liu, Yuqiang; Liu, Wei; Zhao, Guilong

2015-01-01

A brief history of the design of sodium-dependent glucose cotransporter 2 (SGLT2) inhibitors is reviewed. The design of O-glucoside SGLT2 inhibitors by structural modification of phlorizin, a naturally occurring O-glucoside, in the early stage was a process mainly driven by biology with anticipation of improving SGLT2/SGLT1 selectivity and increasing metabolic stability. Discovery of dapagliflozin, a pioneering C-glucoside SGLT2 inhibitor developed by Bristol-Myers Squibb, represents an important milestone in this history. In the second stage, the design of C-glycoside SGLT2 inhibitors by modifications of the aglycone and glucose moiety of dapagliflozin, an original structural template for almost all C-glycoside SGLT2 inhibitors, was mainly driven by synthetic organic chemistry due to the challenge of designing dapagliflozin derivatives that are patentable, biologically active and synthetically accessible. Structure-activity relationships (SAR) of the SGLT2 inhibitors are also discussed.
Extraction, Characterization, Stability and Biological Activity of Flavonoids Isolated from Chamomile Flowers

PubMed Central

Srivastava, Janmejai K; Gupta, Sanjay

2009-01-01

Dried flowers of Chamomile (Matricaria chamomilla) are largely used for their medicinal properties. In the present study, we examined the pharmacological properties of aqueous and methanolic fraction isolated from two varieties of German chamomile. HPLC-MS analysis of chamomile extract confirmed apigenin-7-O-glucoside as the major constituent of chamomile; some minor glycoside components were observed along with essential oils. These glucosides are highly stable in solution at different temperature range and their degradation occurs after long-term storage and extraction conditions at different pH and solvent. Methanolic fraction isolated from chamomile flowers demonstrated higher biologic response in inhibiting cell growth and causing induction of apoptosis in various human cancer cell lines compared to aqueous chamomile fraction. Apigenin glucosides inhibited cancer cell growth through deconjugation of glycosides that occurs in the cellular compartment to produce aglycone, apigenin. Taken together, the pharmacological profile of chamomile extract was dependent upon extraction process, storage conditions which affected the biological activity. PMID:20098626
Enormous Hydrogen Bond Strength Enhancement through π-Conjugation Gain: Implications for Enzyme Catalysis.

PubMed

Wu, Chia-Hua; Ito, Keigo; Buytendyk, Allyson M; Bowen, K H; Wu, Judy I

2017-08-22

Surprisingly large resonance-assistance effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, hydrogen bond donor (XH) forms a hydrogen bond to a charged substrate (Y - ), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH···Y - ] hydrogen bond strength by ≥15 kcal/mol. This reciprocal relationship departs from the widespread pK a concept (i.e., the idea that short, strong hydrogen bonds form when the interacting moieties have matching pK a values), which has been the rationale for enzymic acid-base reactions. The findings presented here provide new insight into how short, strong hydrogen bonds could form in enzymes.
The effect of high hydrostatic pressure treatment on the molecular structure of starches with different amylose content.

PubMed

Szwengiel, Artur; Lewandowicz, Grażyna; Górecki, Adrian R; Błaszczak, Wioletta

2018-02-01

The effect of high hydrostatic pressure processing (650MPa/9min) on molecular mass distribution, and hydrodynamic and structural parameters of amylose (maize, sorghum, Hylon VII) and amylopectin (waxy maize, amaranth) starches was studied. The starches were characterized by high-performance size-exclusion chromatography (HPSEC) equipped with static light scattering and refractive index detectors and by Fourier Transform Infrared (FTIR) spectroscopy. Significant changes were observed in molecular mass distribution of pressurized waxy maize starch. Changes in branches/branch frequency, intrinsic viscosity, and radius of gyration were observed for all treated starches. The combination of SEC and FTIR data showed that α-1,6-glycosidic bonds are more frequently split in pressurized amaranth, Hylon VII, and waxy maize starch, while in sorghum and maize starches, the α-1,4 bonds are most commonly split. Our results show that the structural changes found for pressurized starches were more strongly determined by the starch origin than by the processing applied. Copyright © 2017 Elsevier Ltd. All rights reserved.
In situ coupling of chitosan onto polypropylene foils by an Atmospheric Pressure Air Glow Discharge with a liquid cathode.

PubMed

Nikitin, D; Choukourov, A; Titov, V; Kuzmicheva, L; Lipatova, I; Mezina, E; Aleksandriiskii, V; Shelemin, A; Khalakhan, I; Slavinska, D; Biederman, H

2016-12-10

Atmospheric air plasma treatment of chitosan solutions leads to degradation of chitosan molecules by OH radicals and is accompanied by a predominant cleavage of glycosidic linkages and by a decrease of the molecular weight. The degradation proceeds via first order kinetics with the rate constant of (5.73±0.22)×10(-6)s(-1) and the energetic yield of chitosan bond scission of (2.4±0.2)×10(-8)mol/J. Products of degradation together with intact chitosan molecules adsorb and form coatings on polypropylene foils immersed into the solution that is being plasma treated. The plasma treatment results in strong binding of chitosan to polypropylene due to the formation of covalent bonds between the activated polymer surface and chitosan molecules. Plasma-driven crosslinking is responsible for the accumulation of compressive stress which leads to the development of buckling instabilities in the chitosan coatings. Copyright © 2016 Elsevier Ltd. All rights reserved.
Quercetin and isorhamnetin glycosides in onion (Allium cepa L.): varietal comparison, physical distribution, coproduct evaluation, and long-term storage stability.

PubMed

Lee, Jihyun; Mitchell, Alyson E

2011-02-09

During onion processing, the outer dried protective layer (outer paper layer) and first two fleshy leaf layers are removed. This coproduct material is a potential commercial source of flavonoids especially quercetin. In the following study, the flavonoid composition was determined in coproduct materials and the press cake (material generated after juice extraction) in several commercially important onion varieties grown in California. Flavonoids were characterized and quantified using LC-(ESI)MS/MS and HPLC. The long-term stability of quercetin glycosides was assessed in dried coproduct materials stored at 4 and 22 °C over a 12 month period. In all varieties, the predominant forms of quercetin were the quercetin 3,4'-O-glucoside and 4'-O-glucoside. The first layer had significantly higher levels of flavonoids than the outer paper, second, and inner flesh layers on a DW basis (p < 0.05). Allium cepa "Milestone" contained the highest levels (p < 0.05) of flavonoids (1703 mg/100 g on a dry weight basis (DW). Onion press cake had significantly higher levels of total quercetin as compared with fresh onions (p < 0.05). The levels of 4'-O-glucoside significantly decreased during the first month of storage and remained stable for 12 months of storage at either 4 or 22 °C (p < 0.05).
Effects of flavonoid glycosides obtained from a Ginkgo biloba extract fraction on the physical and oxidative stabilities of oil-in-water emulsions prepared from a stripped structured lipid with a low omega-6 to omega-3 ratio.

PubMed

Yang, Dan; Wang, Xiang-Yu; Gan, Lu-Jing; Zhang, Hua; Shin, Jung-Ah; Lee, Ki-Teak; Hong, Soon-Taek

2015-05-01

In this study, we have produced a structured lipid with a low ω6/ω3 ratio by lipase-catalysed interesterification with perilla and grape seed oils (1:3, wt/wt). A Ginkgo biloba leaf extract was fractionated in a column packed with HP-20 resin, producing a flavonoid glycoside fraction (FA) and a biflavone fraction (FB). FA exhibited higher antioxidant capacity than FB, showing 58.4 mmol gallic acid equivalent (GAE)/g-of-total-phenol-content, 58.8 mg quercetin equivalent (QUE)/g-of-total-flavonoid-content, 4.5 mmol trolox/g-of-trolox-equivalent antioxidant capacity, 0.14 mg extract/mL-of-free-radical-scavenging-activity (DPPH assay, IC50), and 2.3 mmol Fe2SO4 · 7H2O/g-of-ferric-reducing-antioxidant-power. The oil-in-water emulsion containing the stripped structured lipid as an oil phase with FA exhibited the highest stability and the lowest oil globule diameters (d43 and d32), where the aggregation was unnoticeable by Turbiscan and particle size analyses during 30 days of storage. Furthermore, FA was effective in retarding the oxidation of the emulsions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enhanced production of a single domain antibody with an engineered stabilizing extra disulfide bond.

PubMed

Liu, Jinny L; Goldman, Ellen R; Zabetakis, Dan; Walper, Scott A; Turner, Kendrick B; Shriver-Lake, Lisa C; Anderson, George P

2015-10-09

Single domain antibodies derived from the variable region of the unique heavy chain antibodies found in camelids yield high affinity and regenerable recognition elements. Adding an additional disulfide bond that bridges framework regions is a proven method to increase their melting temperature, however often at the expense of protein production. To fulfill their full potential it is essential to achieve robust protein production of these stable binding elements. In this work, we tested the hypothesis that decreasing the isoelectric point of single domain antibody extra disulfide bond mutants whose production fell due to the incorporation of the extra disulfide bond would lead to recovery of the protein yield, while maintaining the favorable melting temperature and affinity. Introduction of negative charges into a disulfide bond mutant of a single domain antibody specific for the L1 antigen of the vaccinia virus led to approximately 3.5-fold increase of protein production to 14 mg/L, while affinity and melting temperature was maintained. In addition, refolding following heat denaturation improved from 15 to 70 %. It also maintained nearly 100 % of its binding function after heating to 85 °C for an hour at 1 mg/mL. Disappointingly, the replacement of neutral or positively charged amino acids with negatively charged ones to lower the isoelectric point of two anti-toxin single domain antibodies stabilized with a second disulfide bond yielded only slight increases in protein production. Nonetheless, for one of these binders the charge change itself stabilized the structure equivalent to disulfide bond addition, thus providing an alternative route to stabilization which is not accompanied by loss in production. The ability to produce high affinity, stable single domain antibodies is critical for their utility. While the addition of a second disulfide bond is a proven method for enhancing stability of single domain antibodies, it frequently comes at the cost of reduced yields. While decreasing the isoelectric point of double disulfide mutants of single domain antibodies may improve protein production, charge addition appears to consistently improve refolding and some charge changes can also improve thermal stability, thus providing a number of benefits making the examination of such mutations worth consideration.
Prenylated flavonol glycosides Epimedium grandiflorum: Cytotoxicity and evaluation against inflammation and metabolic disorders

USDA-ARS?s Scientific Manuscript database

Two new prenylated flavonol glycosides, epimedigrandiosides A and B (1 and 2), and 28 previously known compounds including prenylated flavonol derivatives, flavonol glycoside, megastigmanes, phenyl alkanoids, sesquiterpenoid glycoside, lignan, and hexene glucoside were isolated from the methanol ext...
Aligning, Bonding, and Testing Mirrors for Lightweight X-ray Telescopes

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Zhang, William W.; Saha, Timo T.; McClelland, Ryan S.; Biskach, Michael P.; Niemeyer, Jason; Schofield, Mark J.; Mazzarella, James R.; Kolos, Linette D.; Hong, Melinda M.;

2015-01-01

High-resolution, high throughput optics for x-ray astronomy entails fabrication of well-formed mirror segments and their integration with arc-second precision. In this paper, we address issues of aligning and bonding thin glass mirrors with negligible additional distortion. Stability of the bonded mirrors and the curing of epoxy used in bonding them were tested extensively. We present results from tests of bonding mirrors onto experimental modules, and on the stability of the bonded mirrors tested in x-ray. These results demonstrate the fundamental validity of the methods used in integrating mirrors into telescope module, and reveal the areas for further investigation. The alignment and integration methods are applicable to the astronomical mission concept such as STAR-X, the Survey and Time-domain Astronomical Research Explorer.

DEMONSTRATION BULLETIN: MOLECULAR BONDING SYSTEM FOR HEAVY METALS STABILIZATION - SOLUCORP INDUSTRIES LTD.

EPA Science Inventory

This document presents an evaluation of the Molecular Bonding System (MBS) and its ability to chemically stabilize three metals-contaminated wstes/soils during a SITe demo. The MBS process treated approximately 500 tons each of soil/Fill, Slag, and Miscellaneous Smelter Waste wit...
Stabilization of Quinapril by Incorporating Hydrogen Bonding Interactions

PubMed Central

Roy, B. N.; Singh, G. P.; Godbole, H. M.; Nehate, S. P.

2009-01-01

In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethyl)amino methane. Quinapril free base forms a stable salt with tris(hydroxymethyl)amino methane not reported earlier. Quinapril tris(hydroxymethyl)amino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethyl)amino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation. PMID:20502545
Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

PubMed

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

2017-10-17

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.
Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties

PubMed Central

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M. Aminur; Islam, Mohamad Tofazzal

2017-01-01

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural–activity relationships (SARs) of sea cucumber glycosides are also discussed briefly. PMID:29039760
Bench-Scale Evaluation Of Chemically Bonded Phosphate Ceramic Technology To Stabilize Mercury Waste Mixtures

EPA Science Inventory

This bench-scale study was conducted to evaluate the stabilization of mercury (Hg) and mercuric chloride-containing surrogate test materials by the chemically bonded phosphate ceramics technology. This study was performed as part of a U.S. EPA program to evaluate treatment and d...
Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB.

PubMed

Wei, Wei; Sun, Yang; Zhu, Mingli; Liu, Xiangzhi; Sun, Peiqing; Wang, Feng; Gui, Qiu; Meng, Wuyi; Cao, Yi; Zhao, Jing

2015-12-16

The coordination bond between gold and sulfur (Au-S) has been widely studied and utilized in many fields. However, detailed investigations on the basic nature of this bond are still lacking. A gold-specific binding protein, GolB, was recently identified, providing a unique opportunity for the study of the Au-S bond at the molecular level. We probed the mechanical strength of the gold-sulfur bond in GolB using single-molecule force spectroscopy. We measured the rupture force of the Au-S bond to be 165 pN, much lower than Au-S bonds measured on different gold surfaces (∼1000 pN). We further solved the structures of apo-GolB and Au(I)-GolB complex using X-ray crystallography. These structures showed that the average Au-S bond length in GolB is much longer than the reported average value of Au-S bonds. Our results highlight the dramatic influence of the unique biological environment on the stability and strength of metal coordination bonds in proteins.
Distinct roles of N- and O-glycans in cellulase activity and stability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amore, Antonella; Knott, Brandon C.; Supekar, Nitin T.

In nature, many microbes secrete mixtures of glycoside hydrolases, oxidoreductases, and accessory enzymes to deconstruct polysaccharides and lignin in plants. These enzymes are often decorated with N- and O-glycosylation, the roles of which have been broadly attributed to protection from proteolysis, as the extracellular milieu is an aggressive environment. Glycosylation has been shown to sometimes affect activity, but these effects are not fully understood. In this paper, we examine N- and O-glycosylation on a model, multimodular glycoside hydrolase family 7 cellobiohydrolase (Cel7A), which exhibits an O-glycosylated carbohydrate-binding module (CBM) and an O-glycosylated linker connected to an N- and O-glycosylated catalyticmore » domain (CD) - a domain architecture common to many biomass-degrading enzymes. We report consensus maps for Cel7A glycosylation that include glycan sites and motifs. Additionally, we examine the roles of glycans on activity, substrate binding, and thermal and proteolytic stability. N-glycan knockouts on the CD demonstrate that N-glycosylation has little impact on cellulose conversion or binding, but does have major stability impacts. O-glycans on the CBM have little impact on binding, proteolysis, or activity in the whole-enzyme context. However, linker O-glycans greatly impact cellulose conversion via their contribution to proteolysis resistance. Molecular simulations predict an additional role for linker O-glycans, namely that they are responsible for maintaining separation between ordered domains when Cel7A is engaged on cellulose, as models predict a-helix formation and decreased cellulose interaction for the nonglycosylated linker. In conclusion, this study reveals key roles for N- and O-glycosylation that are likely broadly applicable to other plant cell-wall-degrading enzymes.« less
Structure variations of TBA G-quadruplex induced by 2'-O-methyl nucleotide in K+ and Ca2+ environments.

PubMed

Zhao, Xiaoyang; Liu, Bo; Yan, Jing; Yuan, Ying; An, Liwen; Guan, Yifu

2014-10-01

Thrombin binding aptamer (TBA), a 15-mer oligonucleotide of d(GGTTGGTGTGGTTGG) sequence, folds into a chair-type antiparallel G-quadruplex in the K(+) environment, and each of two G-tetrads is characterized by a syn-anti-syn-anti glycosidic conformation arrangement. To explore its folding topology and structural stability, 2'-O-methyl nucleotide (OMe) with the C3'-endo sugar pucker conformation and anti glycosidic angle was used to selectively substitute for the guanine residues of G-tetrads of TBA, and these substituted TBAs were characterized using a circular dichroism spectrum, thermally differential spectrum, ultraviolet stability analysis, electrophoresis mobility shift assay, and thermodynamic analysis in K(+) and Ca(2+) environments. Results showed that single substitutions for syn-dG residues destabilized the G-quadruplex structure, while single substitutions for anti-dG residues could preserve the G-quadruplex in the K(+) environment. When one or two G-tetrads were modified with OMe, TBA became unstructured. In contrast, in Ca(2+) environment, the native TBA appeared to be unstructured. When two G-tetrads were substituted with OMe, TBA seemed to become a more stable parallel G-4 structure. Further thermodynamic data suggested that OMe-substitutions were an enthalpy-driven event. The results in this study enrich our understanding about the effects of nucleotide derivatives on the G-quadruplex structure stability in different ionic environments, which will help to design G-quadruplex for biological and medical applications. © The Author 2014. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.
Distinct roles of N- and O-glycans in cellulase activity and stability

DOE PAGES

Amore, Antonella; Knott, Brandon C.; Supekar, Nitin T.; ...

2017-12-11

In nature, many microbes secrete mixtures of glycoside hydrolases, oxidoreductases, and accessory enzymes to deconstruct polysaccharides and lignin in plants. These enzymes are often decorated with N- and O-glycosylation, the roles of which have been broadly attributed to protection from proteolysis, as the extracellular milieu is an aggressive environment. Glycosylation has been shown to sometimes affect activity, but these effects are not fully understood. In this paper, we examine N- and O-glycosylation on a model, multimodular glycoside hydrolase family 7 cellobiohydrolase (Cel7A), which exhibits an O-glycosylated carbohydrate-binding module (CBM) and an O-glycosylated linker connected to an N- and O-glycosylated catalyticmore » domain (CD) - a domain architecture common to many biomass-degrading enzymes. We report consensus maps for Cel7A glycosylation that include glycan sites and motifs. Additionally, we examine the roles of glycans on activity, substrate binding, and thermal and proteolytic stability. N-glycan knockouts on the CD demonstrate that N-glycosylation has little impact on cellulose conversion or binding, but does have major stability impacts. O-glycans on the CBM have little impact on binding, proteolysis, or activity in the whole-enzyme context. However, linker O-glycans greatly impact cellulose conversion via their contribution to proteolysis resistance. Molecular simulations predict an additional role for linker O-glycans, namely that they are responsible for maintaining separation between ordered domains when Cel7A is engaged on cellulose, as models predict a-helix formation and decreased cellulose interaction for the nonglycosylated linker. In conclusion, this study reveals key roles for N- and O-glycosylation that are likely broadly applicable to other plant cell-wall-degrading enzymes.« less
Continuous feelings of love? The parental bond from pregnancy to toddlerhood.

PubMed

de Cock, Evi S A; Henrichs, Jens; Vreeswijk, Charlotte M J M; Maas, A Janneke B M; Rijk, Catharina H A M; van Bakel, Hedwig J A

2016-02-01

Both prenatal and postnatal parental bonding (i.e., the affective tie from parent to child) have important effects on parental and child functioning. However, research on the continuity and correlates of parental bonding is lacking. Therefore, the goal of the present study was to examine the stability of bonding levels and to explore distinct bonding patterns with a latent class analysis. Moreover, the correlates of these bonding patterns in the parental-, child-, and contextual domain were studied. Levels of maternal (N = 370) and paternal (N = 292) bonding and potential correlates were assessed at 26 weeks of pregnancy, 6 months, and 24 months postpartum. Results showed moderate stability of bonding from pregnancy to toddlerhood. For both mothers and fathers, 4 distinct bonding patterns were found. Parents with low bonding patterns were characterized by increased anxiety and parenting stress, less partner support, less adaptive personality profiles, and children with difficult temperament. These findings indicate the importance of monitoring young children's parents with poor levels of bonding as their bonding patterns remain stable from pregnancy until toddlerhood and because those parents experience problems in multiple domains. (c) 2016 APA, all rights reserved).
Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases*

PubMed Central

Zhao, Linlin; Pence, Matthew G.; Christov, Plamen P.; Wawrzak, Zdzislaw; Choi, Jeong-Yun; Rizzo, Carmelo J.; Egli, Martin; Guengerich, F. Peter

2012-01-01

N2,3-Ethenoguanine (N2,3-ϵG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2′-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2′-fluoro-N2,3-ϵ-2′-deoxyarabinoguanosine to investigate the miscoding potential of N2,3-ϵG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N2,3-ϵG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N2,3-ϵG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N2,3-ϵG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N2,3-ϵG:dCTP base pair, whereas only one appears to be present in the case of the N2,3-ϵG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N2,3-ϵG. PMID:22910910
Effect of γ-radiation on free radicals formation, structural changes and functional properties of wheat starch.

PubMed

Atrous, Hager; Benbettaieb, Nasreddine; Hosni, Faouzi; Danthine, Sabine; Blecker, Christophe; Attia, Hamadi; Ghorbel, Dorra

2015-09-01

Wheat starch was treated by different γ-radiation doses (3, 5, 10, 20, 35 and 50 kGy). The effects of γ-radiation on structural, thermal, physicochemical, morphological and rheological properties of wheat starch were studied. The presence of free radicals after γ-radiation treatment, which number decreased with time was confirmed. Structural analysis revealed decreases in the intensities of the O-H and C-H stretches and glycosidic linkages indicating the depolymerization of amylose and probably amylopectin into shorter chain molecules, but showed that γ-radiation treatment did not affect the crystalline structure. Differential scanning calorimetric (DSC) thermograms showed the absence of significant differences in the gelatinization temperatures, as well as the corresponding transition enthalpies since the DSC parameters are related to the crystalline ordering within the granules. Apparent amylose content decreased linearly with increasing irradiation dose leading to an increase in water solubility index. An increase in the swelling power was observed after irradiation treatment until 20 kGy, followed by a rapid decrease at higher doses. Microscopic observations showed that the effect of γ-radiation was more visible on starch pastes than on starch granules. Rheological properties of the starch pastes decreased with increasing irradiation dose as a result of glycosidic bond cleavage. Copyright © 2015 Elsevier B.V. All rights reserved.
Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design.

PubMed

Montgomery, Andrew P; Xiao, Kela; Wang, Xingyong; Skropeta, Danielle; Yu, Haibo

2017-01-01

Carbohydrate-active enzymes (CAZymes) are families of essential and structurally related enzymes, which catalyze the creation, modification, and degradation of glycosidic bonds in carbohydrates to maintain essentially all kingdoms of life. CAZymes play a key role in many biological processes underpinning human health and diseases (e.g., cancer, diabetes, Alzheimer's diseases, AIDS) and have thus emerged as important drug targets in the fight against pathogenesis. The realization of the full potential of CAZymes remains a significant challenge, relying on a deeper understanding of the molecular mechanisms of catalysis. Considering numerous unsettled questions in the literature, while with a large amount of structural, kinetic, and mutagenesis data available for CAZymes, there is a pressing need and an abundant opportunity for collaborative computational and experimental investigations with the aim to unlock the secrets of CAZyme catalysis at an atomic level. In this review, we briefly survey key methodology development in computational studies of CAZyme catalysis. This is complemented by selected case studies highlighting mechanistic insights provided by computational glycobiology. Implication for inhibitor design by mimicking the transition state is also illustrated for both glycoside hydrolases and glycosyltransferases. The challenges for such studies will be noted and finally an outlook for future directions will be provided. © 2017 Elsevier Inc. All rights reserved.
A single molecule study of cellulase hydrolysis of crystalline cellulose

NASA Astrophysics Data System (ADS)

Liu, Yu-San; Luo, Yonghua; Baker, John O.; Zeng, Yining; Himmel, Michael E.; Smith, Steve; Ding, Shi-You

2010-02-01

Cellobiohydrolase-I (CBH I), a processive exoglucanase secreted by Trichoderma reesei, is one of the key enzyme components in a commercial cellulase mixture currently used for processing biomass to biofuels. CBH I contains a family 7 glycoside hydrolase catalytic module, a family 1 carbohydrate-binding module (CBM), and a highlyglycosylated linker peptide. It has been proposed that the CBH I cellulase initiates the hydrolysis from the reducing end of one cellulose chain and successively cleaves alternate β-1,4-glycosidic bonds to release cellobiose as its principal end product. The role each module of CBH I plays in the processive hydrolysis of crystalline cellulose has yet to be convincingly elucidated. In this report, we use a single-molecule approach that combines optical (Total Internal Reflection Fluorescence microscopy, or TIRF-M) and non-optical (Atomic Force Microscopy, or AFM) imaging techniques to analyze the molecular motion of CBM tagged with green fluorescence protein (GFP), and to investigate the surface structure of crystalline cellulose and changes made in the structure by CBM and CBH I. The preliminary results have revealed a confined nanometer-scale movement of the TrCBM1-GFP bound to cellulose, and decreases in cellulose crystal size as well as increases in surface roughness during CBH I hydrolysis of crystalline cellulose.
Photochemistry and pharmacology of 9, 19-cyclolanostane glycosides isolated from genus Cimicifuga.

PubMed

Su, Yang; Chi, Wen-Cheng; Wu, Lun; Wang, Qiu-Hong; Kuang, Hai-Xue

2016-10-01

The constituents of Cimicifuga plants have been extensively investigated, and the principal metabolites are 9, 19-cyclolanostane triterpenoid glycosides, which often exhibit extensive pharmacological activities. 9, 19-Cyclolanostane triterpenoid glycosides are distributed widely in genus Cimicifuga rather than in other members of the Ranunculaceae family. So far, more than 140 cycloartane triterpene glycosides have been isolated from Cimicifuga spp.. The aim of this review was to summarize all 9, 19-cyclolanostane triterpenoid glycosides based on the available relevant scientific literatures from 2000 to 2014. Biological studies of cycloartane triterpene glycosides from Cimicifuga spp. are also discussed. Copyright © 2016 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.
Bond Stability of a Universal Adhesive System to Eroded/Abraded Dentin After Deproteinization.

PubMed

Augusto, M G; Torres, Crg; Pucci, C R; Schlueter, N; Borges, A B

Erosive/abrasive challenges can potentially compromise bonding to dentin. Aiming to improve the quality and stability of bonding to this substrate, this study investigated the combined effect of erosion and toothbrush abrasion on the microtensile bond strength (μTBS) stability to dentin using a universal adhesive system in total and self-etching modes, associated or not associated with deproteinization. Bovine dentin specimens were divided into five groups according to the organic matrix condition (n=20): control (C); erosion (E); erosion + abrasion (EA); erosion + sodium hypochlorite (EH); erosion + abrasion + sodium hypochlorite (EAH). The groups were further divided (n=10) according to the mode of application (total or self-etching) of a universal adhesive. After the bonding procedure, composite blocks were built up, and the samples were cut to obtain sticks for μTBS testing. For each specimen, one-half of the sticks was immediately tested, and the other one-half was tested after artificial aging (5000 thermocycles, 5°C and 55°C). Three-way analysis of variance (α=5%) showed a significant difference for the triple interaction ( p=0.0007). Higher μTBS means were obtained for the EH and EAH groups compared with the E and EA groups. The control group showed immediate μTBS values similar to that of the E and EA groups for both bond strategies. Erosion and erosion/abrasion did not significantly influence the immediate μTBS to dentin. Artificial aging reduced μTBS values for the groups C, E, and EA using the total-etching mode. Deproteinization maintained the bond stability to artificially aged eroded and eroded/abraded dentin.
Purification and enzymatic characterization of secretory glycoside hydrolase family 3 (GH3) aryl β-glucosidases screened from Aspergillus oryzae genome.

PubMed

Kudo, Kanako; Watanabe, Akira; Ujiie, Seiryu; Shintani, Takahiro; Gomi, Katsuya

2015-12-01

By a global search of the genome database of Aspergillus oryzae, we found 23 genes encoding putative β-glucosidases, among which 10 genes with a signal peptide belonging to glycoside hydrolase family 3 (GH3) were overexpressed in A. oryzae using the improved glaA gene promoter. Consequently, crude enzyme preparations from three strains, each harboring the genes AO090038000223 (bglA), AO090103000127 (bglF), and AO090003001511 (bglJ), showed a substrate preference toward p-nitrophenyl-β-d-glucopyranoside (pNPGlc) and thus were purified to homogeneity and enzymatically characterized. All the purified enzymes (BglA, BglF, and BglJ) preferentially hydrolyzed aryl β-glycosides, including pNPGlc, rather than cellobiose, and these enzymes were proven to be aryl β-glucosidases. Although the specific activity of BglF toward all the substrates tested was significantly low, BglA and BglJ showed appreciably high activities toward pNPGlc and arbutin. The kinetic parameters of BglA and BglJ for pNPGlc suggested that both the enzymes had relatively higher hydrolytic activity toward pNPGlc among the fungal β-glucosidases reported. The thermal and pH stabilities of BglA were higher than those of BglJ, and BglA was particularly stable in a wide pH range (pH 4.5-10). In contrast, BglJ was the most heat- and alkaline-labile among the three β-glucosidases. Furthermore, BglA was more tolerant to ethanol than BglJ; as a result, it showed much higher hydrolytic activity toward isoflavone glycosides in the presence of ethanol than BglJ. This study suggested that the mining of novel β-glucosidases exhibiting higher activity from microbial genome sequences is of great use for the production of beneficial compounds such as isoflavone aglycones. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Biochemical and Molecular Characterization of a Flavonoid 3-O-glycosyltransferase Responsible for Anthocyanins and Flavonols Biosynthesis in Freesia hybrida

PubMed Central

Sun, Wei; Liang, Lingjie; Meng, Xiangyu; Li, Yueqing; Gao, Fengzhan; Liu, Xingxue; Wang, Shucai; Gao, Xiang; Wang, Li

2016-01-01

The glycosylation of flavonoids increases their solubility and stability in plants. Flowers accumulate anthocyanidin and flavonol glycosides which are synthesized by UDP-sugar flavonoid glycosyltransferases (UFGTs). In our previous study, a cDNA clone (Fh3GT1) encoding UFGT was isolated from Freesia hybrida, which was preliminarily proved to be invovled in cyanidin 3-O-glucoside biosynthesis. Here, a variety of anthocyanin and flavonol glycosides were detected in flowers and other tissues of F. hybrida, implying the versatile roles of Fh3GT1 in flavonoids biosynthesis. To further unravel its multi-functional roles, integrative analysis between gene expression and metabolites was investigated. The results showed expression of Fh3GT1 was positively related to the accumulation of anthocyanins and flavonol glycosides, suggesting its potential roles in the biosynthesis of both flavonoid glycosides. Subsequently, biochemical analysis results revealed that a broad range of flavonoid substrates including flavonoid not naturally occurred in F. hybrida could be recognized by the recombinant Fh3GT1. Both UDP-glucose and UDP-galactose could be used as sugar donors by recombinant Fh3GT1, although UDP-galactose was transferred with relatively low activity. Furthermore, regiospecificity analysis demonstrated that Fh3GT1 was able to glycosylate delphinidin at the 3-, 4-′, and 7- positions in a sugar-dependent manner. And the introduction of Fh3GT1 into Arabidopsis UGT78D2 mutant successfully restored the anthocyanins and flavonols phenotypes caused by lost-of-function of the 3GT, indicating that Fh3GT1 functions as a flavonoid 3-O-glucosyltransferase in vivo. In summary, these results demonstrate that Fh3GT1 is a flavonoid 3-O-glycosyltransferase using UDP-glucose as the preferred sugar donor and may involve in flavonoid glycosylation in F. hybrida. PMID:27064818
Biochemical and Molecular Characterization of a Flavonoid 3-O-glycosyltransferase Responsible for Anthocyanins and Flavonols Biosynthesis in Freesia hybrida.

PubMed

Sun, Wei; Liang, Lingjie; Meng, Xiangyu; Li, Yueqing; Gao, Fengzhan; Liu, Xingxue; Wang, Shucai; Gao, Xiang; Wang, Li

2016-01-01

The glycosylation of flavonoids increases their solubility and stability in plants. Flowers accumulate anthocyanidin and flavonol glycosides which are synthesized by UDP-sugar flavonoid glycosyltransferases (UFGTs). In our previous study, a cDNA clone (Fh3GT1) encoding UFGT was isolated from Freesia hybrida, which was preliminarily proved to be invovled in cyanidin 3-O-glucoside biosynthesis. Here, a variety of anthocyanin and flavonol glycosides were detected in flowers and other tissues of F. hybrida, implying the versatile roles of Fh3GT1 in flavonoids biosynthesis. To further unravel its multi-functional roles, integrative analysis between gene expression and metabolites was investigated. The results showed expression of Fh3GT1 was positively related to the accumulation of anthocyanins and flavonol glycosides, suggesting its potential roles in the biosynthesis of both flavonoid glycosides. Subsequently, biochemical analysis results revealed that a broad range of flavonoid substrates including flavonoid not naturally occurred in F. hybrida could be recognized by the recombinant Fh3GT1. Both UDP-glucose and UDP-galactose could be used as sugar donors by recombinant Fh3GT1, although UDP-galactose was transferred with relatively low activity. Furthermore, regiospecificity analysis demonstrated that Fh3GT1 was able to glycosylate delphinidin at the 3-, 4-', and 7- positions in a sugar-dependent manner. And the introduction of Fh3GT1 into Arabidopsis UGT78D2 mutant successfully restored the anthocyanins and flavonols phenotypes caused by lost-of-function of the 3GT, indicating that Fh3GT1 functions as a flavonoid 3-O-glucosyltransferase in vivo. In summary, these results demonstrate that Fh3GT1 is a flavonoid 3-O-glycosyltransferase using UDP-glucose as the preferred sugar donor and may involve in flavonoid glycosylation in F. hybrida.
Aroma Glycosides in Grapes and Wine.

PubMed

Liu, Jibin; Zhu, Xiao-Lin; Ullah, Niamat; Tao, Yong-Sheng

2017-02-01

The major aroma components in grapes and wine include free volatile compounds and glycosidic nonvolatile compounds. The latter group of compounds is more than 10 times abundant of the former, and constitutes a big aroma reserve in grapes and wine. This review summarizes the research results obtained recently for the identification of aroma glycosides in grapes and wine, including grape glycoside structures, differences in aroma glycosides among grape varieties, hydrolysis mechanisms, and the factors that influence them. It also presents the analytical techniques used to identify the glycosidic aroma precursors. The operational strategies, challenges, and improvements of each step encountered in the analysis of glycosidic aroma precursors are described. This review intends to provide a convenient reference for researchers interested in the methods used for the determination of the aroma glucosides composition and the recognition of their chemical structures. © 2017 Institute of Food Technologists®.
Chemical O‐Glycosylations: An Overview

PubMed Central

2016-01-01

Abstract The development of glycobiology relies on the sources of particular oligosaccharides in their purest forms. As the isolation of the oligosaccharide structures from natural sources is not a reliable option for providing samples with homogeneity, chemical means become pertinent. The growing demand for diverse oligosaccharide structures has prompted the advancement of chemical strategies to stitch sugar molecules with precise stereo‐ and regioselectivity through the formation of glycosidic bonds. This Review will focus on the key developments towards chemical O‐glycosylations in the current century. Synthesis of novel glycosyl donors and acceptors and their unique activation for successful glycosylation are discussed. This Review concludes with a summary of recent developments and comments on future prospects. PMID:27777833
Pulsed laser deposition and characterization of cellulase thin films

NASA Astrophysics Data System (ADS)

Cicco, N.; Morone, A.; Verrastro, M.; Viggiano, V.

2013-08-01

Thin films of cellulase were obtained by pulsed laser deposition (PLD) on an appropriate substrate. Glycoside hydrolase cellulase has received our attention because it emerges among the antifouling enzymes (enzymes being able to remove and prevent the formation of micro-organism biofilms) used in industry and medicine field. Pressed cellulase pellets, used as target material, were ablated with pulses of a Nd-YAG laser working at wavelength of 532 nm. In this work, we evaluated the impact of PLD technique both on molecular structure and hydrolytic activity of cellulase. Characteristic chemical bonds and morphology of deposited layers were investigated by FTIR spectroscopy and SEM respectively. The hydrolytic activity of cellulase thin films was detected by a colorimetric assay.
Evidence for phosphorus bonding in phosphorus trichloride-methanol adduct: a matrix isolation infrared and ab initio computational study.

PubMed

Joshi, Prasad Ramesh; Ramanathan, N; Sundararajan, K; Sankaran, K

2015-04-09

The weak interaction between PCl3 and CH3OH was investigated using matrix isolation infrared spectroscopy and ab initio computations. In a nitrogen matrix at low temperature, the noncovalent adduct was generated and characterized using Fourier transform infrared spectroscopy. Computations were performed at B3LYP/6-311++G(d,p), B3LYP/aug-cc-pVDZ, and MP2/6-311++G(d,p) levels of theory to optimize the possible geometries of PCl3-CH3OH adducts. Computations revealed two minima on the potential energy surface, of which, the global minimum is stabilized by a noncovalent P···O interaction, known as a pnictogen bonding (phosphorus bonding or P-bonding). The local minimum corresponded to a cyclic adduct, stabilized by the conventional hydrogen bonding (Cl···H-O and Cl···H-C interactions). Experimentally, 1:1 P-bonded PCl3-CH3OH adduct in nitrogen matrix was identified, where shifts in the P-Cl modes of PCl3, O-C, and O-H modes of CH3OH submolecules were observed. The observed vibrational frequencies of the P-bonded adduct in a nitrogen matrix agreed well with the computed frequencies. Furthermore, computations also predicted that the P-bonded adduct is stronger than H-bonded adduct by ∼1.56 kcal/mol. Atoms in molecules and natural bond orbital analyses were performed to understand the nature of interactions and effect of charge transfer interaction on the stability of the adducts.
Anomalously enhanced hydration of aqueous electrolyte solution in hydrophobic carbon nanotubes to maintain stability.

PubMed

Ohba, Tomonori

2014-02-24

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Metabolite Profiling of Triterpene Glycosides of the Far Eastern Sea Cucumber Eupentacta fraudatrix and Their Distribution in Various Body Components Using LC-ESI QTOF-MS.

PubMed

Popov, Roman S; Ivanchina, Natalia V; Silchenko, Alexandra S; Avilov, Sergey A; Kalinin, Vladimir I; Dolmatov, Igor Yu; Stonik, Valentin A; Dmitrenok, Pavel S

2017-10-02

The Far Eastern sea cucumber Eupentacta fraudatrix is an inhabitant of shallow waters of the south part of the Sea of Japan. This animal is an interesting and rich source of triterpene glycosides with unique chemical structures and various biological activities. The objective of this study was to investigate composition and distribution in various body components of triterpene glycosides of the sea cucumber E. fraudatrix . We applied LC-ESI MS (liquid chromatography-electrospray mass spectrometry) of whole body extract and extracts of various body components for metabolic profiling and structure elucidation of triterpene glycosides from the E. fraudatrix . Totally, 54 compounds, including 26 sulfated, 18 non-sulfated and 10 disulfated glycosides were detected and described. Triterpene glycosides from the body walls, gonads, aquapharyngeal bulbs, guts and respiratory trees were extracted separately and the distributions of the detected compounds in various body components were analyzed. Series of new glycosides with unusual structural features were described in E. fraudatrix , which allow clarifying the biosynthesis of these compounds. Comparison of the triterpene glycosides contents from the five different body components revealed that the profiles of triterpene glycosides were qualitatively similar, and only some quantitative variabilities for minor compounds were observed.
Polymorphs and polymorphic cocrystals of temozolomide.

PubMed

Babu, N Jagadeesh; Reddy, L Sreenivas; Aitipamula, Srinivasulu; Nangia, Ashwini

2008-07-07

Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.
Flavonol glycosides in the petal of Rosa species as chemotaxonomic markers.

PubMed

Sarangowa, Ochir; Kanazawa, Tsutomu; Nishizawa, Makoto; Myoda, Takao; Bai, Changxi; Yamagishi, Takashi

2014-11-01

Thirteen flavonol glycosides were isolated from the petals of Rosa species belonging to the section Gallicanae, and their structures were identified from their spectroscopic data. These flavonol glycosides, along with two flavonol glycosides isolated from Rosa rugosa, in the petals of 31 Rosa species belonging to sections Gallicanae, Cinnamomeae, Caninae, and Synstylae were quantitatively analyzed by UPLC. The results indicated that the species belonging to these sections could be classified into four types (Type A, B, C and D) based on the pattern of flavonol glycoside contents, whereas the R. rugosa flavonol glycosides were detected only in section Cinnamomeae. A principal components analysis (PCA) calculated from the 15 flavonol glycosides contained in these samples supported the presence of four types. The distribution of the species in Type D (a group of Cinnamomeae) was shown to reflect close interrelationships, but species in Type B (one group of Gallicanae) could be subdivided into two groups, one of which contained species in section Synstylae. Moreover, the flavonol glycosides were grouped by sugar moieties: a disaccharide composed of two hexoses (S1), a hexose (S2), including a hexose with galloyl group, a pentose (S3), and a disaccharide composed of a hexose and a pentose (S4). The ratios of the amounts of S1-S4 to total flavonol glycoside content indicated that differences among the four sections were more distinctive than the amounts of the 15 flavonol glycosides. The 31 samples were divided into Type B, composed of one type of Gallicanae and Synstylae, Type A+C, composed of another type of Gallicanae and Caninae, and Type D, composed of Cinnamomeae. The R. rugosa flavonol glycosides were shown to be important chemotaxonomic markers for the classification of species in Cinnamomeae, and this method of using flavonol glycosides as chemotaxonomic markers could be useful for the identification of Rosa species belonging to sections Gallicanae, Cinnamomeae, Caninae, and Synstylae. Copyright © 2014 Elsevier Ltd. All rights reserved.
The Evaluation of Strain and Stabilization in Molecules Using Isodesmic Reactions.

ERIC Educational Resources Information Center

Fuchs, Richard

1984-01-01

Isodesmic reactions are hypothetical chemical changes in which the number of bonds of a given type are retained but change in relation to one another. Discusses use of these reactions and reaction energy to measure deviations from additivity of bond energy. Also considers relationship of enthalpies to strain and resonance stability. (JM)
Thermally stable, plastic-bonded explosives

DOEpatents

Benziger, Theodore M.

1979-01-01

By use of an appropriate thermoplastic rubber as the binder, the thermal stability and thermal stress characteristics of plastic-bonded explosives may be greatly improved. In particular, an HMX-based explosive composition using an oil-extended styrene-ethylenebutylene-styrene block copolymer as the binder exhibits high explosive energy and thermal stability and good handling safety and physical properties.
Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

NASA Technical Reports Server (NTRS)

Gessner, R. V.; Quigley, G. J.; Wang, A. H.; van der Marel, G. A.; van Boom, J. H.; Rich, A.

1985-01-01

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.
Evaluating the Energetic Driving Force for Cocrystal Formation

PubMed Central

2017-01-01

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol–1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems—hydrogen-bonded, halogen-bonded, and weakly bound cocrystals—finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition—more densely packed cocrystals with stronger hydrogen bonding tend to be more stable—but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems. PMID:29445316
Evaluating the Energetic Driving Force for Cocrystal Formation.

PubMed

Taylor, Christopher R; Day, Graeme M

2018-02-07

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol -1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems-hydrogen-bonded, halogen-bonded, and weakly bound cocrystals-finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition-more densely packed cocrystals with stronger hydrogen bonding tend to be more stable-but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.
Effect of the Anion Activity on the Stability of Li Metal Anodes in Lithium-Sulfur Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Ruiguo; Chen, Junzheng; Han, Kee Sung

2016-03-29

With the significant progress made in the development of cathodes in lithium-sulfur (Li-S) batteries, the stability of Li metal anodes becomes a more urgent challenge in these batteries. Here we report the systematic investigation of the stability of the anode/electrolyte interface in Li-S batteries with concentrated electrolytes containing various lithium salts. It is found that Li-S batteries using LiTFSI-based electrolytes are more stable than those using LiFSI-based electrolytes. The decreased stability is because the N-S bond in the FSI- anion is fairly weak and the scission of this bond leads to the formation of lithium sulfate (LiSOx) in the presencemore » of polysulfide species. In contrast, even the weakest bond (C-S) in the TFSI- anion is stronger than the N-S bond in the FSI- anion. In the LiTFSI-based electrolyte, the lithium metal anode tends to react with polysulfide to form lithium sulfide (LiSx) which is more reversible than LiSOx formed in the LiTFSI-based electrolyte. This fundamental difference in the bond strength of the salt anions in the presence of polysulfide species leads to a large difference in the stability of the anode-electrolyte interface and performance of the Li-S batteries with electrolytes composed of these salts. Therefore, anion selection is one of the key parameters in the search for new electrolytes for stable operation of Li-S batteries.« less
Removal of a C-terminal serine residue proximal to the inter-chain disulfide bond of a human IgG1 lambda light chain mediates enhanced antibody stability and antibody dependent cell-mediated cytotoxicity

PubMed Central

Shen, Yang; Zeng, Lin; Zhu, Aiping; Blanc, Tim; Patel, Dipa; Pennello, Anthony; Bari, Amtul; Ng, Stanley; Persaud, Kris; Kang, Yun (Kenneth); Balderes, Paul; Surguladze, David; Hindi, Sagit; Zhou, Qinwei; Ludwig, Dale L.; Snavely, Marshall

2013-01-01

Optimization of biophysical properties is a critical success factor for the developability of monoclonal antibodies with potential therapeutic applications. The inter-domain disulfide bond between light chain (Lc) and heavy chain (Hc) in human IgG1 lends structural support for antibody scaffold stability, optimal antigen binding, and normal Fc function. Recently, human IgG1λ has been suggested to exhibit significantly greater susceptibility to reduction of the inter Lc-Hc disulfide bond relative to the same disulfide bond in human IgG1κ. To understand the molecular basis for this observed difference in stability, the sequence and structure of human IgG1λ and human IgG1κ were compared. Based on this Lc comparison, three single mutations were made in the λ Lc proximal to the cysteine residue, which forms a disulfide bond with the Hc. We determined that deletion of S214 (dS) improved resistance of the association between Lc and Hc to thermal stress. In addition, deletion of this terminal serine from the Lc of IgG1λ provided further benefit, including an increase in stability at elevated pH, increased yield from transient transfection, and improved in vitro antibody dependent cell-mediated cytotoxicity (ADCC). These observations support the conclusion that the presence of the terminal serine of the λ Lc creates a weaker inter-chain disulfide bond between the Lc and Hc, leading to slightly reduced stability and a potential compromise in IgG1λ function. Our data from a human IgG1λ provide a basis for further investigation of the effects of deleting terminal serine from λLc on the stability and function of other human IgG1λ antibodies. PMID:23567210
Mass spectrometric imaging of flavonoid glycosides and biflavonoids in Ginkgo biloba L.

PubMed

Beck, Sebastian; Stengel, Julia

2016-10-01

Ginkgo biloba L. is known to be rich in flavonoids and flavonoid glycosides. However, the distribution within specific plant organs (e.g. within leaves) is not known. By using HPLC-MS and MS/MS we have identified a number of previously known G. biloba flavonoid glycosides and biflavonoids from leaves. Namely, kaempferol, quercetin, isorhamnetin, myricetin, laricitrin/mearnsetin and apigenin glycosides were identified. Furthermore, biflavonoids like ginkgetin/isoginkgetin were also detected. The application of MALDI mass spectrometric imaging, enabled the compilation of concentration profiles of flavonoid glycosides and biflavonoids in G. biloba L. leaves. Both, flavonoid glycosides and biflavonoids show a distinct distribution in leaf thin sections of G. biloba L. Copyright © 2016 Elsevier Ltd. All rights reserved.
Intramolecular amide bonds stabilize pili on the surface of bacilli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.

Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili.more » We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.« less
New Knowledge About Old Drugs: The Anti-Inflammatory Properties of Cardiac Glycosides.

PubMed

Fürst, Robert; Zündorf, Ilse; Dingermann, Theo

2017-08-01

In the 19th century, cardio-active steroid glycosides, shortly cardiac glycosides, were scientifically established as drugs against heart failure. Their in vivo , cellular, and molecular actions as well as their predominant target, Na + -K + -ATPase, have been comprehensively investigated in the 20th century and the discovery of endogenous cardiac glycosides has fostered this research field. In the last years, however, results from clinical trials and meta-analyses have questioned their therapeutic value due to efficacy and safety issues. This has led to a considerable decline of their usage. Beyond the cardiovascular system, cardiac glycosides have been increasingly recognized as antitumor compounds and Na + -K + -ATPase has evolved into a promising drug target in oncology. A wealth of review articles exists that intensively discuss these topics. Surprisingly, the anti-inflammatory actions of cardiac glycosides, which were discovered in the 1960s, have so far hardly been perceived and have not yet been summarized. This review provides an overview of the in vivo and in vitro actions of cardiac glycosides on inflammatory processes and of the signaling mechanisms responsible for these effects: cardiac glycosides have been found to decrease inflammatory symptoms in different animal models of acute and chronic inflammation. Regarding the underlying mechanisms most research has focused on leukocytes. In these cells, cardiac glycosides primarily inhibit cell proliferation and the secretion of proinflammatory cytokines. Georg Thieme Verlag KG Stuttgart · New York.

Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis.

PubMed

Gupta, Sharad K; Sur, Souvik; Prasad Ojha, Rajendra; Tandon, Vibha

2013-07-01

This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.
Neolignan and flavonoid glycosides in Juniperus communis var. depressa.

PubMed

Nakanishi, Tsutomu; Iida, Naoki; Inatomi, Yuka; Murata, Hiroko; Inada, Akira; Murata, Jin; Lang, Frank A; Iinuma, Munekazu; Tanaka, Toshiyuki

2004-01-01

Two neolignan glycosides (junipercomnosides A and B) were isolated from aerial parts of Juniperus communis var. depressa along with two known neolignan glycosides and seven flavonoid glycosides. The structures of the isolated compounds were determined by spectral analysis, in particular by 2D-NMR analysis. The significance of distribution of flavonoids in the chemotaxonomy of genus Juniperus was also discussed.
Glycosides from Stevia rebaudiana Bertoni Possess Insulin-Mimetic and Antioxidant Activities in Rat Cardiac Fibroblasts

PubMed Central

Prata, Cecilia; Zambonin, Laura; Rizzo, Benedetta; Vieceli Dalla Sega, Francesco

2017-01-01

Stevia rebaudiana Bertoni is a shrub having a high content of sweet diterpenoid glycosides in its leaves, mainly stevioside and rebaudioside A, which are used as noncaloric, natural sweeteners. The aim of this study was to deepen the knowledge about the insulin-mimetic effect exerted by four different mixtures of steviol glycosides, rich in stevioside and rebaudioside A, in neonatal rat cardiac fibroblasts. The potential antioxidant activity of these steviol glycosides was also assessed, as oxidative stress is associated with diabetes. Likewise the insulin effect, steviol glycosides caused an increase in glucose uptake into rat fibroblasts by activating the PI3K/Akt pathway, thus inducing Glut4 translocation to the plasma membrane. The presence of S961, an insulin antagonist, completely abolished these effects, allowing to hypothesize that steviol glycosides could act as ligands of the same receptor engaged by insulin. Moreover, steviol glycosides counteracted oxidative stress by increasing reduced glutathione intracellular levels and upregulating expression and activity of the two antioxidant enzymes superoxide dismutase and catalase. The present work unravels the insulin-mimetic effect and the antioxidant property exerted by steviol glycosides, suggesting their potential beneficial role in the cotreatment of diabetes and in health maintenance. PMID:28947927
The contribution of wine-derived monoterpene glycosides to retronasal odour during tasting.

PubMed

Parker, Mango; Black, Cory A; Barker, Alice; Pearson, Wes; Hayasaka, Yoji; Francis, I Leigh

2017-10-01

This study investigated the sensory significance of monoterpene glycosides during tasting, by retronasal perception of odorant aglycones released in-mouth. Monoterpene glycosides were isolated from Gewürztraminer and Riesling juices and wines, chemically characterised and studied using sensory time-intensity methodology, together with a synthesised monoterpene glucoside. When assessed in model wine at five times wine-like concentration, Gewürztraminer glycosides and geranyl glucoside gave significant fruity flavour, although at wine-like concentrations, or in the presence of wine volatiles, the effect was not significant. Gewürztraminer glycosides, geranyl glucoside and guaiacyl glucoside were investigated using a sensory panel (n=39), revealing large inter-individual variability, with 77% of panellists responding to at least one glycoside. The study showed for the first time that grape-derived glycosides can contribute perceptible fruity flavour, providing a means of enhancing flavour in wines, and confirms the results of previous studies that the effect is highly variable across individuals. Copyright © 2017 Elsevier Ltd. All rights reserved.
Studies on constituents with cytotoxic and cytostatic activity of two Turkish medicinal plants Phlomis armeniaca and Scutellaria salviifolia.

PubMed

Saracoglu, I; Inoue, M; Calis, I; Ogihara, Y

1995-10-01

Ten known glycosidic compounds, betulalbuside A (1), 8-hydroxylinaloyl,3-O-beta-D-glucopyranoside (2) (monoterpen glycosides), ipolamide (3) (iridoid glycoside), acteoside (verbascoside) (4), leucosceptoside A (5), martynoside (6), forsythoside B (7), phlinoside B (8), phlinoside C (9), and teuerioside (10) (phenylpropanoid glycosides) were isolated from methanolic extracts of Phlomis armeniaca and Scutellaria salviifolia (Labiatae). Structure elucidations were carried out using 1H-, 13C-NMR and FAB-MS spectra, as well as chemical evidence. The cytotoxic and cytostatic activities of isolated compounds were investigated by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) method. Among the glycosides obtained here, caffeic acid-containing phenylpropanoid (or phenethyl alcohol, or phenylethanoid) glycosides were found to show activity against several kinds of cancer cells. However, they didn't affect the growth and viability of primary-cultured rat hepatocytes. Study of the structure-activity relationship indicated that ortho-dihydroxy aromatic systems of phenylpropanoid glycosides are necessary for their cytotoxic and cytostatic activities.
Isolation and characterization of a uranium(VI)-nitride triple bond

NASA Astrophysics Data System (ADS)

King, David M.; Tuna, Floriana; McInnes, Eric J. L.; McMaster, Jonathan; Lewis, William; Blake, Alexander J.; Liddle, Stephen T.

2013-06-01

The nature and extent of covalency in uranium bonding is still unclear compared with that of transition metals, and there is great interest in studying uranium-ligand multiple bonds. Although U=O and U=NR double bonds (where R is an alkyl group) are well-known analogues to transition-metal oxo and imido complexes, the uranium(VI)-nitride triple bond has long remained a synthetic target in actinide chemistry. Here, we report the preparation of a uranium(VI)-nitride triple bond. We highlight the importance of (1) ancillary ligand design, (2) employing mild redox reactions instead of harsh photochemical methods that decompose transiently formed uranium(VI) nitrides, (3) an electrostatically stabilizing sodium ion during nitride installation, (4) selecting the right sodium sequestering reagent, (5) inner versus outer sphere oxidation and (6) stability with respect to the uranium oxidation state. Computational analyses suggest covalent contributions to U≡N triple bonds that are surprisingly comparable to those of their group 6 transition-metal nitride counterparts.
Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

PubMed Central

Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua

2012-01-01

Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis. PMID:22267658
Quantitation of sweet steviol glycosides by means of a HILIC-MS/MS-SIDA approach.

PubMed

Well, Caroline; Frank, Oliver; Hofmann, Thomas

2013-11-27

Meeting the rising consumer demand for natural food ingredients, steviol glycosides, the sweet principle of Stevia rebaudiana Bertoni (Bertoni), have recently been approved as food additives in the European Union. As regulatory constraints require sensitive methods to analyze the sweet-tasting steviol glycosides in foods and beverages, a HILIC-MS/MS method was developed enabling the accurate and reliable quantitation of the major steviol glycosides stevioside, rebaudiosides A-F, steviolbioside, rubusoside, and dulcoside A by using the corresponding deuterated 16,17-dihydrosteviol glycosides as suitable internal standards. This quantitation not only enables the analysis of the individual steviol glycosides in foods and beverages but also can support the optimization of breeding and postharvest downstream processing of Stevia plants to produce preferentially sweet and least bitter tasting Stevia extracts.
Synthesis and antibacterial properties of water-dispersible silver nanoparticles stabilized by metal-carbon σ-bonds

NASA Astrophysics Data System (ADS)

Kawai, Koji; Narushima, Takashi; Kaneko, Kotaro; Kawakami, Hayato; Matsumoto, Miyuki; Hyono, Atsushi; Nishihara, Hiroshi; Yonezawa, Tetsu

2012-12-01

The synthesis of 4-diazoniumcarboxylbenzene fluoroborate, a new water-soluble stabilizer for metal nanoparticles (NPs), is described. A stable dispersion of Ag NPs in water was successfully produced by a simultaneous aqueous reduction of this diazonium salt and silver nitrate by NaBH4. UV-vis spectra, TEM images, XRD patterns, and XPS spectra of the obtained Ag NPs revealed that they were stabilized by Ag-C σ-bonds. These NPs showed excellent antimicrobial properties against Staphylococcus aureus.
Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.

PubMed

Huang, Ming; Giese, Timothy J; York, Darrin M

2015-07-05

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.
Nucleic acid reactivity : challenges for next-generation semiempirical quantum models

PubMed Central

Huang, Ming; Giese, Timothy J.; York, Darrin M.

2016-01-01

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity in order to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic diffierential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models are evaluated against high-level quantum mechanical benchmark calculations for seven biologically important data sets. The data sets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling “modified divide-and-conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles within the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggest that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbond interactions. PMID:25943338
Effect of endodontic irrigants on biofilm matrix polysaccharides.

PubMed

Tawakoli, P N; Ragnarsson, K T; Rechenberg, D K; Mohn, D; Zehnder, M

2017-02-01

To specifically investigate the effect of endodontic irrigants at their clinical concentration on matrix polysaccharides of cultured biofilms. Saccharolytic effects of 3% H 2 O 2 , 2% chlorhexidine (CHX), 17% EDTA, 5% NaOCl and 0.9% saline (control) were tested using agarose (α 1-3 and β 1-4 glycosidic bonds) blocks (n = 3) in a weight assay. The irrigants were also applied to three-species biofilms (Streptococcus mutans UAB 159, Streptococcus oralis OMZ 607 and Actinomyces oris OMZ 745) grown anaerobically on hydroxyapatite discs (n = 6). Glycoconjugates in the matrix and total bacterial cell volumes were determined using combined Concanavalin A-/Syto 59-staining and confocal laser-scanning microscopy. Volumes of each scanned area (triplicates/sample) were calculated using Imaris software. Data were compared between groups using one-way anova/Tukey HSD, α = 0.05. The weight assay revealed that NaOCl was the only irrigant under investigation capable of dissolving the agarose blocks. NaOCl eradicated stainable matrix and bacteria in cultured biofilms after 1 min of exposure (P < 0.05 compared to all groups, volumes in means ± standard deviation, 10 -3 mm 3 per 0.6 mm 2 disc; NaOCl matrix: 0.10 ± 0.08, bacteria: 0.03 ± 0.06; saline control matrix: 4.01 ± 1.14, bacteria: 11.56 ± 3.02). EDTA also appeared to have some effect on the biofilm matrix (EDTA matrix: 1.90 ± 0.33, bacteria: 9.26 ± 2.21), whilst H 2 O 2 and CHX merely reduced bacterial cell volumes. Sodium hypochlorite can break glycosidic bonds. It dissolves glycoconjugates in the biofilm matrix. It also lyses bacterial cells. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.
Low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl.

PubMed

Bayat, Parisa; Lesage, Denis; Cole, Richard B

2018-05-29

The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using three techniques shows that, generally, when working with mono-lithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with di-lithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a non-resonant activation technique and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of mono-lithiated and di-lithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages (rearrangement) vs. direct glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on di-lithiated and tri-lithiated sugars reveal that intensities of product ions containing two Li + or three Li + , respectively, are higher than those bearing only one Li + . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl adducted lithiated sugar and NaCl adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system. This article is protected by copyright. All rights reserved.
Epigallocatechin-3-gallate and Epigallocatechin-3-O-(3-O-methyl)-gallate Enhance the Bonding Stability of an Etch-and-Rinse Adhesive to Dentin

PubMed Central

Yu, Hao-Han; Zhang, Ling; Yu, Fan; Li, Fang; Liu, Zheng-Ya; Chen, Ji-Hua

2017-01-01

This study evaluated epigallocatechin-3-gallate (EGCG) and epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG-3Me) modified etch-and-rinse adhesives (Single Bond 2, SB 2) for their antibacterial effect and bonding stability to dentin. EGCG-3Me was isolated and purified with column chromatography and preparative high performance liquid chromatography. EGCG and EGCG-3Me were incorporated separately into the adhesive SB 2 at concentrations of 200, 400, and 600 µg/mL. The effect of cured adhesives on the growth of Streptococcus mutans (S. mutans) was determined with scanning electron microscopy and confocal laser scanning microscopy; the biofilm of bacteria was further quantified via optical density 600 values. The inhibition of EGCG and EGCG-3Me on dentin-originated collagen proteases activities was evaluated with a proteases fluorometric assay kit. The degree of conversion (DC) of the adhesives was tested with micro-Raman spectrum. The immediate and post-thermocycling (5000 cycles) bond strength was assessed through Microtensile Bond Strength (MTBS) test. Cured EGCG/EGCG-3Me modified adhesives inhibit the growth of S. mutans in a concentration-dependent manner. The immediate MTBS of SB 2 was not compromised by EGCG/EGCG-3Me modification. EGCG/EGCG-3Me modified adhesive had higher MTBS than SB 2 after thermocycling, showing no correlation with concentration. The DC of the adhesive system was affected depending on the concentration of EGCG/EGCG-3Me and the depth of the hybrid layer. EGCG/EGCG-3Me modified adhesives could inhibit S. mutans adhesion to dentin–resin interface, and maintain the bonding stability. The adhesive modified with 400 µg/mL EGCG-3Me showed antibacterial effect and enhanced bonding stability without affect the DC of adhesive. PMID:28772546
Epigallocatechin-3-gallate and Epigallocatechin-3-O-(3-O-methyl)-gallate Enhance the Bonding Stability of an Etch-and-Rinse Adhesive to Dentin.

PubMed

Yu, Hao-Han; Zhang, Ling; Yu, Fan; Li, Fang; Liu, Zheng-Ya; Chen, Ji-Hua

2017-02-15

This study evaluated epigallocatechin-3-gallate (EGCG) and epigallocatechin-3- O -(3- O -methyl)-gallate (EGCG-3Me) modified etch-and-rinse adhesives (Single Bond 2, SB 2) for their antibacterial effect and bonding stability to dentin. EGCG-3Me was isolated and purified with column chromatography and preparative high performance liquid chromatography. EGCG and EGCG-3Me were incorporated separately into the adhesive SB 2 at concentrations of 200, 400, and 600 µg/mL. The effect of cured adhesives on the growth of Streptococcus mutans ( S. mutans ) was determined with scanning electron microscopy and confocal laser scanning microscopy; the biofilm of bacteria was further quantified via optical density 600 values. The inhibition of EGCG and EGCG-3Me on dentin-originated collagen proteases activities was evaluated with a proteases fluorometric assay kit. The degree of conversion (DC) of the adhesives was tested with micro-Raman spectrum. The immediate and post-thermocycling (5000 cycles) bond strength was assessed through Microtensile Bond Strength (MTBS) test. Cured EGCG/EGCG-3Me modified adhesives inhibit the growth of S. mutans in a concentration-dependent manner. The immediate MTBS of SB 2 was not compromised by EGCG/EGCG-3Me modification. EGCG/EGCG-3Me modified adhesive had higher MTBS than SB 2 after thermocycling, showing no correlation with concentration. The DC of the adhesive system was affected depending on the concentration of EGCG/EGCG-3Me and the depth of the hybrid layer. EGCG/EGCG-3Me modified adhesives could inhibit S. mutans adhesion to dentin-resin interface, and maintain the bonding stability. The adhesive modified with 400 µg/mL EGCG-3Me showed antibacterial effect and enhanced bonding stability without affect the DC of adhesive.
The crystallization and structural analysis of cellulases (and other glycoside hydrolases): strategies and tactics.

PubMed

Roberts, Shirley M; Davies, Gideon J

2012-01-01

The three-dimensional (3-D) structures of cellulases, and other glycoside hydrolases, are a central feature of research in carbohydrate chemistry and biochemistry. 3-D structure is used to inform protein engineering campaigns, both academic and industrial, which are typically used to improve the stability or activity of an enzyme. Examples of classical protein engineering goals include higher thermal stability, reduced metal-ion dependency, detergent and protease resistance, decreased product inhibition, and altered specificity. 3-D structure may also be used to interpret the behavior of enzyme variants that are derived from screening or random mutagenesis approaches, with a view to establishing an iterative design process. In other areas, 3-D structure is used as one of the many tools to probe enzymatic catalysis, typically dovetailing with physical organic chemistry approaches to provide complete reaction mechanisms for enzymes by visualizing catalytic site interactions at different stages of the reaction. Such mechanistic insight is not only fundamentally important, impacting on inhibitor and drug design approaches with ramifications way beyond cellulose hydrolysis, but also provides the framework for the design of enzyme variants to use as biocatalysts for the synthesis of bespoke oligosaccharides. Here we review some of the strategies and tactics that may be applied to the X-ray structure solution of cellulases (and other carbohydrate-active enzymes). The general approach is first to decide why you are doing the work, then to establish correct domain boundaries for truncated constructs (typically the catalytic domain only), and finally to pursue crystallization of pure, homogeneous, and monodisperse protein with appropriate ligand and additive combinations. Cellulase-specific strategies are important for the delineation of domain boundaries, while glycoside hydrolases generally also present challenges and opportunities for the selection and optimization of ligands to both aid crystallization, and also provide structural and mechanistic insight. As the many roles for plant cell wall degrading enzymes increase, so does the need for rapid high-quality structure determination to provide a sound structural foundation for understanding mechanism and specificity, and for future protein engineering strategies. Copyright © 2012 Elsevier Inc. All rights reserved.
Dynamic stability of stacked disk type flywheels

NASA Astrophysics Data System (ADS)

Younger, F. C.

1981-04-01

A flywheel assembly formed from adhesively bonded stacked fiber composite disks was analyzed. The stiffness and rigidity of the assembly required to prevent uncontrolled growth in the deformations due to centrifugal force was determined. It is shown that stacked disk type flywheels become unstable when the speed exceeds a critical value. This critical value of speed depends upon the stiffness of the bonded attachments between the disks. It is found that elastomeric bonds do not provide adequate stiffness to insure dynamic stability for high speed stacked disk type flywheels.
New lignan glycosides from Justicia procumbens.

PubMed

Jin, Hong; Yang, Shu; Dong, Jun-Xing

2017-01-01

Four new lignan glycosides (1-4), named procumbenosides I, K, L, and M, together with cleistanthin B (5) reported for the first time in the genus Justicia, and 5 other known arylnaphthalene lignan glycosides (6-10) were isolated from the whole plant of Justicia procumbens. The structures of the new compounds were elucidated by extensive one-dimensional (1D) and two-dimensional (2D) NMR experiments and mass spectrometry. Procumbenoside M (4) was a rare sesquilignan glycoside never previously reported in the species of Justicia. The paper also provided insight into the conformational equilibria existing in the lignan glycosides of the plant.
[Digoxin as a cause of chromatopsia and depression in a patient with heart failure and hyperthyroidism].

PubMed

Chyrek, R; Jabłecka, A; Pupek-Musialik, D; Lowicki, Z

2000-08-01

67 year old patient with chronic heart failure and persistent atrial fibrillation had overdosed glycosides for several months. The symptoms of gastrointestinal system and nervous system appeared after long term therapy with toxic doses of glycosides. Originally depression was diagnosed based on the central nervous system disturbances. Even though overdose of glycosides was diagnosed the blood serum glycoside level was within the therapeutic limits. Based on the precise analysis of the data, it was concluded that the reason for normal blood serum glycoside level in this case was coexisting hyperthyreosis.
Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

PubMed Central

Wolters, Lando P; Bickelhaupt, F Matthias

2012-01-01

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A− arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A− and the σ* orbital of D–X. PMID:24551497

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.
Agrobacterium Mediated Transient Gene Silencing (AMTS) in Stevia rebaudiana: Insights into Steviol Glycoside Biosynthesis Pathway

PubMed Central

Guleria, Praveen; Yadav, Sudesh Kumar

2013-01-01

Background Steviol glycoside biosynthesis pathway has emerged as bifurcation from ent-kaurenoic acid, substrate of methyl erythritol phosphate pathway that also leads to gibberellin biosynthesis. However, the genetic regulation of steviol glycoside biosynthesis has not been studied. So, in present study RNA interference (RNAi) based Agrobacterium mediated transient gene silencing (AMTS) approach was followed. SrKA13H and three SrUGTs (SrUGT85C2, SrUGT74G1 and SrUGT76G1) genes encoding ent-kaurenoic acid-13 hydroxylase and three UDP glycosyltransferases of steviol glycoside biosynthesis pathway were silenced in Stevia rebaudiana to understand its molecular mechanism and association with gibberellins. Methodology/Principal Findings RNAi mediated AMTS of SrKA13H and three SrUGTs has significantly reduced the expression of targeted endogenous genes as well as total steviol glycoside accumulation. While gibberellins (GA3) content was significantly enhanced on AMTS of SrUGT85C2 and SrKA13H. Silencing of SrKA13H and SrUGT85C2 was found to block the metabolite flux of steviol glycoside pathway and shifted it towards GA3 biosynthesis. Further, molecular docking of three SrUGT proteins has documented highest affinity of SrUGT76G1 for the substrates of alternate pathways synthesizing steviol glycosides. This could be a plausible reason for maximum reduction in steviol glycoside content on silencing of SrUGT76G1 than other genes. Conclusions SrKA13H and SrUGT85C2 were identified as regulatory genes influencing carbon flux between steviol glycoside and gibberellin biosynthesis. This study has also documented the existence of alternate steviol glycoside biosynthesis route. PMID:24023961
Importance of interlayer H bonding structure to the stability of layered minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.

Layered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulkmore » and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.« less
Importance of interlayer H bonding structure to the stability of layered minerals

DOE PAGES

Conroy, Michele; Soltis, Jennifer A.; Wittman, Rick S.; ...

2017-10-16

Layered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulkmore » and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.« less
Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

PubMed

Honda, Ryo

2018-02-27

Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Characterization of single-domain antibodies with an engineered disulfide bond.

PubMed

Hussack, Greg; Mackenzie, C Roger; Tanha, Jamshid

2012-01-01

Camelidae single-domain antibodies (VHHs) represent a unique class of emerging therapeutics. Similar to other recombinant antibody fragments (e.g., Fabs, scFvs), VHHs are amenable to library screening and selection, but benefit from superior intrinsic biophysical properties such as high refolding efficiency, high solubility, no tendency for aggregation, resistance to proteases and chemical denaturants, and high expression, making them ideal agents for antibody-based drug design. Despite these favorable biophysical characteristics, further improvements to VHH stability are desirable when considering applications in adverse environments like high heat, low humidity, pH extremes, and the acidic, protease-rich gastrointestinal tract. Recently, the introduction of a disulfide bond into the hydrophobic core of camelid VHHs increased antibody thermal and conformational stability. Here, we present additional protocols for characterizing the effects of the introduced disulfide bond on a panel of llama VHHs. Specifically, we employ mass spectrometry fingerprinting analysis of VHH peptides to confirm the presence of the introduced disulfide bond, size exclusion chromatography, and surface plasmon resonance to examine the effects on aggregation state and target affinity, and circular dichroism spectroscopy and protease digestion assays to assess the effects on thermal and proteolytic stability. The disulfide bond stabilization strategy can be incorporated into antibody library design and should lead to hyperstabilized single-domain antibodies (VHHs, VHs), and possibly Fabs and scFvs, if selection pressures such as denaturants or proteases are introduced during antibody selection.
A Report of Undergraduates' Bonding Misconceptions.

ERIC Educational Resources Information Center

Nicoll, Gayle

2001-01-01

Describes misconceptions related to electronegativity, bonding, geometry, and microscopic representations that undergraduate students hold. Investigates the stability of misconceptions as a function of educational level, indicating that some students' misconceptions relating to bonding are resistant to change despite increased chemistry education.…
Influence of ageing on self-etch adhesives: one-step vs. two-step systems.

PubMed

Marchesi, Giulio; Frassetto, Andrea; Visintini, Erika; Diolosà, Marina; Turco, Gianluca; Salgarello, Stefano; Di Lenarda, Roberto; Cadenaro, Milena; Breschi, Lorenzo

2013-02-01

The aim of this study was to evaluate microtensile bond strength (μTBS) to dentine, interfacial nanoleakage expression, and stability after ageing, of two-step vs. one-step self-etch adhesives. Human molars were cut to expose middle/deep dentine, assigned to groups (n = 15), and treated with the following bonding systems: (i) Optibond XTR (a two-step self-etch adhesive; Kerr), (ii) Clearfil SE Bond (a two-step self-etch adhesive; Kuraray), (iii) Adper Easy Bond (a one-step self-etch adhesive; 3M ESPE), and (iv) Bond Force (a one-step self-etch adhesive; Tokuyama). Specimens were processed for μTBS testing after 24 h, 6 months, or 1 yr of storage in artificial saliva at 37°C. Nanoleakage expression was examined in similarly processed additional specimens. At baseline the μTBS results ranked in the following order: Adper Easy Bond = Optibond XTR ≥Clearfil SE = Bond Force, and interfacial nanoleakage analysis showed Clearfil SE Bond = Adper Easy Bond = Optibond XTR> Bond Force. After 1 yr of storage, Optibond XTR, Clearfil SE Bond, and Adper Easy Bond showed higher μTBS and lower interfacial nanoleakage expression compared with Bond Force. In conclusion, immediate bond strength, nanoleakage expression, and stability over time were not related to the number of steps of the bonding systems, but to their chemical formulations. © 2012 Eur J Oral Sci.
Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.

PubMed

Teplitsky, A; Mechaly, A; Stojanoff, V; Sainz, G; Golan, G; Feinberg, H; Gilboa, R; Reiland, V; Zolotnitsky, G; Shallom, D; Thompson, A; Shoham, Y; Shoham, G

2004-05-01

Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.
Synthesis and anti-fungal activity of acetylated glycosides of 1,4-naphthoquinone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polonik, S.G.; Tolkach, A.M.; Uvarova, N.I.

1986-12-01

The authors synthesize a series of glycoside derivatives of 1,4-naphthoquinones (VIII-XXII) and study their anti-fungal activity in a search for more effective preparations for the medical and food industries. The structures of the newly prepared glycosides were verified by IR and /sup 1/H and /sup 13/C NMR spectroscopy. The properties of acetylated 1,4-naphthoquinone glycosides are presented.
Bonding properties and bond activation of ylides: recent findings and outlook.

PubMed

Urriolabeitia, Esteban P

2008-11-14

The interaction of phosphorus and nitrogen ylides with metallic precursors has been examined from different points of view. The first one is related to the bonding properties of the ylides. Ylides with a unique stabilizing group bond through different atoms (the Calpha or the heteroatoms); while ylides with two stabilizing groups never coordinate through the Calpha atom. In the second section we examine the cause of the stereoselective coordination of bisylides of phosphorus, nitrogen and arsenic, and of mixed bisylides. We describe here the very interesting conformational preferences found in these systems, which have been determined and characterized. The DFT study of these bisylides has allowed for the characterization of strong intramolecular PO and AsO interactions, as well as moderate CHO[double bond, length as m-dash]C hydrogen bonds as the source of these conformational preferences. The third topic is related to the amazing reactivity of phosphorus ylides in bond activation processes. Depending on the nature of the metallic precursors, ylides can behave as sources of carbenes, of phosphine derivatives, of other ylides or of orthometallated complexes through P[double bond, length as m-dash]C, P-C or C-H bond activation reactions.
Complementary action of jasmonic acid on salicylic acid in mediating fungal elicitor-induced flavonol glycoside accumulation of Ginkgo biloba cells.

PubMed

Xu, Maojun; Dong, Jufang; Wang, Huizhong; Huang, Luqi

2009-08-01

The antagonistic action between jasmonic acid (JA) and salicylic acid (SA) in plant defence responses has been well documented. However, their relationship in secondary metabolite production is largely unknown. Here, we report that PB90, a protein elicitor from Phytophthora boehmeriae, triggers JA generation, SA accumulation and flavonol glycoside production of Ginkgo biloba cells. JA inhibitors suppress not only PB90-triggered JA generation, but also the elicitor-induced flavonol glycoside production. However, the elicitor can still enhance flavonol glycoside production even though the JA generation is totally inhibited. Over-expression of SA hydrolase gene NahG not only abolishes SA accumulation, but also suppresses the elicitor-induced flavonol glycoside production when JA signalling is inhibited. Interestingly, expression of NahG does not inhibit the elicitor-induced flavonol glycoside accumulation in the absence of JA inhibitors. Moreover, JA levels are significantly enhanced when SA accumulation is impaired in the transgenic cells. Together, the data suggest that both JA and SA are involved in PB90-induced flavonol glycoside production. Furthermore, we demonstrate that JA signalling might be enhanced to substitute for SA to mediate the elicitor-induced flavonol glycoside accumulation when SA signalling is impaired, which reveals an unusual complementary relationship between JA and SA in mediating plant secondary metabolite production.
Effects of protein in wheat flour on retrogradation of wheat starch.

PubMed

Xijun, Lian; Junjie, Guo; Danli, Wang; Lin, Li; Jiaran, Zhu

2014-08-01

Albumins, globulins, gliadins, and glutenins were isolated from wheat flour and the effects of those proteins on retrogradation of wheat starch were investigated. The results showed that only glutenins retarded retrogradation of wheat starch and other 3 proteins promoted it. The results of IR spectra proved that no S-S linkage formed during retrogradation of wheat starch blended with wheat proteins. Combination of wheat starch and globulins or gliadins through glucosidic bonds hindered the hydrolysis of wheat starch by α-amylase. The melting peak temperatures of retrograded wheat starch attached to different proteins were 128.46, 126.14, 132.03, 121.65, and 134.84 °C for the control with no protein, albumins, glutenins, globulins, gliadins groups, respectively, and there was no second melting temperature for albumins group. Interaction of wheat proteins and starch in retrograded wheat starch greatly decreased the endothermic enthalpy (△H) of retrograded wheat starch. Retrograded wheat starch bound to gliadins might be a new kind of resistant starch based on glycosidic bond between starch and protein. © 2014 Institute of Food Technologists®
Enhancing protein stability with extended disulfide bonds

DOE PAGES

Liu, Tao; Wang, Yan; Luo, Xiaozhou; ...

2016-05-09

Disulfide bonds play an important role in protein folding and stability. However, the cross-linking of sites within proteins by cysteine disulfides has significant distance and dihedral angle constraints. In this paper, we report the genetic encoding of noncanonical amino acids containing long side-chain thiols that are readily incorporated into both bacterial and mammalian proteins in good yields and with excellent fidelity. These amino acids can pair with cysteines to afford extended disulfide bonds and allow cross-linking of more distant sites and distinct domains of proteins. To demonstrate this notion, we preformed growth-based selection experiments at nonpermissive temperatures using a librarymore » of random β-lactamase mutants containing these noncanonical amino acids. A mutant enzyme that is cross-linked by one such extended disulfide bond and is stabilized by ~9 °C was identified. Finally, this result indicates that an expanded set of building blocks beyond the canonical 20 amino acids can lead to proteins with improved properties by unique mechanisms, distinct from those possible through conventional mutagenesis schemes.« less
Metabolic stability of new anticonvulsants in body fluids and organ homogenates.

PubMed

Marszałek, Dorota; Goldnik, Anna; Pluciński, Franciszek; Mazurek, Aleksander P; Jakubiak, Anna; Lis, Ewa; Tazbir, Piotr; Koziorowska, Agnieszka

2012-01-01

The stability as a function of time of compounds with established anticonvulsant activity: picolinic acid benzylamide (Pic-BZA), picolinic acid 2-fluorobenzylamide (Pic-2-F-BZA), picolinic acid 3-fluorobenzylamide (Pic-3-F-BZA), picolinic acid 4-fluorobenzylamide (Pic-4-F-BZA) and picolinic acid 2-methylbenzylamide (Pic-2-Me-BZA) in body fluids and homogenates of body organs were determined after incubation. It was found that they decompose relatively rapidly in liver and kidney and are stable against enzymes present in body fluids and some organs. These results are consistent with the bond strength expressed as total energy of amide bonds (calculated by quantum chemical methods) in the studied anticonvulsants. The calculated values of the amide bond energy are: 199.4 kcal/mol, 200.2 kcal/mol, 207.5 kcal/mol, 208.4 kcal/mol and 198.2 kcal/mol, respectively. The strength of the amide bonds in the studied anticonvulsants correctly reflects their stability in liver or kidney.
Iodine bonding stabilizes iodomethane in MIDAS pesticide. Theoretical study of intermolecular interactions between iodomethane and chloropicrin.

PubMed

Glaser, Rainer; Prugger, Kaitlan

2012-02-22

The results are reported of a theoretical study of iodomethane (H(3)C-I, 1) and chloropicrin (Cl(3)C-NO(2), 2), of the heterodimers 3-6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3-5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding.
Fecalase: a model for activation of dietary glycosides to mutagens by intestinal flora

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamura, G.; Gold, C.; Ferro-Luzzi, A.

1980-08-01

Many substances in the plant kingdom and in man's diet occur as glycosides. Recent studies have indicated that many glycosides that are not mutagenic in tests such as the Salmonella test become mutagenic upon hydrolysis of the glycosidic linkages. The Salmonella test utilizes a liver homogenate to approximate mammalian metabolism but does not provide a source of the enzymes present in intestinal bacterial flora that hydrolyze the wide variety of glycosides present in nature. We describe a stable cell-free extract of human feces, fecalase, which is shown to contain various glycosidases that allow the in vitro activation of many naturalmore » glycosides to mutagens in the Salmonella/liver homogenate test. Many beverages, such as red wine (but apparently not white wine) and tea, contain glycosides of the mutagen quercetin. Red wine, red grape juice, and teas were mutagenic in the test when fecalase was added, and red wine contained considerable direct mutagenic activity in the absence of fecalase. The implications of quercetin mutagenicity and carcinogenicity are discussed.« less
Transition of phenolics and cyanogenic glycosides from apricot and cherry fruit kernels into liqueur.

PubMed

Senica, Mateja; Stampar, Franci; Veberic, Robert; Mikulic-Petkovsek, Maja

2016-07-15

Popular liqueurs made from apricot/cherry pits were evaluated in terms of their phenolic composition and occurrence of cyanogenic glycosides (CGG). Analyses consisted of detailed phenolic and cyanogenic profiles of cherry and apricot seeds as well as beverages prepared from crushed kernels. Phenolic groups and cyanogenic glycosides were analyzed with the aid of high-performance liquid chromatography (HPLC) and mass spectrophotometry (MS). Lower levels of cyanogenic glycosides and phenolics have been quantified in liqueurs compared to fruit kernels. During fruit pits steeping in the alcohol, the phenolics/cyanogenic glycosides ratio increased and at the end of beverage manufacturing process higher levels of total analyzed phenolics were detected compared to cyanogenic glycosides (apricot liqueur: 38.79 μg CGG per ml and 50.57 μg phenolics per ml; cherry liqueur 16.08 μg CGG per ml and 27.73 μg phenolics per ml). Although higher levels of phenolics are characteristic for liqueurs made from apricot and cherry pits these beverages nevertheless contain considerable amounts of cyanogenic glycosides. Copyright © 2016 Elsevier Ltd. All rights reserved.
[Separation and identification of 5 glycosidic flavor precursors in tobacco by ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry].

PubMed

Wu, Xinhua; Zhu, Ruizhi; Ren, Zhuoying; Wang, Kai; Mou, Dingrong; Wei, Wanzhi; Miao, Mingming

2009-11-01

A qualitative method for the identification of 5 main glycosidic flavor precursors in tobacco was developed by using ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI MS/MS) and gas chromatography-mass spectrometry (GC-MS). The glycosidic flavor precursors in tobacco were extracted with methanol, cleaned up with an XAD-2 column. The aglycones were later released by enzyme-mediated hydrolysis under the condition of pH 5. The 5 volatile aglycone moieties were identified by GC-MS standard spectra library. The precursor ions of glycosides were determined by using electrospray ionization mass spectrometry in negative ion mode, then the 5 glycosidic flavor precursors were identified by using product ion scan (MS2) finally, using UPLC-ESI MS/MS, separation and identification of 5 glycosidic flavor precursors were accomplished on an RP-C,8 column in the multiple reaction monitoring (MRM) mode by using methanol and acetic acid-ammonium acetate aqueous solution as eluent. This work lays a foundation for the analysis of glycosidic flavor precursors without the standards by using liquid chromatography-mass spectrometry.
A Triatomic Silicon(0) Cluster Stabilized by a Cyclic Alkyl(amino) Carbene.

PubMed

Mondal, Kartik Chandra; Roy, Sudipta; Dittrich, Birger; Andrada, Diego M; Frenking, Gernot; Roesky, Herbert W

2016-02-24

Reduction of the neutral carbene tetrachlorosilane adduct (cAAC)SiCl4 (cAAC=cyclic alkyl(amino) carbene :C(CMe2)2 (CH2)N(2,6-iPr2C6H3) with potassium graphite produces stable (cAAC)3Si3, a carbene-stabilized triatomic silicon(0) molecule. The Si-Si bond lengths in (cAAC)3Si3 are 2.399(8), 2.369(8) and 2.398(8) Å, which are in the range of Si-Si single bonds. Each trigonal pyramidal silicon atom of the triangular molecule (cAAC)3Si3 possesses a lone pair of electrons. Its bonding, stability, and electron density distributions were studied by quantum chemical calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methylene Homologues of Artemisone: An Unexpected Structure-Activity Relationship and a Possible Implication for the Design of C10-Substituted Artemisinins.

PubMed

Wu, Yuet; Wu, Ronald Wai Kung; Cheu, Kwan Wing; Williams, Ian D; Krishna, Sanjeev; Slavic, Ksenija; Gravett, Andrew M; Liu, Wai M; Wong, Ho Ning; Haynes, Richard K

2016-07-05

We sought to establish if methylene homologues of artemisone are biologically more active and more stable than artemisone. The analogy is drawn with the conversion of natural O- and N-glycosides into more stable C-glycosides that may possess enhanced biological activities and stabilities. Dihydroartemisinin was converted into 10β-cyano-10-deoxyartemisinin that was hydrolyzed to the α-primary amide. Reduction of the β-cyanide and the α-amide provided the respective methylamine epimers that upon treatment with divinyl sulfone gave the β- and α-methylene homologues, respectively, of artemisone. Surprisingly, the compounds were less active in vitro than artemisone against P. falciparum and displayed no appreciable activity against A549, HCT116, and MCF7 tumor cell lines. This loss in activity may be rationalized in terms of one model for the mechanism of action of artemisinins, namely the cofactor model, wherein the presence of a leaving group at C10 assists in driving hydride transfer from reduced flavin cofactors to the peroxide during perturbation of intracellular redox homeostasis by artemisinins. It is noted that the carba analogue of artemether is less active in vitro than the O-glycoside parent toward P. falciparum, although extrapolation of such activity differences to other artemisinins at this stage is not possible. However, literature data coupled with the leaving group rationale suggest that artemisinins bearing an amino group attached directly to C10 are optimal compounds. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Effect of polarization on the stability of a helix dimer

NASA Astrophysics Data System (ADS)

Wang, Xing Y.; Zhang, John Z. H.

2011-01-01

Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.
Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

ERIC Educational Resources Information Center

Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

2016-01-01

Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…
Broad control of disulfide stability through microenvironmental effects and analysis in complex redox environments.

PubMed

Wu, Chuanliu; Wang, Shuo; Brülisauer, Lorine; Leroux, Jean-Christophe; Gauthier, Marc A

2013-07-08

Disulfide bonds stabilize the tertiary- and quaternary structure of proteins. In addition, they can be used to engineer redox-sensitive (bio)materials and drug-delivery systems. Many of these applications require control of the stability of the disulfide bond. It has recently been shown that the charged microenvironment of the disulfide can be used to alter their stability by ∼3 orders of magnitude in a predictable and finely tunable manner at acidic pH. The aim of this work is to extend these findings to physiological pH and to demonstrate the validity of this approach in complex redox milieu. Disulfide microenvironments were manipulated synergistically with steric hindrance herein to control disulfide bond stability over ∼3 orders of magnitude at neutral pH. Control of disulfide stability through microenvironmental effects could also be observed in complex redox buffers (including serum) and in the presence of cells. Such fine and predictable control of disulfide properties is not achievable using other existing approaches. These findings provide easily implementable and general tools for controlling the responsiveness of biomaterials and drug delivery systems toward various local endogenous redox environments.
A Second β-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans*

PubMed Central

Robb, Melissa; Robb, Craig S.; Higgins, Melanie A.; Hobbs, Joanne K.; Paton, James C.; Boraston, Alisdair B.

2015-01-01

An important facet of the interaction between the pathogen Streptococcus pneumoniae (pneumococcus) and its human host is the ability of this bacterium to process host glycans. To achieve cleavage of the glycosidic bonds in host glycans, S. pneumoniae deploys a wide array of glycoside hydrolases. Here, we identify and characterize a new family 20 glycoside hydrolase, GH20C, from S. pneumoniae. Recombinant GH20C possessed the ability to hydrolyze the β-linkages joining either N-acetylglucosamine or N-acetylgalactosamine to a wide variety of aglycon residues, thus revealing this enzyme to be a generalist N-acetylhexosaminidase in vitro. X-ray crystal structures were determined for GH20C in a ligand-free form, in complex with the N-acetylglucosamine and N-acetylgalactosamine products of catalysis and in complex with both gluco- and galacto-configured inhibitors O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino N-phenyl carbamate (PUGNAc), O-(2-acetamido-2-deoxy-d-galactopyranosylidene)amino N-phenyl carbamate (GalPUGNAc), N-acetyl-d-glucosamine-thiazoline (NGT), and N-acetyl-d-galactosamine-thiazoline (GalNGT) at resolutions from 1.84 to 2.7 Å. These structures showed N-acetylglucosamine and N-acetylgalactosamine to be recognized via identical sets of molecular interactions. Although the same sets of interaction were maintained with the gluco- and galacto-configured inhibitors, the inhibition constants suggested preferred recognition of the axial O4 when an aglycon moiety was present (Ki for PUGNAc > GalPUGNAc) but preferred recognition of an equatorial O4 when the aglycon was absent (Ki for GalNGT > NGT). Overall, this study reveals GH20C to be another tool that is unique in the arsenal of S. pneumoniae and that it may implement the effort of the bacterium to utilize and/or destroy the wide array of host glycans that it may encounter. PMID:26491009
Macromolecules of extracellular matrix: determination of selective structures and their functional significance.

PubMed

Butler, William T

2008-01-01

In this brief review, I recount events and scientific endeavors in which I have been privileged to participate. The descriptive information includes discovery and characterization of hydroxylysine glycosides from collagen, isolation of dentin sialoprotein (DSP), investigations on dentin phosphoprotein (DPP), and the discovery of a single gene for both DSP and DPP that requires posttranslational proteolytic cleavage of the parent DSPP molecule to generate the two fragments. Finally, I address our unexpected finding of fragments of DMP1 in bone extracts. These fragments are from the NH2-terminal (37 kDa) and COOH-terminal (57 kDa) regions of DMP1. Our studies showed that, similar to DSPP, DMP1 is proteolytically processed by cleavages at X-Asp bonds.
Chemoselective Reactions for the Synthesis of Glycoconjugates from Unprotected Carbohydrates.

PubMed

Villadsen, Klaus; Martos-Maldonado, Manuel C; Jensen, Knud J; Thygesen, Mikkel B

2017-04-04

Glycobiology is the comprehensive biological investigation of carbohydrates. The study of the role and function of complex carbohydrates often requires the attachment of carbohydrates to surfaces, their tagging with fluorophores, or their conversion into natural or non-natural glycoconjugates, such as glycopeptides or glycolipids. Glycobiology and its "omics", glycomics, require easy and robust chemical methods for the construction of these glycoconjugates. This review gives an overview of the rapidly expanding field of chemical reactions that selectively convert unprotected carbohydrates into glycoconjugates through the anomeric position. The discussion is divided in terms of the anomeric bond type of the newly formed glycoconjugates, including O-, N-, S-, and C-glycosides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Design, fabrication and actuation of a MEMS-based image stabilizer for photographic cell phone applications

NASA Astrophysics Data System (ADS)

Chiou, Jin-Chern; Hung, Chen-Chun; Lin, Chun-Ying

2010-07-01

This work presents a MEMS-based image stabilizer applied for anti-shaking function in photographic cell phones. The proposed stabilizer is designed as a two-axis decoupling XY stage 1.4 × 1.4 × 0.1 mm3 in size, and adequately strong to suspend an image sensor for anti-shaking photographic function. This stabilizer is fabricated by complex fabrication processes, including inductively coupled plasma (ICP) processes and flip-chip bonding technique. Based on the special designs of a hollow handle layer and a corresponding wire-bonding assisted holder, electrical signals of the suspended image sensor can be successfully sent out with 32 signal springs without incurring damage during wire-bonding packaging. The longest calculated traveling distance of the stabilizer is 25 µm which is sufficient to resolve the anti-shaking problem in a three-megapixel image sensor. Accordingly, the applied voltage for the 25 µm moving distance is 38 V. Moreover, the resonant frequency of the actuating device with the image sensor is 1.123 kHz.
Phenolic glycosides and ionone glycoside from the stem of Sargentodoxa cuneata.

PubMed

Chang, Jun; Case, Ryan

2005-12-01

Four phenolic glycosides, cuneatasides A-D (1-4), and one ionone glycoside cuneataside E (5), together with seven known phenolic compounds (6-12) were isolated from the water-soluble constituents of the stem of Sargentodoxa cuneata (Sargentodoxaceae). Their structures were elucidated by spectroscopic analysis. In vitro tests for antimicrobial activity showed compounds 1 and 2 to possess significant activity against two Gram-positive organisms, Staphylococcus aureus and Micrococcus epidermidis.
Pregnane glycosides from Sansevieria trifasciata.

PubMed

Mimaki, Y; Inoue, T; Kuroda, M; Sashida, Y

1997-01-01

Phytochemical analysis of the whole plant of Sansevieria trifasciata, one of the most common Agavaceae plants, has resulted in the isolation of four new pregnane glycosides. Their structures have been determined by spectroscopic analysis and acid- and alkaline-catalysed hydrolysis to be 1 beta,3 beta-dihydroxypregna-5,16-dien-20-one glycosides. This is believed to be the first report of the isolation of the pregnane glycosides from a plant of the family Agavaceae.
Stability and electronic structure of the low- Σ grain boundaries in CdTe: a density functional study

DOE PAGES

Park, Ji-Sang; Kang, Joongoo; Yang, Ji-Hui; ...

2015-01-15

Using first-principles density functional calculations, we investigate the relative stability and electronic structure of the grain boundaries (GBs) in zinc-blende CdTe. Among the low-Σ-value symmetric tilt Σ3 (111), Σ3 (112), Σ5 (120), and Σ5 (130) GBs, we show that the Σ3 (111)GB is always the most stable due to the absence of dangling bonds and wrong bonds. The Σ5 (120) GBs, however, are shown to be more stable than the Σ3 (112) GBs, even though the former has a higher Σ value, and the latter is often used as a model system to study GB effects in zinc-blende semiconductors. Furthermore,more » we find that although containing wrong bonds, the Σ5 (120) GBs are electrically benign due to the short wrong bond lengths, and thus are not as harmful as the Σ3 (112) GBs also having wrong bonds but with longer bond lengths.« less
New benzophenone and quercetin galloyl glycosides from Psidium guajava L.

PubMed

Matsuzaki, Keiichi; Ishii, Rie; Kobiyama, Kaori; Kitanaka, Susumu

2010-07-01

New benzophenone and flavonol galloyl glycosides were isolated from an 80% MeOH extract of Psidium guajava L. (Myrtaceae) together with five known quercetin glycosides. The structures of the novel glycosides were elucidated to be 2,4,6-trihydroxybenzophenone 4-O-(6''-O-galloyl)-beta-D: -glucopyranoside (1, guavinoside A), 2,4,6-trihydroxy-3,5-dimethylbenzophenone 4-O-(6''-O-galloyl)-beta-D: -glucopyranoside (2, guavinoside B), and quercetin 3-O-(5''-O-galloyl)-alpha-L: -arabinofuranoside (3, guavinoside C) by NMR, MS, UV, and IR spectroscopies. Isolated phenolic glycosides showed significant inhibitory activities against histamine release from rat peritoneal mast cells, and nitric oxide production from a murine macrophage-like cell line, RAW 264.7.
Structure Elucidation of New Acetylated Saponins, Lessoniosides A, B, C, D, and E, and Non-Acetylated Saponins, Lessoniosides F and G, from the Viscera of the Sea Cucumber Holothuria lessoni

PubMed Central

Bahrami, Yadollah; Franco, Christopher M. M.

2015-01-01

Sea cucumbers produce numerous compounds with a wide range of chemical structural diversity. Among these, saponins are the most diverse and include sulfated, non-sulfated, acetylated and methylated congeners with different aglycone and sugar moieties. In this study, MALDI and ESI tandem mass spectrometry, in the positive ion mode, were used to elucidate the structure of new saponins extracted from the viscera of H. lessoni. Fragmentation of the aglycone provided structural information on the presence of the acetyl group. The presence of the O-acetyl group was confirmed by observing the mass transition of 60 u corresponding to the loss of a molecule of acetic acid. Ion fingerprints from the glycosidic cleavage provided information on the mass of the aglycone (core), and the sequence and type of monosaccharides that constitute the sugar moiety. The tandem mass spectra of the saponin precursor ions [M + Na]+ provided a wealth of detailed structural information on the glycosidic bond cleavages. As a result, and in conjunction with existing literature, we characterized the structure of five new acetylated saponins, Lessoniosides A–E, along with two non-acetylated saponins Lessoniosides F and G at m/z 1477.7, which are promising candidates for future drug development. The presented strategy allows a rapid, reliable and complete analysis of native saponins. PMID:25603350
Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT-GIAO calculations

NASA Astrophysics Data System (ADS)

Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona

2009-09-01

Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.
Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

PubMed

Wang, Lu; Fried, Stephen D; Boxer, Steven G; Markland, Thomas E

2014-12-30

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.
A stable silicon(0) compound with a Si=Si double bond.

PubMed

Wang, Yuzhong; Xie, Yaoming; Wei, Pingrong; King, R Bruce; Schaefer, Henry F; von R Schleyer, Paul; Robinson, Gregory H

2008-08-22

Dative, or nonoxidative, ligand coordination is common in transition metal complexes; however, this bonding motif is rare in compounds of main group elements in the formal oxidation state of zero. Here, we report that the potassium graphite reduction of the neutral hypervalent silicon-carbene complex L:SiCl4 {where L: is:C[N(2,6-Pri2-C6H3)CH]2 and Pri is isopropyl} produces L:(Cl)Si-Si(Cl):L, a carbene-stabilized bis-silylene, and L:Si=Si:L, a carbene-stabilized diatomic silicon molecule with the Si atoms in the formal oxidation state of zero. The Si-Si bond distance of 2.2294 +/- 0.0011 (standard deviation) angstroms in L:Si=Si:L is consistent with a Si=Si double bond. Complementary computational studies confirm the nature of the bonding in L:(Cl)Si-Si(Cl):L and L:Si=Si:L.
Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

PubMed Central

Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

2014-01-01

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367
A new furostanol glycoside from Tribulus terrestris.

PubMed

Xu, Yajuan; Liu, Yonghong; Xu, Tunhai; Xie, Shengxu; Si, Yunshan; Liu, Yue; Zhou, Haiou; Liu, Tonghua; Xu, Dongming

2010-01-27

Besides two known glycosides, a new furostanol glycoside was isolated from the Fruits of Tribulus terrestris L. The structure of the new furostanol glycoside was established as 26-O-beta-D-glucopyranosyl-(25S)-5alpha-furostane-20(22)-en-12-one-3beta, 26-diol-3-O-alpha-L-rhamnopyranosyl-(1-->2)-[beta-D-glucopyranosyl-(1-->4)]-beta-D-galactopyranoside (1) on the basis of 1D and 2D-NMR techniques, including COSY, HMBC, and HMQC correlations.
Flavonoids of Lotus (Nelumbo nucifera) Seed Embryos and Their Antioxidant Potential.

PubMed

Zhu, Mingzhi; Liu, Ting; Zhang, Chunyun; Guo, Mingquan

2017-08-01

Flavonoids from lotus (Nelumbo nucifera) seed embryos were fractionated over a macroporous resin chromatography into 2 main fractions (I and II), and subsequently identified by high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS 2 ). Sixteen flavonoids were identified in lotus seed embryos, including 8 flavonoid C-glycosides and 8 flavonoid O-glycosides, in which the flavonoid C-glycosides were the main flavonoids. Among them, 2 flavonoid O-glycosides (luteolin 7-O-neohesperidoside and kaempferol 7-O-glucoside) were identified in lotus seed embryos for the 1st time. For further elucidating the effects of flavonoid C-glycosides to the bioactivities of lotus seed embryos, we compared the differences of the flavonoids and their antioxidant activities between leaves and seed embryos of lotus using the same methods. The results showed the antioxidant activity of flavonoids in lotus seed embryos was comparable or higher than that in lotus leaves, whereas the total flavonoid content in seed embryos was lower than lotus leaves which only contained flavonoid O-glycosides. The flavonoid C-glycosides of lotus seed embryos had higher antioxidant properties than the flavonoid O-glycosides presented in lotus leaves. This study suggested that the lotus seed embryos could be promising sources with antioxidant activity and used as dietary supplements for health promotion. © 2017 Institute of Food Technologists®.
The effect of flavonol glycosides on opiate withdrawal.

PubMed

Capasso, Anna

2007-07-01

Our interest has been centered on flavonol glycosides from Croton Menthodorus (Euphorbiaceae) and Aristeguietia discolor (Asteraceae). In this respect, the effect of flavonol glycosides from Croton Menthodorus (Euphorbiaceae) and Aristeguietia discolor (Asteraceae) was investigated on the naloxone-precipitated withdrawal contracture of the acute morphine-dependent guinea-pig ileum in vitro. Furthermore, the effect of these flavonol glycosides was also considered on DAGO (highly selective micro-agonist) and U50-488H (highly selective k-agonist) withdrawal to test whether the possible interaction of flavonol glycosides on opioid withdrawal involves micro- and/or k-opioid receptors. Flavonol glycosides from Croton Menthodorus (1 x 10(-5), 5 x 10(-5) and 1 x 10(-4) M) and from Aristeguietia discolor (1 x 10(-7)-1 x 10(-6)-1 x 10(-5) M) before or after the opioid agonists were able to both prevent and reverse the naloxone-induced contracture after exposure to micro (morphine and DAGO) or k (U50-488H) opiate agonists in a concentration-dependent fashion. Both acetylcholine response and electrical stimulation were reduced by flavonol glycosides treatment as well as the final opiate withdrawal was still reduced. The results of the present study indicate that flavonol glycosides were able to produce significant influence on the opiate withdrawal in vitro and these compounds were able to exert their effects both at micro and k opioid agonists.

[Formation of protodioscin and deltoside isomers in suspension cultures of Nepal yam (Dioscorea deltoidea Wall.) cells].

PubMed

Khandy, M T; Titova, M V; Konstantinova, S V; Kochkin, D V; Ivanov, I M; Nosov, A M

2016-01-01

Changes in the content of the furostanol glycosides protodioscin and deltoside, particularly that of the (25S)-isomers of the glycosides, during suspension cultivation of different lines of Nepal yam (Dioscorea deltoidea Wall.) cells of the strain IFR-DM-0.5 has been investigated. The composition of furostanol glycosides has been characterized, and the dynamics of the accumulation of individual glycosides during lengthy subcultivation of cells maintained in flasks or in a barbotage bioreactor has been analyzed. A positive correlation between the growth and accumulation of substances that belonged to the class of furostanol glycosides has been demonstrated for cultured dioscorea cells, whereas the content of some of the individual glycosides varied considerably between the lines of the strain, cultures maintained under different conditions, and even between cells in different phases of the growth cycle. The increased content of (25R)-forms of the glycosides (protodioscin and deltoside) was correlated with a decrease in the cellular growth rate, whereas an increase in culture growth intensity occurred concomitantly to an increase of the amount of (25S)-isomers. This may be indicative of the specific stimulatory effect of (25S)-glycosides, but not the (25R)-forms, on cell proliferation in vitro. Thus, the concentration of (25S)-forms may increase due to the autoselection of cells capable of intensive division during prolonged cultivation.
In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

PubMed Central

2017-01-01

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events. PMID:29181193
Monoterpene glycosides from Paeonia veitchii.

PubMed

Fu, Qiang; Tan, Mao-Ling; Yuan, Hai-Mei; Chen, Jiang; Fu, Jia

2017-01-01

The EtOH extract of the roots of Paeonia veitchii afforded two new monoterpene glycosides paeonidanin I (1) and paeonidanin J (2), and a new dimeric monoterpene glycoside paeonidanin K (3). Their structures were elucidated on the basis of spectroscopic means and hydrolysis products.
An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins

PubMed Central

Cao, Zheng; Bowie, James U

2014-01-01

Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as –7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by –4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies. PMID:24501090
Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178
Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

PubMed

Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

2017-04-18

The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.
An insight into current concepts and techniques in resin bonding to high strength ceramics.

PubMed

Luthra, R; Kaur, P

2016-06-01

Reliable bonding between high strength ceramics and resin composite cement is difficult to achieve because of their chemical inertness and lack of silica content. The aim of this review was to assess the current literature describing methods for resin bonding to ceramics with high flexural strength such as glass-infiltrated alumina and zirconia, densely sintered alumina and yttria-partially stabilized tetragonal zirconia polycrystalline ceramic (Y-TZP) with respect to bond strength and bond durability. Suitable peer reviewed publications in the English language were identified through searches performed in PubMed, Google Search and handsearches. The keywords or phrases used were 'resin-ceramic bond', 'silane coupling agents', 'air particle abrasion', 'zirconia ceramic' and 'resin composite cements'. Studies from January 1989 to June 2015 were included. The literature demonstrated that there are multiple techniques available for surface treatments but bond strength testing under different investigations have produced conflicting results. Within the scope of this review, there is no evidence to support a universal technique of ceramic surface treatment for adhesive cementation. A combination of chemical and mechanical treatments might be the recommended solution. The hydrolytic stability of the resin ceramic bond should be enhanced. © 2016 Australian Dental Association.
Identification and characterization of chlorogenic acids, chlorogenic acid glycosides and flavonoids from Lonicera henryi L. (Caprifoliaceae) leaves by LC-MSn.

PubMed

Jaiswal, Rakesh; Müller, Heiko; Müller, Anja; Karar, Mohamed Gamaleldin Elsadig; Kuhnert, Nikolai

2014-12-01

The chlorogenic acids, chlorogenic acid glycosides and flavonoids of the leaves of Lonicera henryi L. (Caprifoliaceae) were investigated qualitatively by liquid chromatography tandem mass spectrometry. Thirty-one chlorogenic acids and their glycosides were detected and characterized to their regioisomeric level on the basis of their unique fragmentation pattern in the negative ion mode tandem MS spectra. All of them were extracted for the first time from this source and thirteen of them were not reported previously in nature. For the positive identification of chlorogenic acid glycosides by LC-MS(n), multiple reaction monitoring and targeted MS(n) experiments were performed. We have developed an LC-MS(n) method for the systematic identification of chlorogenic acid glycosides and were also able to discriminate between chlorogenic acids and their isobaric glycosides. It was also possible to discriminate between 5-O-(3'-O-caffeoyl glucosyl)quinic acid and 5-O-(4'-O-caffeoyl glucosyl)quinic acid by LC-MS(n). This method can be applied for the rapid and positive identification of chlorogenic acids and their glycosides in plant materials, food and beverages. Copyright © 2014 Elsevier Ltd. All rights reserved.
Flavonol glycosides in berries of two major subspecies of sea buckthorn (Hippophaë rhamnoides L.) and influence of growth sites.

PubMed

Ma, Xueying; Laaksonen, Oskar; Zheng, Jie; Yang, Wei; Trépanier, Martin; Kallio, Heikki; Yang, Baoru

2016-06-01

Flavonol glycosides of wild sea buckthorn (Hippophaë rhamnoides ssp. sinensis) berries from China and cultivated berries (H. rhamnoides ssp. mongolica) from Finland and Canada were identified and quantified. Twenty-six flavonol glycosides were found with isorhamnetin and quercetin as the major aglycones. The contents of flavonol glycosides ranged 23-250 mg/100 g fresh berries and were significantly higher in the berries of ssp. sinensis than in those of ssp. mongolica. Among the cultivars of ssp. mongolica, the berries of 'Oranzhevaya' had the lowest (23 mg/100 g) content, and those of 'Prevoshodnaya' the highest content of flavonol glycosides (80 mg/100 g). Within the ssp. mongolica, the samples from Kittilä (Northern Finland) had higher levels of most flavonol glycosides than those from Turku (Southern Finland) and Québec. Among the ssp. sinensis berries of different growth sites, increasing trends were detected in the contents of most of the compounds as the altitude increased and as the latitude decreased. The wild berries (ssp. sinensis) from Sichuan had remarkably high contents and unique profiles of flavonol glycosides. Copyright © 2016 Elsevier Ltd. All rights reserved.
Synthesis and Biological Testing of Novel Glucosylated Epigallocatechin Gallate (EGCG) Derivatives.

PubMed

Zhang, Xin; Wang, Jing; Hu, Jiang-Miao; Huang, Ye-Wei; Wu, Xiao-Yun; Zi, Cheng-Ting; Wang, Xuan-Jun; Sheng, Jun

2016-05-11

Epigallocatechin gallate (EGCG) is the most abundant component of green tea catechins and has strong physiological activities. In this study, two novel EGCG glycosides (EGCG-G1 and EGCG-G2) were chemoselectively synthesized by a chemical modification strategy. Each of these EGCG glycosides underwent structure identification, and the structures were assigned as follows: epigallocatechin gallate-4''-O-β-d-glucopyranoside (EGCG-G1, 2) and epigallocatechin gallate-4',4''-O-β-d-gluco-pyranoside (EGCG-G2, 3). The EGCG glycosides were evaluated for their anticancer activity in vitro against two human breast cell lines (MCF-7 and MDA-MB-231) using MTT assays. The inhibition rate of EGCG glycosides (EGCG-G1 and EGCG-G2) is not obvious. The EGCG glycosides are more stable than EGCG in aqueous solutions, but exhibited decreasing antioxidant activity in the DPPH radical-scavenging assay (EGCG > EGCG-G2 > EGCG-G1). Additionally, the EGCG glycosides exhibited increased water solubility: EGCG-G2 and EGCG-G1 were 15 and 31 times as soluble EGCG, respectively. The EGCG glycosides appear to be useful, and further studies regarding their biological activity are in progress.
Quasi-Monolithic Structures for Spaceflight Using Hydroxide-Catalysis Bonding

NASA Technical Reports Server (NTRS)

Preston, Alix; Thorpe, J. Ira; Miner, Linda

2012-01-01

Future space-based missions will take measurements of the universe with unprecedented results. To do this, these missions will require materials and bonding techniques with ever-increasing stability in order to make their measurements. As an example, the Laser Interferometer Space Antenna (LISA) will detect and observe gravitational waves in the 0.1 mHz to 1 Hz frequency range with strain sensitivities on the order of 10(exp -21) at its most sensitive frequency. To make these measurements, critical components such as the optical bench or telescope support structure, will need to have path-length stabilities of better than 1 pm/(square root)Hz. The baseline construction method for the LISA optical bench is to affix fused silica optical components to a Zerodur baseplate using hydroxide-catalysis bonding (HCB). HCB is a recently developed technique that allows the bonding of glasses, some metals, and silicon carbide with significant strength and stability with a bond thickness of less than a few micrometers. In addition, a wide range of surface profiles can be bonded using only a small amount of hydroxide solution. These characteristics make HCB ideal for adhering optical components in complex optical systems. In addition to being used to construct the LISA optical bench, the HCB technique shows great promise for constructing other structures such as hollow retroreflectors to be used for lunar laser ranging, or a visible nulling coronograph to be used for exo-planet detection. Here we present construction techniques that could be used to make an optical bench, hollow retroreflector, nulling coronograph, or other quasi-monolithic structures using HCB. In addition, we present dimensional stability results of an optical bench that was made using HCB, as well as HCB strength measurements.
Acylated-oxypregnane glycosides from the roots of Asclepias syriaca.

PubMed

Warashina, Tsutomu; Noro, Tadataka

2009-02-01

Twenty new pregnane glycosides were obtained from the roots of Asclepias syriaca L. (Asclepiadaceae). These glycosides were confirmed to contain ikemagenin, 12-O-nicotinoyllineolon, 5alpha,6-dihydroikemagenin, and 12-O-tigloylisolineolon, as their aglycones, using both spectroscopic and chemical methods.
The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

2017-10-01

A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.
Can HN[double bond, length as m-dash]NH, FN[double bond, length as m-dash]NH, or HN[double bond, length as m-dash]CHOH bridge the σ-hole and the lone pair at P in binary complexes with H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H?

PubMed

Del Bene, Janet E; Alkorta, Ibon; Elguero, José

2015-11-11

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the properties of complexes formed between H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H, and the possible bridging molecules HN[double bond, length as m-dash]NH, FN[double bond, length as m-dash]NH, and HN[double bond, length as m-dash]CHOH. H2XP:HNNH and H2XP:FNNH complexes are stabilized by PN pnicogen bonds, except for H2(CH3)P:FNNH and H3P:FNNH which are stabilized by N-HP hydrogen bonds. H2XP:HNCHOH complexes are stabilized by PN pnicogen bonds and nonlinear O-HP hydrogen bonds. For a fixed H2XP molecule, binding energies decrease in the order HNCHOH > HNNH > FNNH, except for the binding energies of H2(CH3)P and H3P with HNNH and FNNH. Binding energies of complexes with HNCHOH and HNNH increase as the P-N1 distance decreases, but binding energies of complexes with FNNH show little dependence on this distance. The large binding energies of H2XP:HNCHOH complexes arise from a cooperative effect involving electron-pair acceptance by P to form a pnicogen bond, and electron-pair donation by P to form a hydrogen bond. The dominant charge-transfer interaction in these complexes involves electron-pair donation by N across the pnicogen bond, except for complexes in which X is one of the more electropositive substituents, CCH, CH3, and H. For these, lone-pair donation by P across the hydrogen bond dominates. AIM and NBO data for these complexes are consistent with their bonding characteristics, showing molecular graphs with bond critical points and charge-transfer interactions associated with hydrogen and pnicogen bonds. EOM-CCSD spin-spin coupling constants (1p)J(P-N) across the pnicogen bond for each series of complexes correlate with the P-N distance. In contrast, (2h)J(O-P) values for complexes H2XP:HNCHOH do not correlate with the O-P distance, a consequence of the nonlinearity of these hydrogen bonds.
An enzyme-linked immunosorbant assay using monoclonal antibody against bacoside A₃ for determination of jujubogenin glycosides in Bacopa monnieri (L.) Wettst.

PubMed

Tothiam, Charinrat; Phrompittayarat, Watoo; Putalun, Waraporn; Tanaka, Hiroyuki; Sakamoto, Seiichi; Khan, Ikhlas A; Ingkaninan, Kornkanok

2011-01-01

In Ayurvedic medicines, Bacopa monnieri (L.) Wettst. (brahmi) is known as a medicinal plant used for memory enhancement. Its active compounds are classified as pseudojujubogenin and jujubogenin glycosides. Owing to the lack of chromophore in the saponin glycoside structures, HPLC-UV-vis gives low sensitivity for determination of such compounds. In the case of the detection of small amounts of saponin glycosides, immunological assay could be a suitable method. To develop and validate a sensitive enzyme-linked immunosorbant assay (ELISA) using monoclonal antibody (MAb) against bacoside A₃, the major jujubogenin glycoside found in brahmi. An immunogen was prepared by conjugating bacoside A₃ with a bovine serum albumin (BSA). To determine its immunogenicity, the ratio of hapten in bacoside A₃-BSA conjugate was determined by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS). After immunisation in mice, hybridomas secreting MAbs against bacoside A₃ were produced by fusing the immunised splenocytes with SP2/0- Ag14 myeloma cells. The antibody was raised specifically against jujubogenin glycosides. The ELISA using anti-bacoside A₃ MAb was developed. Bacoside A₃ in the range of 3.05-97.70 ng mL⁻¹ could be detected by ELISA using anti-bacoside A₃ MAb. The assay showed a detection limit of 0.48 ng mL⁻¹ (0.517 nm). The validation study showed that the method was precise, accurate and sensitive. Interestingly, the MAb showed cross-reactivity with the other jujubogenin glycosides, bacopaside X and IV. However, it did not show cross-reactivity with any of pseudojujubogenin glycosides. The study demonstrated that ELISA using anti-bacoside A₃ MAb can be used for determination of total jujubogenin glycosides in brahmi. Copyright © 2011 John Wiley & Sons, Ltd.
Evaluation of the potential carcinogenic activity of Senna and Cascara glycosides for the rat colon.

PubMed

Mereto, E; Ghia, M; Brambilla, G

1996-03-19

Anthraquinone glycosides of Senna and Cascara were investigated for their ability to induce aberrant crypt foci (ACF) in the rat colon mucosa, which are considered putative preneoplastic lesions. Dietary exposure to high doses of these glycosides for 56 successive days did not cause the appearance of ACF or increase in incidence of ACF induced by 1,2-dimethyl-hydrazine (DMH). However, in rats treated with both DMH and the highest dose of glycosides, the average number of aberrant crypts per focus, considered a consistent predictor of tumor outcome, was higher than in rats given DMH alone. These findings suggest that Senna and Cascara glycoside might behave as weak promoters in rat colon carcinogenesis.
New 8,12;8,20-diepoxy-8,14-secopregnane hexa- and hepta-glycosides from the roots of Asclepias tuberosa.

PubMed

Warashina, Tsutomu; Miyase, Toshio

2018-01-01

Previously, phytochemical investigation of the roots of Asclepias tuberosa (Asclepiadaceae) led to the isolation of some 8,12;8,20-diepoxy-8,14-secopregnane tri-, tetra-, and penta-glycosides. An additional eight new minor 8,12;8,20-diepoxy-8,14-secopregnane glycosides were afforded in the recent investigation of this plant. These glycosides consisted of six or seven 2,6-dideoxy-hexopyranoses together with the aglycone, tuberogenin. The structures of each of these compounds were established using NMR, mass spectroscopic analysis and chemical evidence. As 8,12;8,20-diepoxy-8,14-secopregnane-type glycosides were observed only in A. tuberosa, these compounds were considered to be characteristic phytochemicals of this plant.
[Flavonols and flavones of vegetables. VII. Flavonols of leek, chive and garlic (author's transl)].

PubMed

Starke, H; Herrmann, K

1976-01-01

Green leaves of leek and chive mainly contain kaempferol glycosides, with mono- and di-glycosides dominating in leek and di- and tri-glycosides in chive. In leek glucose is dominant as sugar component compared to xylose; in chive we found glucose and galactose. Kaempferol-3-beta-D-glucoside and kaempferol-3-xylosyl-beta-D-glucoside were isolated from leek and the 3-beta-D-glucosides of kaempferol, quercetin and isorhamnetin as by-glycosides from chive. In leek traces of quercetin-3-glucoside were identified by tlc, but no spiraeoside (quercetin-4'-glucoside) could be detected in the two species. The bulbs of garlic and leek contain only few milligram of glycosides of kaempferol and quercetin per kg fresh weight.
Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.
78 FR 36029 - CDFI Bond Guarantee Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-14

... the extent a Secondary Loan is financed on a corporate finance basis (i.e., through a Credit... Issue. Bonds will be used to finance Bond Loans to Eligible CDFIs for Eligible Purposes for a period not... financial strength, stability, durability and liquidity as reflected in its corporate credit ratings and...

Influence of Hydrogen Bonding on the Kinetic Stability of Vapor Deposited Glasses of Triazine Derivatives

DOE Data Explorer

Laventure, Audrey [Departement de chimie, Universite de Montreal, C.P. 6128, Succ. Centre-Ville, Montreal, Quebec H3C 3J7, Canada] (ORCID:0000000208670231); Gujral, Ankit [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States] (ORCID:0000000250652694); Lebel, Olivier [Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, Ontario K7K 7B4] (ORCID:0000000217376843); Ediger, Mark [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States] (ORCID:0000000347158473); Pellerin, Christian [Departement de chimie, Universite de Montreal, C.P. 6128, Succ. Centre-Ville, Montreal, Quebec H3C 3J7, Canada] (ORCID:0000000161441318)

2017-02-01

It has recently been established that physical vapor deposition (PVD) can produce organic glasses with enhanced kinetic stability, high density, and anisotropic packing, with the substrate temperature during deposition (Tsubstrate) as the key control parameter. The influence of hydrogen bonding on the formation of PVD glasses has not been fully explored. Herein, we use a high-throughput preparation method to vapor-deposit three triazine derivatives over a wide range of Tsubstrate, from 0.69 to 1.08Tg, where Tg is the glass transition temperature. These model systems are structural analogues containing a functional group with different H-bonding capability at the 2-position of a triazine ring: (1) 2-methylamino-4,6-bis(3,5-dimethyl-phenylamino)-1,3,5-triazine (NHMe) (H-bond donor), (2) 2-methoxy-4,6-bis(3,5-dimethyl-phenylamino)-1,3,5-triazine (OMe) (H-bond acceptor), and (3) 2-ethyl-4,6-bis(3,5-dimethyl-phenylamino)-1,3,5-triazine (Et) (none). Using spectroscopic ellipsometry, we find that the Et and OMe compounds form PVD glasses with relatively high kinetic stability, with the transformation time (scaled by the α-relaxation time) on the order of 103, comparable to other highly stable glasses formed by PVD. In contrast, PVD glasses of NHMe are only slightly more stable than the corresponding liquid-cooled glass. Using IR spectroscopy, we find that both the supercooled liquid and the PVD glasses of the NHMe derivative show a higher average number of bonded NH per molecule than that in the other two compounds. These results suggest that H-bonds hinder the formation of stable glasses, perhaps by limiting the surface mobility. Interestingly, despite this difference in kinetic stability, all three compounds show properties typically observed in highly stable glasses prepared by PVD, including a higher density and anisotropic molecular packing (as characterized by IR and wide-angle X-ray scattering).
Nickel-catalyzed proton-deuterium exchange (HDX) procedures for glycosidic linkage analysis of complex carbohydrates

USDA-ARS?s Scientific Manuscript database

The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of non-carbohydrate substituents. The glycosidic linkage positions are often de...
Plant-derived cardiac glycosides: Role in heart ailments and cancer management.

PubMed

Patel, Seema

2016-12-01

Cardiac glycosides, the cardiotonic steroids such as digitalis have been in use as heart ailment remedy since ages. They manipulate the renin-angiotensin axis to improve cardiac output. However; their safety and efficacy have come under scrutiny in recent times, as poisoning and accidental mortalities have been observed. In order to better understand and exploit them as cardiac ionotropes, studies are being pursued using different cardiac glycosides such as digitoxin, digoxin, ouabain, oleandrin etc. Several cardiac glycosides as peruvoside have shown promise in cancer control, especially ovary cancer and leukemia. Functional variability of these glycosides has revealed that not all cardiac glycosides are alike. Apart from their specific affinity to sodium-potassium ATPase, their therapeutic dosage and behavior in poly-morbidity conditions needs to be considered. This review presents a concise account of the key findings in recent years with adequate elaboration of the mechanisms. This compilation is expected to contribute towards management of cardiac, cancer, even viral ailments. Copyright © 2016 Elsevier Masson SAS. All rights reserved.
Use of qNMR for speciation of flaxseeds (Linum usitatissimum) and quantification of cyanogenic glycosides.

PubMed

Roulard, Romain; Fontaine, Jean-Xavier; Jamali, Arash; Cailleu, Dominique; Tavernier, Reynald; Guillot, Xavier; Rhazi, Larbi; Petit, Emmanuel; Molinie, Roland; Mesnard, François

2017-12-01

This report describes a routine method taking less than 20 min to quantify cyanogenic glycosides such as linustatin and neolinustatin from flaxseeds (Linum usitatissimum L.) using 1 H nuclear magnetic resonance. After manual dehulling, a higher linustatin content was shown in the almond fraction, while neolinustatin and total cyanogenic glycoside contents were significantly higher in hulls. Linustatin and neolinustatin were quantified in seven cultivars grown in two locations in three different years. Linustatin, neolinustatin, and total cyanogenic glycosides ranged between 91 and 267 mg/100 g, 78-272 mg/100 g, and 198-513 mg/100 g dry weight flaxseeds, respectively. NMR revealed differences of up to 70% between samples with standard deviation variations lower than 6%. This study shows that NMR is a very suitable tool to perform flaxseed varietal selection for the cyanogenic glycoside content. Graphical abstract qNMR can be used to perform flaxseed varietal selection for the cyanogenic glycoside content.
Quantification of flavonol glycosides in Camellia sinensis by MRM mode of UPLC-QQQ-MS/MS.

PubMed

Wu, Yahui; Jiang, Xiaolan; Zhang, Shuxiang; Dai, Xinlong; Liu, Yajun; Tan, Huarong; Gao, Liping; Xia, Tao

2016-04-01

Phenolic compounds are major components of tea flavour, in which catechins and flavonol glycosides play important roles in the astringent taste of tea infusion. However, the flavonol glycosides are difficult to quantify because of the large variety, as well as the inefficient seperation on chromatography. In this paper, a total of 15 flavonol glycosides in the tea plant (Camellia sinensis) were identified by the high performance liquid chromatography (HPLC) coupled to a time-of-flight mass spectrometer (TOF-MS), and a quantitative method was established based on multiple reaction monitoring (MRM) mode of ultra-high performance liquid chromatography (UPLC) coupled to a triple quadrupole mass spectrometer (QQQ-MS/MS). It provided the limit of detection and quantification to the order of picogram, which was more sensitive than the HPLC detection of the order of nanogram. The relative standard deviations of the intra- and inter-day variations in retention time and signal intensity (peak area) of six analytes were less than 0.26% and 4%, respectively. The flavonol glycosides of four tea cultivars were relatively quantified using the signal intensity (peak area) of product ion, in which six flavonol glycosides were quantified by the authentic standards. The results showed that the flavonol mono-, di- and tri-glycoside mostly accumulated in young leaves of the four tea cultivars. Notably, the myricetin 3-O-galactoside was the major component among the six flavonol glycosides detected. Copyright © 2016 Elsevier B.V. All rights reserved.
Quantification of appetite suppressing steroid glycosides from Hoodia gordonii in dried plant material, purified extracts and food products using HPLC-UV and HPLC-MS methods.

PubMed

Janssen, Hans-Gerd; Swindells, Chris; Gunning, Philip; Wang, Weijun; Grün, Christian; Mahabir, Krishna; Maharaj, Vinesh J; Apps, Peter J

2008-06-09

High-performance liquid chromatography (HPLC)-UV and HPLC-Mass Spectrometry (MS) methods were developed for the quantitative analysis of the family of Hoodia gordonii steroid glycosides with appetite suppressing properties in dried plant material, in purified and enriched extracts and in various prototype food-products fortified with H. gordonii extracts. For solid materials, e.g. dried plants or for non-fatty foods, extraction of the steroid glycosides is performed using methanol. For products where the steroid glycosides are present in an oil matrix, direct injection of the oil after dilution in tetrahydrofuran is applied. The HPLC separation is performed on an octyl-modified reversed-phase column in the gradient mode with UV detection at lambda = 220 nm. Quantification is performed against an external calibration line prepared using either one of the pure steroid glycosides or geranyl-tiglate. Short- and long-term repeatabilities of the methods are better than 3 and 6%, respectively. Recoveries are better than 85%, even in the analysis of the least abundant steroid glycosides in a complex yoghurt drink. Linearity is better than 3-4 orders of magnitude and the detection limits are below approximately 2 microg g(-1) for the individual steroid glycosides in dried plant material and food products. HPLC-MS is used to confirm that the steroid glycosides contain the characteristic steroid core, the carbohydrate chain and the tigloyl group.
Stability Limits and Dynamics of Nonaxisymmetric Liquid Bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.

1998-01-01

Theoretical and experimental investigation of the stability of nonaxisymmetric and nonaxisymmetric bridges contained between equal and unequal radii disks as a function of Bond and Weber number with emphasis on the transition from unstable axisymmetric to stable nonaxisymmetric shapes. Numerical analysis of the stability of nonaxisymmetric bridges for various orientations of the gravity vector for equal and unequal disks. Experimental and theoretical investigation of large (nonaxisymmetric) oscillations and breaking of liquid bridges. This project involves both experimental and theoretical work. Static and dynamic experiments are conducted in a Plateau tank which makes a range of static Bond numbers accessible.
Phytosteryl glycosides reduce cholesterol absorption: mechanisms in mice

USDA-ARS?s Scientific Manuscript database

Phytosteryl glycosides occur in natural foods but little is known about their metabolism and bioactivity. Purified acylated steryl glycosides (ASG) were compared with phytosteryl esters (PSE) in mice. Animals on a phytosterol-free diet received ASG or PSE by gavage in purified soybean oil along with...
[Effect of three aging challenges on the bonding stability of resin-dentin interface using an etch-and-rinse adhesive].

PubMed

Xu, Shuai; Zhang, Ling; Li, Fang; Zhou, Wei; Chen, Yujiang; Chen, Jihua

2014-06-01

To systematically investigate the aging effect of thermocycling, water storage and bacteria aggression on the stability of resin-dentin bonds. Forty molars were sectioned perpendicularly to the axis of the teeth to expose the middle-coronal dentin surfaces. The dentin surfaces were then treated with Single Bond 2 and made a core build-up. According to random digits table, the bonding specimens were divided into four groups (n = 10) as follows: immediate control group, aging group with thermocycling for 5 000 times, aging group with artificial saliva storage for 6 months and aging group with bacteria aggression for 14 days. The specimens in each group were then subjected to microtensile bond strengths (µTBS) testing and nanoleakage evaluation respectively. After aging treatments, the three aging groups showed significantly lower µTBS than the immediate control group [(44.24 ± 12.75) MPa, P < 0.05]. The immediate control group also showed the lowest value of nanoleakage. The µTBS of aging group with bacteria aggression [(25.53 ± 7.39) MPa] was significantly lower than those of the other aging groups with artificial saliva storage[(29.72 ± 6.51) MPa] and thermocycling [(31.92 ± 11.87) MPa, P < 0.05]. There were no differences in the nanoleakage values among the three aging groups (P > 0.05). All the aging treatments with artificial saliva storage, thermocycling and bacteria aggression could accelerate the degradation of bonding interfaces between an etch-and-rinse adhesive and dentin. Bacteria aggression showed the most impairing effect on the stability of resin-dentin bonds.
Energetics of short hydrogen bonds in photoactive yellow protein.

PubMed

Saito, Keisuke; Ishikita, Hiroshi

2012-01-03

Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK(a) values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK(a) difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK(a) of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
Evaluation of Disulfide Bond Position to Enhance the Thermal Stability of a Highly Stable Single Domain Antibody

PubMed Central

Zabetakis, Dan; Olson, Mark A.; Anderson, George P.; Legler, Patricia M.; Goldman, Ellen R.

2014-01-01

Single domain antibodies are the small recombinant variable domains derived from camelid heavy-chain-only antibodies. They are renowned for their stability, in large part due to their ability to refold following thermal or chemical denaturation. In addition to refolding after heat denaturation, A3, a high affinity anti-Staphylococcal Enterotoxin B single domain antibody, possesses a melting temperature of ∼84°C, among the highest reported for a single domain antibody. In this work we utilized the recently described crystal structure of A3 to select locations for the insertion of a second disulfide bond and evaluated the impact that the addition of this second bond had on the melting temperature. Four double-disulfide versions of A3 were constructed and each was found to improve the melting temperature relative to the native structure without reducing affinity. Placement of the disulfide bond at a previously published position between framework regions 2 and 3 yielded the largest improvement (>6°C), suggesting this location is optimal, and seemingly provides a universal route to raise the melting temperature of single domain antibodies. This study further demonstrates that even single domain antibodies with extremely high melting points can be further stabilized by addition of disulfide bonds. PMID:25526640
Independent of Their Localization in Protein the Hydrophobic Amino Acid Residues Have No Effect on the Molten Globule State of Apomyoglobin and the Disulfide Bond on the Surface of Apomyoglobin Stabilizes This Intermediate State

PubMed Central

Melnik, Tatiana N.; Majorina, Maria A.; Larina, Daria S.; Kashparov, Ivan A.; Samatova, Ekaterina N.; Glukhov, Anatoly S.; Melnik, Bogdan S.

2014-01-01

At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin. PMID:24892675
Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state.

PubMed

Melnik, Tatiana N; Majorina, Maria A; Larina, Daria S; Kashparov, Ivan A; Samatova, Ekaterina N; Glukhov, Anatoly S; Melnik, Bogdan S

2014-01-01

At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to "strengthen" the protein) can result in destabilization of the protein native state of apomyoglobin.
New cardenolide and acylated lignan glycosides from the aerial parts of Asclepias curassavica.

PubMed

Warashina, Tsutomu; Shikata, Kimiko; Miyase, Toshio; Fujii, Satoshi; Noro, Tadataka

2008-08-01

Three new cardenolide glycosides and six new acylated lignan glycosides were obtained along with nineteen known compounds from the aerial parts of Asclepias curassavica L. (Asclepiadaceae). The structure of each compound was determined based on interpretations of NMR and MS measurements and chemical evidence.
Rapid analysis of the main components of the total glycosides of Ranunculus japonicus by UPLC/Q-TOF-MS.

PubMed

Rui, Wen; Chen, Hongyuan; Tan, Yuzhi; Zhong, Yanmei; Feng, Yifan

2010-05-01

A rapid method for the analysis of the main components of the total glycosides of Ranunculus japonicus (TGOR) was developed using ultra-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOF-MS). The separation analysis was performed on a Waters Acquity UPLC system and the accurate mass of molecules and their fragment ions were determined by Q-TOF MS. Twenty compounds, including lactone glycosides, flavonoid glycosides and flavonoid aglycones, were identified and tentatively deduced on the basis of their elemental compositions, MS/MS data and relevant literature. The results demonstrated that lactone glycosides and flavonoids were the main constituents of TGOR. Furthermore, an effective and rapid pattern was established allowing for the comprehensive and systematic characterization of the complex samples.
Cycloartenol triterpenoid saponins from Cimicifuga simplex (Ranunculaceae) and their biological effects.

PubMed

Wu, Lun; Chen, Zhi-Li; Su, Yang; Wang, Qiu-Hong; Kuang, Hai-Xue

2015-02-01

The constituents of Cimicifuga plants have been extensively investigated, and the principal metabolites are 9,19-cyclolanostane triterpenoid glycosides, which are distributed widely in Cimicifuga plants, but not in other members of the Ranunculaceae family, and are considered to be characteristics of the Cimicifuga genus. This type of triterpenoid glycoside possesses several important biological activities. More than 120 cycloartane triterpene glycosides have been isolated from Cimicifuga simplex Wormsk. The aim of this review article is to summarize all the major findings based on the available scientific literatures on C. simplex, with a focus on the identified 9,19-cyclolanostane triterpenoid glycosides. Biological studies of cycloartane triterpene glycosides from Cimicifuga spp. are also discussed. Copyright © 2015 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.
Hemi bonds and noncovalent interactions in the cational systems (XH2P: SHY)+

NASA Astrophysics Data System (ADS)

Li, Xiang; Li, An Yong

2016-08-01

Quantum chemistry ab initio MP2 and CCSD calculations were performed to investigate the P⋯S hemi bonds and noncovalent interactions in the radical cational systems (H3P:SH2)+, (FH2P:SH2)+ and (H3P:SHF)+. The hydride dimer (H3P:SH2)+ has a P⋯S hemi bonding structure and a H-bonding structure, (FH2P:SH2)+ has two hemi bonding structures and a proton-transferred H-bonding structure, (H3P:SHF)+ has two hemi bonding structures and three noncovalent structures. It is remarkable that these hemi bonds also have characters of pnicogen and chalcogen bonds. The binding energy, stability and bonding nature of the hemi bonds were presented.
A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.
Investigation of non-covalent and hydrogen bonding interactions on the formation of crystalline networks and supramolecular synthons of a series of α-aminophosphonates: Crystallography and DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Masoud; Eshghi, Hossein; Akhlaghi Bagherjeri, Fateme; Mirzaei, Mahdi; Farhadipour, Abolghasem

2018-07-01

α-Aminophosphonates have been rarely explored in the field of crystal engineering. These organic molecules are capable of forming reliable and reproducible supramolecular synthons through non-covalent interactions that can be employed for designing high dimensional supramolecular architectures. Here, we systematically study the influence of conventional and unconventional hydrogen bonding interactions on the formation of these synthons and stability of the crystal packing. The theoretical studies were employed to further confirm the presence of these synthons by comparing the stabilization energies of the dimers and monomers. The dependence of the stability of NH⋯O hydrogen bonds to the aromatic substituents were investigated using NBO analysis. The most stable compound was determined by comparing the HOMO-LUMO energy gap of all compounds and compared with NBO analysis.
GDAP: a web tool for genome-wide protein disulfide bond prediction.

PubMed

O'Connor, Brian D; Yeates, Todd O

2004-07-01

The Genomic Disulfide Analysis Program (GDAP) provides web access to computationally predicted protein disulfide bonds for over one hundred microbial genomes, including both bacterial and achaeal species. In the GDAP process, sequences of unknown structure are mapped, when possible, to known homologous Protein Data Bank (PDB) structures, after which specific distance criteria are applied to predict disulfide bonds. GDAP also accepts user-supplied protein sequences and subsequently queries the PDB sequence database for the best matches, scans for possible disulfide bonds and returns the results to the client. These predictions are useful for a variety of applications and have previously been used to show a dramatic preference in certain thermophilic archaea and bacteria for disulfide bonds within intracellular proteins. Given the central role these stabilizing, covalent bonds play in such organisms, the predictions available from GDAP provide a rich data source for designing site-directed mutants with more stable thermal profiles. The GDAP web application is a gateway to this information and can be used to understand the role disulfide bonds play in protein stability both in these unusual organisms and in sequences of interest to the individual researcher. The prediction server can be accessed at http://www.doe-mbi.ucla.edu/Services/GDAP.

Pauling's electronegativity equation and a new corollary accurately predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.

PubMed

Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A

2003-04-18

Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite accurately homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not reproduce experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously observed empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant.
The lignan glycosides lyoniside and saracoside poison the unusual type IB topoisomerase of Leishmania donovani and kill the parasite both in vitro and in vivo.

PubMed

Saha, Sourav; Mukherjee, Tulika; Chowdhury, Sayan; Mishra, Amartya; Chowdhury, Somenath Roy; Jaisankar, Parasuraman; Mukhopadhyay, Sibabrata; Majumder, Hemanta K

2013-12-15

Lignans are diphenyl propanoids with vast range of biological activities. The present study provides an important insight into the anti-leishmanial activities of two lignan glycosides, viz. lyoniside and saracoside. These compounds inhibit catalytic activities of topoisomerase IB (LdTopIB) of Leishmania donovani in non-competitive manner and stabilize the LdTopIB mediated cleavage complex formation both in vitro and in Leishmania promastigotes and subsequently inhibit the religation of cleaved strand. These two compounds not only poison LdTopIB but also can interact with the free enzyme LdTopIB. We have also shown that lyoniside and saracoside are cytotoxic to promastigotes and intracellular amastigotes. The protein-DNA complex formation leads to double strand breaks in DNA which ultimately triggers apoptosis-like cell death in the parasite. Along with their cytotoxicity towards sodium antimony gluconate (SAG) sensitive AG83 strain, their ability to kill SAG resistant GE1 strain makes these two compounds potential anti-leishmanial candidates. Not only they effectively kill L. donovani amastigotes inside macrophages in vitro, lyoniside and saracoside demonstrated strong anti-leishmanial efficacies in BALB/c mice model of leishmaniasis. Treatment with these lignan glycosides produce nitric oxide and reactive oxygen species which result in almost complete clearance of the liver and splenic parasite burden. These compounds do not inhibit human topoisomerase IB upto 200μM concentrations and had poor cytotoxic effect on uninfected cultured murine peritoneal macrophages upto 100μM concentrations. Taken together it can be concluded that these compounds can be developed into excellent therapeutic agent against deadly disease leishmaniasis. Copyright © 2013 Elsevier Inc. All rights reserved.
α-Dihydroxychalcone-glycoside (α-DHC) isolated from the heartwood of Pterocarpus marsupium inhibits LPS induced MAPK activation and up regulates HO-1 expression in murine RAW 264.7 macrophage.

PubMed

Chakraborty, Prarthana; Saraswat, Ghungroo; Kabir, Syed N

2014-05-15

Three phenolic glycosides isolated from the heartwood of Pterocarpus marsupium showed significant free radical and superoxide ion scavenging activity and antioxidant potential that were comparable to, or several folds higher than those of standard antioxidants, trolox and ascorbic acid. The effective concentrations of these compounds were far below their cytotoxic levels. Compound 3, which was characterized to be α-dihydroxychalcone-glycoside (α-DHC), was the most potent one. Subsequent studies demonstrated that α-DHC effectively reduced nitric oxide and cytokine production by the LPS stimulated RAW 264.7 mouse macrophage cell line. The compound effectively attenuated the expression of inflammation-mediating enzymes COX-2 and iNOS at the mRNA as well as protein levels in a concentration dependent manner. It prevented phosphorylation of all the three MAPKs (JNK, ERK, p38) and eventually blocked the activation of downstream elements contributing to inflammation. Phosphorylation of IκB-α and subsequent translocation of NF-κB into the nucleus were restricted, while the expression of stress responsive gene HO-1 was up-regulated. α-DHC targeted Keap-1 by modifying its cysteine thiols, dissociating it from Nrf-2 and facilitating nuclear entry of the latter; and this in turn induced HO-1 expression. Thus α-DHC exerts its anti-inflammatory activity in a dual manner: by down regulating MAPKs and restricting nuclear stabilization of NF-κB at one end, and by disrupting Nrf-2-Keap-1 complex on the other. In conclusion, the anti-inflammatory potential together with its high therapeutic index envisages α-DHC as a prospective candidate molecule for the development of therapeutic strategy against inflammatory disorders. Copyright © 2014 Elsevier Inc. All rights reserved.
Adhesives for Achieving Durable Bonds with Acetylated Wood

Treesearch

Charles Frihart; Rishawn Brandon; James Beecher; Rebecca Ibach

2017-01-01

Acetylation of wood imparts moisture durability, decay resistance, and dimensional stability to wood; however, making durable adhesive bonds with acetylated wood can be more difficult than with unmodified wood. The usual explanation is that the acetylated surface has fewer hydroxyl groups, resulting in a harder-to-wet surface and in fewer hydrogen bonds between wood...
A Simple Visualization of Double Bond Properties: Chemical Reactivity and UV Fluorescence

ERIC Educational Resources Information Center

Grayson, Scott M.

2012-01-01

A simple, easily visualized thin-layer chromatography (TLC) staining experiment is presented that highlights the difference in reactivity between aromatic double bonds and nonaromatic double bonds. Although the stability of aromatic systems is a major theme in organic chemistry, the concept is rarely reinforced "visually" in the undergraduate…
Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome.

PubMed

El Kaoutari, Abdessamad; Armougom, Fabrice; Leroy, Quentin; Vialettes, Bernard; Million, Matthieu; Raoult, Didier; Henrissat, Bernard

2013-01-01

Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.
Purification, crystallization and preliminary X-ray analysis of uracil-DNA glycosylase from Sulfolobus tokodaii strain 7

PubMed Central

Kawai, Akito; Higuchi, Shigesada; Tsunoda, Masaru; Nakamura, Kazuo T.; Miyamoto, Shuichi

2012-01-01

Uracil-DNA glycosylase (UDG) specifically removes uracil from DNA by catalyzing hydrolysis of the N-glycosidic bond, thereby initiating the base-excision repair pathway. Although a number of UDG structures have been determined, the structure of archaeal UDG remains unknown. In this study, a deletion mutant of UDG isolated from Sulfolobus tokodaii strain 7 (stoUDGΔ) and stoUDGΔ complexed with uracil were crystallized and analyzed by X-ray crystallography. The crystals were found to belong to the orthorhombic space group P212121, with unit-cell parameters a = 52.2, b = 52.3, c = 74.7 Å and a = 52.1, b = 52.2, c = 74.1 Å for apo stoUDGΔ and stoUDGΔ complexed with uracil, respectively. PMID:22949205
A promptly approach from monosaccharides of biomass to oligosaccharides via sharp-quenching thermo conversion (SQTC).

PubMed

Liu, Xiao; Wei, Weiqi; Wu, Shubin; Lei, Ming; Liu, Ying

2018-06-01

In this study, a novel and facile approach of conversion monosaccharides (glucose and xylose) to oligosaccharides (Cello-oligosaccharides and Xylo-oligosaccharides) was demonstrated. The approach did not introduce any chemical reagent and the preparation process could be environmentally friendly. Identification and quantification by ion chromatography (IC) and high performance liquid chromatography (HPLC) showed that the yields of COS and XOS reached to 44.62% (38 s) and 47.09% (30 s) respectively at 500 °C reaction temperature coupled with sharp-quenching method. Structural characterization indicated that such oligosaccharides showed a degree of polymerization (DP) with 2-6, and the units mainly linked by β-(1 → 4)-glycosidic bond. Copyright © 2018 Elsevier Ltd. All rights reserved.
Chemical Characterization of Potentially Prebiotic Oligosaccharides in Brewed Coffee and Spent Coffee Grounds.

PubMed

Tian, Tian; Freeman, Samara; Corey, Mark; German, J Bruce; Barile, Daniela

2017-04-05

Oligosaccharides are indigestible carbohydrates widely present in mammalian milk and in some plants. Milk oligosaccharides are associated with positive health outcomes; however, oligosaccharides in coffee have not been extensively studied. We investigated the oligosaccharides and their monomeric composition in dark roasted coffee beans, brewed coffee, and spent coffee grounds. Oligosaccharides with a degree of polymerization ranging from 3 to 15, and their constituent monosaccharides, were characterized and quantified. The oligosaccharides identified were mainly hexoses (potentially galacto-oligosaccharides and manno-oligosaccharides) containing a heterogeneous mixture of glucose, arabinose, xylose, and rhamnose. The diversity of oligosaccharides composition found in these coffee samples suggests that they could have selective prebiotic activity toward specific bacterial strains able to deconstruct the glycosidic bonds and utilize them as a carbon source.
Polysaccharide‐Based Controlled Release Systems for Therapeutics Delivery and Tissue Engineering: From Bench to Bedside

PubMed Central

Miao, Tianxin; Wang, Junqing; Zeng, Yun; Chen, Xiaoyuan

2018-01-01

Abstract Polysaccharides or polymeric carbohydrate molecules are long chains of monosaccharides that are linked by glycosidic bonds. The naturally based structural materials are widely applied in biomedical applications. This article covers four different types of polysaccharides (i.e., alginate, chitosan, hyaluronic acid, and dextran) and emphasizes their chemical modification, preparation approaches, preclinical studies, and clinical translations. Different cargo fabrication techniques are also presented in the third section. Recent progresses in preclinical applications are then discussed, including tissue engineering and treatment of diseases in both therapeutic and monitoring aspects. Finally, clinical translational studies with ongoing clinical trials are summarized and reviewed. The promise of new development in nanotechnology and polysaccharide chemistry helps clinical translation of polysaccharide‐based drug delivery systems. PMID:29721408
A minimalist approach to stereoselective glycosylation with unprotected donors.

PubMed

Le Mai Hoang, Kim; He, Jing-Xi; Báti, Gábor; Chan-Park, Mary B; Liu, Xue-Wei

2017-10-27

Mechanistic study of carbohydrate interactions in biological systems calls for the chemical synthesis of these complex structures. Owing to the specific stereo-configuration at each anomeric linkage and diversity in branching, significant breakthroughs in recent years have focused on either stereoselective glycosylation methods or facile assembly of glycan chains. Here, we introduce the unification approach that offers both stereoselective glycosidic bond formation and removal of protection/deprotection steps required for further elongation. Using dialkylboryl triflate as an in situ masking reagent, a wide array of glycosyl donors carrying one to three unprotected hydroxyl groups reacts with various glycosyl acceptors to furnish the desired products with good control over regioselectivity and stereoselectivity. This approach demonstrates the feasibility of straightforward access to important structural scaffolds for complex glycoconjugate synthesis.
Synthesis of the tetrasaccharide outer core fragment of Burkholderia multivorans lipooligosaccharide.

PubMed

Ziaco, Marcello; De Castro, Cristina; Silipo, Alba; Corsaro, Maria Michela; Molinaro, Antonio; Iadonisi, Alfonso; Lanzetta, Rosa; Parrilli, Michelangelo; Bedini, Emiliano

2015-02-11

The first synthesis of the outer core fragment of Burkholderia multivorans lipooligosaccharide [β-D-Glc-(1→3)-α-D-GalNAc-(1→3)-β-D-GalNAc-(1→3)-L-Rha] as α-allyl tetrasaccharide was accomplished. The glycosylations involving GalNAc units were studied in depth testing them under several conditions. This allowed the building of both the α- and the β-configured glycosidic bonds by employing the same GalNAc glycosyl donor, thus considerably shortening the total number of synthetic steps. The target tetrasaccharide was synthesized with an allyl aglycone to allow its future conjugation with an immunogenic protein en route to the development of a synthetic neoglycoconjugate vaccine against the Burkholderia cepacia pathogens. Copyright © 2014 Elsevier Ltd. All rights reserved.
Assessment of increased wet wood bonding for epoxy-bonded samples using a melamine-urea-formaldehyde priming agent

Treesearch

Jermal G. Chandler; Charles R. Frihart

2005-01-01

Is the hydroxymethylated resorcinol (HMR) primer unique or can a melamine- based primer also increase the wet wood strength of epoxy bonds? Although the exact reason for poor durability with some wood adhesives is not known, the HMR priming agent was found to facilitate durable bonds in most cases tested. A model of cell wall stabilization that is believed to be the...
The relationship between bond ionicity, lattice energy, coefficient of thermal expansion and microwave dielectric properties of Nd(Nb(1-x)Sb(x))O4 ceramics.

PubMed

Zhang, Ping; Zhao, Yonggui; Wang, Xiuyu

2015-06-28

The crystalline structure refinement, chemical bond ionicity, lattice energy and coefficient of thermal expansion were carried out for Nd(Nb(1-x)Sb(x))O4 ceramics with a monoclinic fergusonite structure to investigate the correlations between the crystalline structure, phase stability, bond ionicity, lattice energy, coefficient of thermal expansion, and microwave dielectric properties. The bond ionicity, lattice energy, and coefficient of thermal expansion of Nd(Nb(1-x)Sb(x))O4 ceramics were calculated using a semiempirical method based on the complex bond theory. The phase structure stability varied with the lattice energy which was resulted by the substitution constant of Sb(5+). With the increasing of the Sb(5+) contents, the decrease of Nb/Sb-O bond ionicity was observed, which could be contributed to the electric polarization. The ε(r) had a close relationship with the Nb/Sb-O bond ionicity. The increase of the Q×f and |τ(f)| values could be attributed to the lattice energy and the coefficient of thermal expansion. The microwave dielectric properties of Nd(Nb(1-x)Sb(x))O4 ceramics with the monoclinic fergusonite structure were strongly dependent on the chemical bond ionicity, lattice energy and coefficient of thermal expansion.
Two‐Dimensional Fluorinated Graphene: Synthesis, Structures, Properties and Applications

PubMed Central

Long, Peng; Feng, Yiyu; Li, Yu

2016-01-01

Fluorinated graphene, an up‐rising member of the graphene family, combines a two‐dimensional layer‐structure, a wide bandgap, and high stability and attracts significant attention because of its unique nanostructure and carbon–fluorine bonds. Here, we give an extensive review of recent progress on synthetic methods and C–F bonding; additionally, we present the optical, electrical and electronic properties of fluorinated graphene and its electrochemical/biological applications. Fluorinated graphene exhibits various types of C–F bonds (covalent, semi‐ionic, and ionic bonds), tunable F/C ratios, and different configurations controlled by synthetic methods including direct fluorination and exfoliation methods. The relationship between the types/amounts of C–F bonds and specific properties, such as opened bandgap, high thermal and chemical stability, dispersibility, semiconducting/insulating nature, magnetic, self‐lubricating and mechanical properties and thermal conductivity, is discussed comprehensively. By optimizing the C–F bonding character and F/C ratios, fluorinated graphene can be utilized for energy conversion and storage devices, bioapplications, electrochemical sensors and amphiphobicity. Based on current progress, we propose potential problems of fluorinated graphene as well as the future challenge on the synthetic methods and C‐F bonding character. This review will provide guidance for controlling C–F bonds, developing fluorine‐related effects and promoting the application of fluorinated graphene. PMID:27981018
Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

PubMed

Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

2018-07-05

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Density functional theory meta-GGA + U study of water incorporation in the metal-organic framework material Cu-BTC.

PubMed

Cockayne, Eric; Nelson, Eric B

2015-07-14

Water absorption in the metal-organic framework (MOF) material Cu-BTC, up to a concentration of 3.5 H2O per Cu ion, is studied via density functional theory at the meta-GGA + U level. The stable arrangements of water molecules show chains of hydrogen-bonded water molecules and a tendency to form closed cages at high concentration. Water clusters are stabilized primarily by a combination of water-water hydrogen bonding and Cu-water oxygen interactions. Stability is further enhanced by van der Waals interactions, electric field enhancement of water-water bonding, and hydrogen bonding of water to framework oxygens. We hypothesize that the tendency to form such stable clusters explains the particularly strong affinity of water to Cu-BTC and related MOFs with exposed metal sites.
Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

PubMed

Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment. Copyright © 2012 Elsevier B.V. All rights reserved.
Ultrastable assembly and integration technology for ground- and space-based optical systems.

PubMed

Ressel, Simon; Gohlke, Martin; Rauen, Dominik; Schuldt, Thilo; Kronast, Wolfgang; Mescheder, Ulrich; Johann, Ulrich; Weise, Dennis; Braxmaier, Claus

2010-08-01

Optical metrology systems crucially rely on the dimensional stability of the optical path between their individual optical components. We present in this paper a novel adhesive bonding technology for setup of quasi-monolithic systems and compare selected characteristics to the well-established state-of-the-art technique of hydroxide-catalysis bonding. It is demonstrated that within the measurement resolution of our ultraprecise custom heterodyne interferometer, both techniques achieve an equivalent passive path length and tilt stability for time scales between 0.1 mHz and 1 Hz. Furthermore, the robustness of the adhesive bonds against mechanical and thermal inputs has been tested, making this new bonding technique in particular a potential option for interferometric applications in future space missions. The integration process itself is eased by long time scales for alignment, as well as short curing times.
Stability of the bond between two resin cements and an yttria-stabilized zirconia ceramic after six months of aging in water.

PubMed

da Silva, Eduardo M; Miragaya, Luciana; Sabrosa, Carlos Eduardo; Maia, Lucianne C

2014-09-01

The behavior of the luting cement and the cementation protocol are essential in the clinical success of ceramic restorations. The purpose of this study was to evaluate the bond stability of 2 resin cements and a yttria-stabilized tetragonal polycrystalline zirconia (Y-TZP) ceramic submitted to 2 surface treatments. Sixty plates of a Y-TZP ceramic were assigned to 3 groups according to the surface treatments: control, as sintered surface; methacryloxydecyl dihydrogen phosphate (MDP), coated with an MDP-based primer, and tribochemical silica-coating (TSC), coated with tribochemical silica. The plates of each group were further divided into 2 subgroups according to the resin cement as follows: RelyX adhesive resin cement (conventional) and RelyX Unicem (self-adhesive). Cylinders of resin cements (∅=0.75 mm × 0.5 mm in height) were built up on the ceramic surfaces, and the plates stored in distilled water at 37°C for either 24 hours or 6 months before being submitted to a microshear bond strength test. The data were submitted to 3-way ANOVA and the Tukey honestly significant difference test (α=.05). Three-way ANOVA showed statistical significance for the 3 independent factors: resin cement, surface treatment, and period of water immersion (P<.001). Unicem presented the highest microshear bond strength after 24 hours (MDP, 37.4 ±2.3 and TSC, 36.2 ±2.1 MPa). Except for RelyX adhesive resin cement applied on ceramic surfaces treated with TSC, the microshear bond strength of all the other groups decreased after 6 months of aging in water. The microshear bond strength decreased most in the control groups (-81.5% for ARC and -93.1% for Unicem). In the group treated with TSC, the microshear bond strength for Unicem decreased by 54.8% and in that treated with MDP-based primer by -42.5%. In the group treated with MDP-based primer, the microshear bond strength for RelyX ARC decreased by -52.8%. Irrespective of surface treatments, self-adhesive resin cement was not able to maintain the bond to Y-TZP ceramic after 6 months of aging in water. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli.

PubMed

Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V; Beal, Nathan J; O'Malley, Patrick J; Tajkhorshid, Emad; Gennis, Robert B; Dikanov, Sergei A

2016-10-11

The respiratory cytochrome bo 3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQ H ), which is a transient intermediate during the electron-mediated reduction of O 2 to water. It is known that SQ H is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQ H was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1 H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo 3 in a H 2 O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor T z' = 11.8 MHz, whereas for H2, T z' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo 3 Q H site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.
Thermal stability relationships between PMR-15 resin and its composites

NASA Technical Reports Server (NTRS)

Bowles, Kenneth J.; Jayne, Douglas; Leonhardt, Todd A.; Bors, Dennis

1993-01-01

A study was conducted to investigate the relationship between the thermo-oxidative stability of PMR-15 matrix resin and the stability of graphite-fiber-reinforced composites that contain this resin as the matrix material. Three areas were investigated. The first was the effect of fiber/matrix interfacial bond strength on the isothermal aging weight loss of composites. By using type-A graphite fibers produced by Hercules, it was possible to study composites reinforced with fibers that were processed to receive different surface treatments. One of the fibers was untreated, a second fiber was treated by oxidation to enhance fiber/matrix bonding, and the third type of fiber was coated with an epoxy sizing. These treatments produced three significantly different interfacial bond strengths. The epoxy sizing on the third fiber was quickly oxidized from the bare fiber surfaces at 288, 316, and 343 C. The weight loss due to the removal of the sizing was constant at 1.5 percent. This initial weight loss was not observed in thermo-oxidative stability studies of composites. The PMR-15 matrix satisfactorily protected the reinforcemnt at all three temperatures.
Enhanced thermal stability of RuO2/polyimide interface for flexible device applications

NASA Astrophysics Data System (ADS)

Music, Denis; Schmidt, Paul; Chang, Keke

2017-09-01

We have studied the thermal stability of RuO2/polyimide (Kapton) interface using experimental and theoretical methods. Based on calorimetric and spectroscopic analyses, this inorganic-organic system does not exhibit any enthalpic peaks as well as all bonds in RuO2 and Kapton are preserved up to 500 °C. In addition, large-scale density functional theory based molecular dynamics, carried out in the same temperature range, validates the electronic structure and points out that numerous Ru-C and a few Ru-O covalent/ionic bonds form across the RuO2/Kapton interface. This indicates strong adhesion, but there is no evidence of Kapton degradation upon thermal excitation. Furthermore, RuO2 does not exhibit any interfacial bonds with N and H in Kapton, providing additional evidence for the thermal stability notion. It is suggested that the RuO2/Kapton interface is stable due to aromatic architecture of Kapton. This enhanced thermal stability renders Kapton an appropriate polymeric substrate for RuO2 containing systems in various applications, especially for flexible microelectronic and energy devices.
Preparation and Bond Properties of Thermal Barrier Coatings on Mg Alloy with Sprayed Al or Diffused Mg-Al Intermetallic Interlayer

NASA Astrophysics Data System (ADS)

Fan, Xizhi; Wang, Ying; Zou, Binglin; Gu, Lijian; Huang, Wenzhi; Cao, Xueqiang

2014-02-01

Sprayed Al or diffused Mg-Al layer was designed as interlayer between the thermal barrier coatings (TBCs) and Mg alloy substrate. The effects of the interlayer on the bond properties of the coats were investigated. Al layers were prepared by arc spraying and atmospheric plasma spraying (APS), respectively. Mg-Al diffused layer was obtained after the heat treatment of the sprayed sample (Mg alloy with APS Al coat) at 400 °C. The results show that sprayed Al interlayer does not improve the bond stability of TBCs. The failure of the TBCs on Mg alloy with Al interlayer occurs mainly due to the low strength of Al layer. Mg-Al diffused layer improves corrosion resistance of substrate and the bond interface. The TBCs on Mg alloy with Mg-Al diffused interlayer shows better bond stability than the sample of which the TBCs is directly sprayed on Mg alloy substrate by APS.
Nitrogen: A New Class of π-Bonding Partner in Hetero π-Stacking Interaction.

PubMed

Ramanathan, N; Sankaran, K; Sundararajan, K

2017-11-30

Spectroscopy under isolated conditions at low temperatures is an excellent tool to characterize the aggregates stabilized through weak interactions. Within the framework of weak interactions, the π-stacking interactions are considered unconventional with the limited experimental proofs, wherein the bonding associates are either aromatic and heterocyclic compounds or their combinations. Besides aromatic compounds, π-stacking networks can even be realized with molecules possessing electron rich π-clouds. In this work, the N 2 molecule as a possible π-bonding partner is explored for the first time in which hetero π-stacking was achieved between pyrrole and N 2 precursors. The matrix isolation experiments performed by seeding pyrrole and N 2 mixtures in an Ar matrix at low temperatures with subsequent infrared spectral characterization revealed the generation of adducts stabilized through a π(pyrrole)···π(N 2 ) interaction. Under identical conditions with the likelihood of two competing π-stacking and hydrogen-bonding interactions in pyrrole-N 2 associates, π-stacking dominates energetically over hydrogen-bonding interaction.
Caecal absorption of vitexin-2-O-xyloside and its aglycone apigenin, in the rat

USDA-ARS?s Scientific Manuscript database

The in vivo bioavailability of the flavone-C-glycosides has been little studied compared to their O-glycoside analogues, which are both more common in nature and considered more easily hydrolyzed than C-glycosides, by enterocytes and gut microbiota. In this study, we used vitexin-2-O-xyloside (VOX),...
Determination of triterpene glycosides in sea cucumber (Stichopus japonicus) and its related products by high-performance liquid chromatography.

PubMed

Dong, Ping; Xue, Chang-Hu; Yu, Lin-Fang; Xu, Jie; Chen, Shi-Guo

2008-07-09

A creative and sensitive method has been developed for the determination of triterpene glycosides concentrations in sea cucumber ( Stichopus japonicus) and related products by using d-quinovose (6-deoxyglucose) as the measurement standard by reverse-phase high-performance liquid chromatography (HPLC) and variable-wavelength detection. d-quinovose, which is a unique monosaccharide in holostane triterpene glycosides, was liberated by acid hydrolysis and precolumn derivatized by 1-phenyl-3-methyl-5-pyrazolone (PMP). PMP-quinovose was analyzed by HPLC with 22% acetonitrile in 0.05 M KH2PO4 aquatic solution (pH 5.2) as mobile phase. The calibration curves of d-quinovose were linear within the range of 6.56-164 mg/L (r(2) > 0.995). The contents of triterpene glycosides in various S. japonicus products were determined after appropriate pretreatment methods. The concentration of triterpene glycosides was calculated by the formula C = C(qui) x alpha (alpha = 8.5). The result showed that this method was a simple, rapid, and stable method for the determination of triterpene glycosides in S. japonicus products.
Fragmentation study of iridoid glycosides including epimers by liquid chromatography-diode array detection/electrospray ionization mass spectrometry and its application in metabolic fingerprint analysis of Gardenia jasminoides Ellis.

PubMed

Zhou, Tingting; Liu, Hua; Wen, Jun; Fan, Guorong; Chai, Yifeng; Wu, Yutian

2010-09-15

A high-performance liquid chromatography-diode array detection/electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS) method was applied to the characterization of ten iridoid glycosides in Gardenia jasminoides Ellis, a traditional Chinese medicine. During the process of structural elucidation, two groups of isomers including two epimers were structurally characterized and differentiated according to their distinctive fragmentation patterns which were closely related to their isomeric differentiations. Subsequently, the major compounds were purified by multi-dimensional chromatography and semi-preparative HPLC and the structure identification was confirmed with NMR techniques. The major fragmentation pathways of iridoid glycosides in Gardenia jasminoides Ellis obtained through the MS data were schemed systematically, which provided the best sensitivity and specificity for characterization of the iridoid glycosides especially the isomers so far. Based on the fragmentation patterns of iridoid glycosides concluded, seven major iridoid glycosides were characterized in rat plasma after intravenous administration of Gardenia jasminoides Ellis. Copyright 2010 John Wiley & Sons, Ltd.
Pressurized hot water extraction (PHWE) for the green recovery of bioactive compounds and steviol glycosides from Stevia rebaudiana Bertoni leaves.

PubMed

Bursać Kovačević, Danijela; Barba, Francisco J; Granato, Daniel; Galanakis, Charis M; Herceg, Zoran; Dragović-Uzelac, Verica; Putnik, Predrag

2018-07-15

Stevia rebaudiana Bertoni leaves are a natural source of diterpenic glycosides, and various bioactive compounds. The objectives were to characterize antioxidants and steviol glycosides in the extracts obtained from Stevia after "green" pressurized hot water extraction (PHWE). PHWE extracts were obtained at different temperatures (100, 130, 160 °C); static extraction times (5 and 10 min), and cycle numbers (1, 2, 3) using a constant pressure of 10.34 MPa. Temperature was the most important parameter for extraction, where the highest recoveries of all bioactive compounds (except for carotenoids) were at 160 °C. Extracts obtained at longer static times had more steviol glycosides, condensed tannins, and chlorophyll A. Higher amounts of total phenols, condensed tannins, and steviol glycosides were obtained under higher cycle numbers. This study indicated that PHWE is useful for recovering polar and nonpolar antioxidants and steviol glycosides. PHWE may be a suitable technique for scale-up to industrial applications. Copyright © 2018 Elsevier Ltd. All rights reserved.
Advances in the biotechnological glycosylation of valuable flavonoids.

PubMed

Xiao, Jianbo; Muzashvili, Tamar S; Georgiev, Milen I

2014-11-01

The natural flavonoids, especially their glycosides, are the most abundant polyphenols in foods and have diverse bioactivities. The biotransformation of flavonoid aglycones into their glycosides is vital in flavonoid biosynthesis. The main biological strategies that have been used to achieve flavonoid glycosylation in the laboratory involve metabolic pathway engineering and microbial biotransformation. In this review, we summarize the existing knowledge on the production and biotransformation of flavonoid glycosides using biotechnology, as well as the impact of glycosylation on flavonoid bioactivity. Uridine diphosphate glycosyltransferases play key roles in decorating flavonoids with sugars. Modern metabolic engineering and proteomic tools have been used in an integrated fashion to generate numerous structurally diverse flavonoid glycosides. In vitro, enzymatic glycosylation tends to preferentially generate flavonoid 3- and 7-O-glucosides; microorganisms typically convert flavonoids into their 7-O-glycosides and will produce 3-O-glycosides if supplied with flavonoid substrates having a hydroxyl group at the C-3 position. In general, O-glycosylation reduces flavonoid bioactivity. However, C-glycosylation can enhance some of the benefits of flavonoids on human health, including their antioxidant and anti-diabetic potential. Copyright © 2014 Elsevier Inc. All rights reserved.
Preparative isolation of flavonoid glycosides from Sphaerophysa salsula using hydrophilic interaction solid-phase extraction coupled with two-dimensional preparative liquid chromatography.

PubMed

Jiao, Lijin; Tao, Yanduo; Wang, Weidong; Shao, Yun; Mei, Lijuan; Wang, Qilan; Dang, Jun

2017-10-01

An offline preparative two-dimensional reversed-phase liquid chromatography/hydrophilic interaction liquid chromatography coupled with hydrophilic interaction solid-phase extraction method was developed for the preparative isolation of flavonoid glycosides from a crude sample of Sphaerophysa salsula. First, the non-flavonoids were removed using an XAmide solid-phase extraction cartridge. Based on the separation results of three different chromatographic stationary phases, the first-dimensional preparation was performed on an XAqua C18 prep column, and 15 fractions were obtained from the 5.2 g target sample. Then, three representative fractions were selected for additional purification on an XAmide preparative column to further isolate the flavonoid glycosides. In all, eight flavonoid glycosides were isolated in purities over 97%. The results demonstrated that the two-dimensional liquid chromatography method used in this study was effective for the preparative separation of flavonoid glycosides from Sphaerophysa salsula. Additionally, this method showed great potential for the separation of flavonoid glycosides from other plant materials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Effects of Pregnane Glycosides on Food Intake Depend on Stimulation of the Melanocortin Pathway and BDNF in an Animal Model

PubMed Central

Komarnytsky, Slavko; Esposito, Debora; Rathinasabapathy, Thirumurugan; Poulev, Alexander; Raskin, Ilya

2013-01-01

Pregnane glycosides appear to modulate food intake by possibly affecting the hypothalamic feeding circuits; however, the mechanisms of the appetite-regulating effect of pregnane glycosides remain obscure. Here, we show that pregnane glycoside-enriched extracts from swamp milkweed Asclepias incarnata at 25–100 mg/kg daily attenuated food intake (up to 47.1 ± 8.5% less than controls) and body weight gain in rats (10% for males and 9% for females, respectively) by activating melanocortin signaling and inhibiting gastric emptying. The major milkweed pregnane glycoside, ikemagenin, exerted its appetite-regulating effect by decreasing levels of agouti-related protein (0.6-fold) but not NPY satiety peptides. Ikemagenin treatment also increased secretion of brain-derived neurotropic factor (BDNF) downstream of melanocortin receptors in the hypothalamus (1.4-fold) and in the C6 rat glioma cell culture in vitro (up to 6-fold). These results support the multimodal effects of pregnane glycosides on feeding regulation, which depends on the activity of the melanocortin signaling pathway and BDNF. PMID:23308358
Effects of pregnane glycosides on food intake depend on stimulation of the melanocortin pathway and BDNF in an animal model.

PubMed

Komarnytsky, Slavko; Esposito, Debora; Rathinasabapathy, Thirumurugan; Poulev, Alexander; Raskin, Ilya

2013-02-27

Pregnane glycosides appear to modulate food intake by possibly affecting the hypothalamic feeding circuits; however, the mechanisms of the appetite-regulating effect of pregnane glycosides remain obscure. Here, we show that pregnane glycoside-enriched extracts from swamp milkweed Asclepias incarnata at 25-100 mg/kg daily attenuated food intake (up to 47.1 ± 8.5% less than controls) and body weight gain in rats (10% for males and 9% for females, respectively) by activating melanocortin signaling and inhibiting gastric emptying. The major milkweed pregnane glycoside, ikemagenin, exerted its appetite-regulating effect by decreasing levels of agouti-related protein (0.6-fold) but not NPY satiety peptides. Ikemagenin treatment also increased secretion of brain-derived neurotropic factor (BDNF) downstream of melanocortin receptors in the hypothalamus (1.4-fold) and in the C6 rat glioma cell culture in vitro (up to 6-fold). These results support the multimodal effects of pregnane glycosides on feeding regulation, which depends on the activity of the melanocortin signaling pathway and BDNF.
Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation

PubMed Central

2017-01-01

Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution. PMID:28581720
On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution

PubMed Central

Rios, Andro C.

2014-01-01

The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases. PMID:25284884
Characterisation of soy isoflavones and screening for novel malonyl glycosides using high-performance liquid chromatography-electrospray ionisation-mass spectrometry.

PubMed

Gu, L; Gu, W

2001-01-01

HPLC combined with electrospray ionisation (ESI)-MS and photodiode array detection has been employed to study the isoflavone components of soy. All of the known soy isoflavones separated by HPLC were identified and characterised, and three novel isoflavones were detected and screened out. These minor isoflavones were deduced to be isomers of 6"-O-malonyl isoflavone glycosides, based on the ESI-MS and UV data, in which the malonyl group is attached at a position other than the 6" position of the glycosyl moiety of the molecule. These novel malonyl glycosides are as thermally labile as the 6"-O-malonyl glycosides, being converted into known isoflavone glycosides after heating in aqueous ethanol. The advantages of HPLC-ESI-MS in detection of novel isoflavones from plant extracts are reviewed.
Role of plant β-glucosidases in the dual defense system of iridoid glycosides and their hydrolyzing enzymes in Plantago lanceolata and Plantago major.

PubMed

Pankoke, Helga; Buschmann, Torsten; Müller, Caroline

2013-10-01

The typical defense compounds of Plantaginaceae are the iridoid glycosides, which retard growth and/or enhance mortality of non-adapted herbivores. In plants, glycosidic defense compounds and hydrolytic enzymes often form a dual defense system, in which the glycosides are activated by the enzymes to exert biological effects. Yet, little is known about the activating enzymes in iridoid glycoside-containing plants. To examine the role of plant-derived β-glucosidases in the dual defense system of two common plantain species, Plantago lanceolata and Plantago major, we determined the concentration of iridoid glycosides as well as the β-glucosidase activity in leaves of different age. To investigate the presence of other leaf metabolites potentially involved in plant defense, we used a metabolic fingerprinting approach with ultra-high performance liquid chromatography coupled with time-of-flight-mass spectrometry. According to the optimal defense hypothesis, more valuable parts such as young leaves should be better protected than less valuable parts. Therefore, we expected that both, the concentrations of defense compounds as well as the β-glucosidase activity, should be highest in younger leaves and decrease with increasing leaf age. Both species possessed β-glucosidase activity, which hydrolyzed aucubin, one of the two most abundant iridoid glycosides in both plant species, with high activity. In line with the optimal defense hypothesis, the β-glucosidase activity in both Plantago species as well as the concentration of defense-related metabolites such as iridoid glycosides correlated negatively to leaf age. When leaf extracts were incubated with bovine serum albumin and aucubin, SDS-PAGE revealed a protein-denaturing effect of the leaf extracts of both plantain species, suggesting that iridoid glycosides and plant β-glucosidase interact in a dual defense system. Copyright © 2013 Elsevier Ltd. All rights reserved.
Change of supercooling capability in solutions containing different kinds of ice nucleators by flavonol glycosides from deep supercooling xylem parenchyma cells in trees.

PubMed

Kuwabara, Chikako; Kasuga, Jun; Wang, Donghui; Fukushi, Yukiharu; Arakawa, Keita; Koyama, Toshie; Inada, Takaaki; Fujikawa, Seizo

2011-12-01

Deep supercooling xylem parenchyma cells (XPCs) in Katsura tree contain flavonol glycosides with high supercooling-facilitating capability in solutions containing the ice nucleation bacterium (INB) Erwinia ananas, which is thought to have an important role in deep supercooling of XPCs. The present study, in order to further clarify the roles of these flavonol glycosides in deep supercooling of XPCs, the effects of these supercooling-facilitating (anti-ice nucleating) flavonol glycosides, kaempferol 3-O-β-D-glucopyranoside (K3Glc), kaempferol 7-O-β-D-glucopyranoside (K7Glc) and quercetin 3-O-β-D-glucopyranoside (Q3Glc), in buffered Milli-Q water (BMQW) containing different kinds of ice nucleators, including INB Xanthomonas campestris, silver iodide and phloroglucinol, were examined by a droplet freezing assay. The results showed that all of the flavonol glycosides promoted supercooling in all solutions containing different kinds of ice nucleators, although the magnitudes of supercooling capability of each flavonol glycoside changed in solutions containing different kinds of ice nucleators. On the other hand, these flavonol glycosides exhibited complicated nucleating reactions in BMQW, which did not contain identified ice nucleators but contained only unidentified airborne impurities. Q3Glc exhibited both supercooling-facilitating and ice nucleating capabilities depending on the concentrations in such water. Both K3Glc and K7Glc exhibited only ice nucleation capability in such water. It was also shown by an emulsion freezing assay in BMQW that K3Glc and Q3Glc had no effect on homogeneous ice nucleation temperature, whereas K7Glc increased ice nucleation temperature. The results indicated that each flavonol glycoside affected ice nucleation by very complicated and varied reactions. More studies are necessary to determine the exact roles of these flavonol glycosides in deep supercooling of XPCs in which unidentified heterogeneous ice nucleators may exist. Copyright © 2011 Elsevier Inc. All rights reserved.
Approach to the study of flavone di-C-glycosides by high performance liquid chromatography-tandem ion trap mass spectrometry and its application to characterization of flavonoid composition in Viola yedoensis.

PubMed

Cao, Jie; Yin, Chengle; Qin, Yan; Cheng, Zhihong; Chen, Daofeng

2014-10-01

The mass spectrometric (MS) analysis of flavone di-C-glycosides has been a difficult task due to pure standards being unavailable commercially and to that the reported relative intensities of some diagnostic ions varied with MS instruments. In this study, five flavone di-C-glycoside standards from Viola yedoensis have been systematically studied by high performance liquid chromatography-electrospray ionization-tandem ion trap mass spectrometry (HPLC-ESI-IT-MS(n)) in the negative ion mode to analyze their fragmentation patterns. A new MS(2) and MS(3) hierarchical fragmentation for the identification of the sugar nature (hexoses or pentoses) at C-6 and C-8 is presented based on previously established rules of fragmentation. Here, for the first time, we report that the MS(2) and MS(3) structure-diagnostic fragments about the glycosylation types and positions are highly dependent on the configuration of the sugars at C-6 and C-8. The base peak ((0,2) X1 (0,2) X(2)(-) ion) in MS(3) spectra of di-C-glycosides could be used as a diagnostic ion for flavone aglycones. These newly proposed fragmentation behaviors have been successfully applied to the characterization of flavone di-C-glycosides found in V. yedoensis. A total of 35 flavonoid glycosides, including 1 flavone mono-C-hexoside, 2 flavone 6,8-di-C-hexosides, 11 flavone 6,8-di-C-pentosides, 13 flavone 6,8-C-hexosyl-C-pentosides, 5 acetylated flavone C-glycosides and 3 flavonol O-glycosides, were identified or tentatively identified on the base of their UV profiles, MS and MS(n) (n = 5) data, or by comparing with reference substances. Among these, the acetylated flavone C-glycosides were reported from V. yedoensis for the first time. Copyright © 2014 John Wiley & Sons, Ltd.
Plasma-sprayed CaTiSiO5 ceramic coating on Ti-6Al-4V with excellent bonding strength, stability and cellular bioactivity.

PubMed

Wu, Chengtie; Ramaswamy, Yogambha; Liu, Xuanyong; Wang, Guocheng; Zreiqat, Hala

2009-02-06

Novel Ca-Si-Ti-based sphene (CaTiSiO5) ceramics possess excellent chemical stability and cytocompatibility. The aim of this study was to prepare sphene coating on titanium alloy (Ti-6Al-4V) for orthopaedic applications using the plasma spray method. The phase composition, surface and interface microstructure, coating thickness, surface roughness and bonding strength of the plasma-sprayed sphene coating were analysed using X-ray diffraction, scanning electron microscopy, atomic force microscopy and the standard mechanical testing of the American Society for Testing and Materials, respectively. The results indicated that sphene coating was obtained with a uniform and dense microstructure at the interface of the Ti-6Al-4V surface and the thickness and surface roughness of the coating were approximately 150 and 10 microm, respectively. Plasma-sprayed sphene coating on Ti-6Al-4V possessed a significantly improved bonding strength and chemical stability compared with plasma-sprayed hydroxyapatite (HAp) coating. Plasma-sprayed sphene coating supported human osteoblast-like cell (HOB) attachment and significantly enhanced HOB proliferation and differentiation compared with plasma-sprayed HAp coating and uncoated Ti-6Al-4V. Taken together, plasma-sprayed sphene coating on Ti-6Al-4V possessed excellent bonding strength, chemical stability and cellular bioactivity, indicating its potential application for orthopaedic implants.

Plasma-sprayed CaTiSiO5 ceramic coating on Ti-6Al-4V with excellent bonding strength, stability and cellular bioactivity

PubMed Central

Wu, Chengtie; Ramaswamy, Yogambha; Liu, Xuanyong; Wang, Guocheng; Zreiqat, Hala

2008-01-01

Novel Ca-Si-Ti-based sphene (CaTiSiO5) ceramics possess excellent chemical stability and cytocompatibility. The aim of this study was to prepare sphene coating on titanium alloy (Ti-6Al-4V) for orthopaedic applications using the plasma spray method. The phase composition, surface and interface microstructure, coating thickness, surface roughness and bonding strength of the plasma-sprayed sphene coating were analysed using X-ray diffraction, scanning electron microscopy, atomic force microscopy and the standard mechanical testing of the American Society for Testing and Materials, respectively. The results indicated that sphene coating was obtained with a uniform and dense microstructure at the interface of the Ti-6Al-4V surface and the thickness and surface roughness of the coating were approximately 150 and 10 μm, respectively. Plasma-sprayed sphene coating on Ti-6Al-4V possessed a significantly improved bonding strength and chemical stability compared with plasma-sprayed hydroxyapatite (HAp) coating. Plasma-sprayed sphene coating supported human osteoblast-like cell (HOB) attachment and significantly enhanced HOB proliferation and differentiation compared with plasma-sprayed HAp coating and uncoated Ti-6Al-4V. Taken together, plasma-sprayed sphene coating on Ti-6Al-4V possessed excellent bonding strength, chemical stability and cellular bioactivity, indicating its potential application for orthopaedic implants. PMID:18664431
Relative Stabilities and Reactivities of Isolated Versus Conjugated Alkenes: Reconciliation Via a Molecular Orbital Approach

NASA Astrophysics Data System (ADS)

Sotiriou-Leventis, Chariklia; Hanna, Samir B.; Leventis, Nicholas

1996-04-01

The well-accepted practice of generating a pair of molecular orbitals, one of lower energy and another of higher energy than the original pair of overlapping atomic orbitals, and the concept of a particle in a one-dimensional box are implemented in a simplified, nonmathematical method that explains the relative stabilities and reactivities of alkenes with conjugated versus isolated double bonds. In this method, Huckel-type MO's of higher polyenes are constructed by energy rules of linear combination of atomic orbitals. One additional rule is obeyed: bonding molecular orbitals overlap only with bonding molecular orbitals, and antibonding molecular orbitals overlap only with antibonding molecular orbitals.
Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

NASA Astrophysics Data System (ADS)

Lichtenberg, Dennis L.

During this period some important breakthroughs were accomplished in understanding the relationships between molecular ionization energies and bond energies in transition metal complexes, in understanding the electronic factors of carbon-hydrogen bond activation by transition metals, in characterizing small molecule bonding interactions with transition metals, and in investigating intermolecular interactions in thin films of transition metal complexes. The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies was developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. The relationship was used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. The ionization energies were also used to correlate the rates of carbonyl substitution reactions of (eta(sup 5)-C5H4X)Rh(CO)2 complexes, and to reveal the factors that control the stability of the transition state. The investigations of the fundamental interactions of C-H sigma and sigma* orbitals metals were continued with study of eta(sup 3)-1-methylallyl metal complexes. Direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal was obtained. The ability to observe the electronic effects of intermolecular interactions by comparing the ionizations of metal complexes in the gas phase with the ionizations of thin solid organometallic films prepared in ultra-high vacuum was established. Most significantly, the scanning tunneling microscope imaging of these thin films was accomplished.
Multilayer biomimetics: reversible covalent stabilization of a nanostructured biofilm.

PubMed

Li, Bingyun; Haynie, Donald T

2004-01-01

Designed polypeptides and electrostatic layer-by-layer self-assembly form the basis of promising research in bionanotechnology and medicine on development of polyelectrolyte multilayer films (PEMs). We show that PEMs can be formed from oppositely charged 32mers containing several cysteine residues. The polypeptides in PEMs become cross-linked under mild oxidizing conditions. This mimicking of disulfide (S-S) bond stabilization of folded protein structure confers on the PEMs a marked increase in resistance to film disassembly at acidic pH. The reversibility of S-S bond stabilization of PEMs presents further advantages for controlling physical properties of films, coatings, and other applications involving PEMs.
Caterpillar chemical defense and parasitoid success: Cotesia congregata parasitism of Ceratomia catalpae.

PubMed

Lampert, Evan C; Dyer, Lee A; Bowers, M Deane

2010-09-01

Sequestration of plant compounds by herbivorous insects as a defense against predators is well documented; however, few studies have examined the effectiveness of sequestration as a defense against parasitoids. One assumption of the "nasty host" hypothesis is that sequestration of plant defense compounds is deleterious to parasitoid development. We tested this hypothesis with larvae of the sequestering sphingid Ceratomia catalpae, which is heavily parasitized by the endoparasitoid Cotesia congregata, despite sequestering high concentrations of the iridoid glycoside catalpol from their catalpa host plants. We collected C. catalpae and catalpa leaves from six populations in the Eastern US, and allowed any C. congregata to emerge in the lab. Leaf iridoid glycosides and caterpillar iridoid glycosides were quantified, and we examined associations between sequestered caterpillar iridoid glycosides and C. congregata performance. Caterpillar iridoid glycosides were not associated with C. congregata field parasitism or number of offspring produced. Although wasp survival was over 90% in all populations, there was a slight negative relationship between caterpillar iridoid glycosides and wasp survival. Iridoid glycosides were present in caterpillars at levels that are deterrent to a variety of vertebrate and invertebrate predators. Thus, our results support the alternative hypothesis that unpalatable, chemically defended hosts are "safe havens" for endoparasitoids. Future trials examining the importance of catalpol sequestration to potential natural enemies of C. congregata and C. catalpae are necessary to strengthen this conclusion.
Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans

NASA Astrophysics Data System (ADS)

Hecht, Elizabeth S.; Loziuk, Philip L.; Muddiman, David C.

2017-04-01

Understanding the rearrangement of gas-phase ions via tandem mass spectrometry is critical to improving manual and automated interpretation of complex datasets. N-glycan analysis may be carried out under collision induced (CID) or higher energy collision dissociation (HCD), which favors cleavage at the glycosidic bond. However, fucose migration has been observed in tandem MS, leading to the formation of new bonds over four saccharide units away. In the following work, we report the second instance of saccharide migration ever to occur for N-glycans. Using horseradish peroxidase as a standard, the beta-1,2 xylose was observed to migrate from a hexose to a glucosamine residue on the (Xyl)Man3GlcNac2 glycan. This investigation was followed up in a complex N-linked glycan mixture derived from stem differentiating xylem tissue, and the rearranged product ion was observed for 75% of the glycans. Rearrangement was not favored in isomeric glycans with a core or antennae fucose and unobserved in glycans predicted to have a permanent core-fucose modification. As the first empirical observation of this rearrangement, this work warrants dissemination so it may be searched in de novo sequencing glycan workflows.
Aryl C—H···Cl– Hydrogen Bonding in a Fluorescent Anion Sensor

PubMed Central

Tresca, Blakely W.; Zakharov, Lev N.; Carroll, Calden N.; Johnson, Darren W.; Haley, Michael M.

2014-01-01

A new phenyl-acetylene receptor containing a carbonaceous hydrogen bond donor activates anion binding in conjunction with two stabilizing ureas. The unusual CH···Cl– hydrogen bond is apparent in solution by large 1H NMR chemical shifts and by a short, linear contact in the solid state. PMID:23843050
Effects of chemically modified wood on bond durability

Treesearch

Rishawn Brandon; Rebecca E. Ibach; Charles R. Frihart

2005-01-01

Chemical modification of wood can improve its dimensional stability and resistance to biological degradation and moisture, but modification can also create a new surface for bonding. Acetylation of wood results in the loss of hydroxyl groups, making the wood more hydrophobic and reduces its ability to hydrogen-bond with the adhesive. In contrast, reacting wood with...
New megastigmane glycoside and aromadendrane derivative from the aerial part of Piper elongatum.

PubMed

Masuoka, Chikako; Ono, Masateru; Ito, Yasuyuki; Okawa, Masafumi; Nohara, Toshihiro

2002-10-01

A new megastigmane glycoside, called pipeloside A, and a new aromadendrane type sesquiterpenoid, pipelol A, were isolated from the MeOH extract of the aerial part of Piper elongatum VAHL. along with a known megastigmane glycoside, byzantionoside B. The structures of these compounds were elucidated on the basis of spectroscopic data and chemical evidence.
Steroidal glycosides from the roots of Asclepias curassavica.

PubMed

Warashina, Tsutomu; Noro, Tadataka

2008-03-01

Twenty-six new acylated-oxypregnane glycosides were obtained along with three known cardenolide glycosides from the roots of Asclepias curassavica (Asclepiadaceae). The new compounds were confirmed to contain 12-O-benzoylsarcostin, 12-O-benzoyldeacylmetaplexigenin, kidjolanin, and 12-O-benzoyltayloron, and one new acylated-oxypregnane, 12-O-(E)-cinnamoyltayloron, as their aglycones, using both spectroscopic and chemical methods.
Effects of Fruit Toxins on Intestinal and Microbial β-Glucosidase Activities of Seed-Predating and Seed-Dispersing Rodents (Acomys spp.).

PubMed

Kohl, Kevin D; Samuni-Blank, Michal; Lymberakis, Petros; Kurnath, Patrice; Izhaki, Ido; Arad, Zeev; Karasov, William H; Dearing, M Denise

2016-01-01

Plant secondary compounds (PSCs) have profound influence on the ecological interaction between plants and their consumers. Glycosides, a class of PSC, are inert in their intact form and become toxic on activation by either plant β-glucosidase enzymes or endogenous β-glucosidases produced by the intestine of the plant-predator or its microbiota. Many insect herbivores decrease activities of endogenous β-glucosidases to limit toxin exposure. However, such an adaptation has never been investigated in nonmodel mammals. We studied three species of spiny mice (Acomys spp.) that vary in their feeding behavior of the glycoside-rich fruit of Ochradenus baccatus. Two species, the common (Acomys cahirinus) and Crete (Acomys minous) spiny mice, behaviorally avoid activating glycosides, while the golden spiny mouse (Acomys russatus) regularly consumes activated glycosides. We fed each species a nontoxic diet of inert glycosides or a toxic diet of activated fruit toxins and investigated the responses of intestinal and microbial β-glucosidase activities. We found that individuals feeding on activated toxins had lower intestinal β-glucosidase activity and that the species that behaviorally avoid activating glycosides also had lower intestinal β-glucosidase activity regardless of treatment. The microbiota represented a larger source of toxin liberation, and the toxin-adapted species (golden spiny mouse) exhibited almost a fivefold increase in microbial β-glucosidase when fed activated toxins, while other species showed slight decreases. These results are contrary to those in insects, where glycoside-adapted species have lower β-glucosidase activity. The glycoside-adapted golden spiny mouse may have evolved tolerance mechanisms such as enhanced detoxification rather than avoidance mechanisms.
Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism

PubMed Central

Kim, Seonah; Ståhlberg, Jerry; Sandgren, Mats; Paton, Robert S.; Beckham, Gregg T.

2014-01-01

Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η1-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η1) to copper, and that a copper-oxyl–mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds. PMID:24344312
Interaction model of steviol glycosides from Stevia rebaudiana (Bertoni) with sweet taste receptors: A computational approach.

PubMed

Mayank; Jaitak, Vikas

2015-08-01

Docking studies were performed on natural sweeteners from Stevia rebaudiana by constructing homology models of T1R2 and T1R3 subunits of human sweet taste receptors. Ramachandran plot, PROCHECK results and ERRAT overall quality factor were used to validate the quality of models. Furthermore, docking results of steviol glycosides (SG's) were correlated significantly with data available in the literature which enabled to predict the exact sweetness rank order of SG's. The binding pattern indicated that Asn 44, Ans 52, Ala 345, Pro 343, Ile 352, Gly 346, Gly 47, Ala 354, Ser 336, Thr 326 and Ser 329 are the main interacting amino acid residues in case of T1R2 and Arg 56, Glu 105, Asp 215, Asp 216, Glu 148, Asp 258, Lys 255, Ser 104, Glu 217, Leu 51, Arg 52 for T1R3, respectively. Amino acids interact with SG's mainly by forming hydrogen bonds with the hydroxyl group of glucose moieties. Significant variation in docked poses of all the SG's were found. In this study, we have proposed the mechanism of the sweetness of the SG's in the form of multiple point stimulation model by considering the diverse binding patterns of various SG's, as well as their structural features. It will give further insight in understanding the differences in the quality of taste and will be used to improve the taste of SG's using semi-synthetic approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.
Genomics Review of Holocellulose Deconstruction by Aspergilli

PubMed Central

Segato, Fernando; Damásio, André R. L.; de Lucas, Rosymar C.; Squina, Fabio M.

2014-01-01

SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases. PMID:25428936
Mapping the Reactivity and Selectivity of 2-Azidofucosyl Donors for the Assembly of N-Acetylfucosamine-Containing Bacterial Oligosaccharides.

PubMed

Hagen, Bas; Ali, Sara; Overkleeft, Herman S; van der Marel, Gijsbert A; Codée, Jeroen D C

2017-01-20

The synthesis of complex oligosaccharides is often hindered by a lack of knowledge on the reactivity and selectivity of their constituent building blocks. We investigated the reactivity and selectivity of 2-azidofucosyl (FucN 3 ) donors, valuable synthons in the synthesis of 2-acetamido-2-deoxyfucose (FucNAc) containing oligosaccharides. Six FucN 3 donors, bearing benzyl, benzoyl, or tert-butyldimethylsilyl protecting groups at the C3-O and C4-O positions, were synthesized, and their reactivity was assessed in a series of glycosylations using acceptors of varying nucleophilicity and size. It was found that more reactive nucleophiles and electron-withdrawing benzoyl groups on the donor favor the formation of β-glycosides, while poorly reactive nucleophiles and electron-donating protecting groups on the donor favor α-glycosidic bond formation. Low-temperature NMR activation studies of Bn- and Bz-protected donors revealed the formation of covalent FucN 3 triflates and oxosulfonium triflates. From these results, a mechanistic explanation is offered in which more reactive acceptors preferentially react via an S N 2-like pathway, while less reactive acceptors react via an S N 1-like pathway. The knowledge obtained in this reactivity study was then applied in the construction of α-FucN 3 linkages relevant to bacterial saccharides. Finally, a modular synthesis of the Staphylococcus aureus type 5 capsular polysaccharide repeating unit, a trisaccharide consisting of two FucNAc units, is described.
An updated review of dietary isoflavones: Nutrition, processing, bioavailability and impacts on human health.

PubMed

Zaheer, Khalid; Humayoun Akhtar, M

2017-04-13

Isoflavones (genistein, daidzein, and glycitein) are bioactive compounds with mildly estrogenic properties and often referred to as phytoestrogen. These are present in significant quantities (up to 4-5 mg·g -1 on dry basis) in legumes mainly soybeans, green beans, mung beans. In grains (raw materials) they are present mostly as glycosides, which are poorly absorbed on consumption. Thus, soybeans are processed into various food products for digestibility, taste and bioavailability of nutrients and bioactives. Main processing steps include steaming, cooking, roasting, microbial fermentation that destroy protease inhibitors and also cleaves the glycoside bond to yield absorbable aglycone in the processed soy products, such as miso, natto, soy milk, tofu; and increase shelf lives. Processed soy food products have been an integral part of regular diets in many Asia-Pacific countries for centuries, e.g. China, Japan and Korea. However, in the last two decades, there have been concerted efforts to introduce soy products in western diets for their health benefits with some success. Isoflavones were hailed as magical natural component that attribute to prevent some major prevailing health concerns. Consumption of soy products have been linked to reduction in incidence or severity of chronic diseases such as cardiovascular, breast and prostate cancers, menopausal symptoms, bone loss, etc. Overall, consuming moderate amounts of traditionally prepared and minimally processed soy foods may offer modest health benefits while minimizing potential for any adverse health effects.
Solubility Enhancement of Steviol Glycosides and Characterization of Their Inclusion Complexes with Gamma-Cyclodextrin

PubMed Central

Upreti, Mani; Strassburger, Ken; Chen, You L.; Wu, Shaoxiong; Prakash, Indra

2011-01-01

Steviol glycosidesrebaudioside (reb) A, C and D have low aqueous solubilities. To improve their aqueous solubilities, inclusion complex of steviol glycosides, reb A, C and D and gamma cyclodextrin were prepared by freeze drying method and further characterized by means of differential scanning calorimetry, Fourier transform infrared spectroscopy and Raman spectroscopy. The effect of gamma cyclodextrin on chemical shifts of the steviol glycosides was also studied in proton NMR experiments as well as in solid state 13C CP/MAS NMR experiments. These results indicated that the steviol glycosides were clearly in inclusion complex formation with the gamma cyclodextrin which also results in solubility enhancement of these steviol glycosides. Phase solubility studies showed that amounts of soluble reb A, C and D increased with increasing amounts of gamma cyclodextrin indicating formation of 1:1 stoichiometric and higher order inclusion complexes. PMID:22174615
Plant-derived isoprenoid sweeteners: recent progress in biosynthetic gene discovery and perspectives on microbial production.

PubMed

Seki, Hikaru; Tamura, Keita; Muranaka, Toshiya

2018-06-01

Increased public awareness of negative health effects associated with excess sugar consumption has triggered increasing interest in plant-derived natural sweeteners. Steviol glycosides are a group of highly sweet diterpene glycosides contained in the leaves of stevia (Stevia rebaudiana). Mogrosides, extracted from monk fruit (Siraitia grosvenorii), are a group of cucurbitane-type triterpenoid glycosides. Glycyrrhizin is an oleanane-type triterpenoid glycoside derived from the underground parts of Glycyrrhiza plants (licorice). This review focuses on the natural isoprenoid sweetening agents steviol glycosides, mogrosides, and glycyrrhizin, and describes recent progress in gene discovery and elucidation of the catalytic functions of their biosynthetic enzymes. Recently, remarkable progress has been made in engineering the production of various plant-specialized metabolites in microbial hosts such as Saccharomyces cerevisiae via the introduction of biosynthetic enzyme genes. Perspectives on the microbial production of plant-derived natural sweeteners are also discussed.
Steroidal Saponins

NASA Astrophysics Data System (ADS)

Sahu, N. P.; Banerjee, S.; Mondal, N. B.; Mandal, D.

The medicinal activities of plants are generally due to the secondary metabolites (1) which often occur as glycosides of steroids, terpenoids, phenols etc. Saponins are a group of naturally occurring plant glycosides, characterized by their strong foam-forming properties in aqueous solution. The cardiac glycosides also possess this, property but are classified separately because of their specific biological activity. Unlike the cardiac glycosides, saponins generally do not affect the heart. These are classified as steroid or triterpenoid saponins depending on the nature of the aglycone. Steroidal glycosides are naturally occurring sugar conjugates of C27 steroidal compounds. The aglycone of a steroid saponin is usually a spirostanol or a furostanol. The glycone parts of these compounds are mostly oligosaccharides, arranged either in a linear or branched fashion, attached to hydroxyl groups through an acetal linkage (2, 3). Another class of saponins, the basic steroid saponins, contain nitrogen analogues of steroid sapogenins as aglycones.
Enzymatically modified starch up-regulates expression of incretins and sodium-coupled monocarboxylate transporter in jejunum of growing pigs.

PubMed

Metzler-Zebeli, B U; Ertl, R; Grüll, D; Molnar, T; Zebeli, Q

2017-07-01

Dietary effects on the host are mediated via modulation of the intestinal mucosal responses. The present study investigated the effect of an enzymatically modified starch (EMS) product on the mucosal expression of genes related to starch digestion, sugar and short-chain fatty acid (SCFA) absorption and incretins in the jejunum and cecum in growing pigs. Moreover, the impact of the EMS on hepatic expression of genes related to glucose and lipid metabolism, and postprandial serum metabolites were assessed. Barrows (n=12/diet; initial BW 29 kg) were individually fed three times daily with free access to a diet containing either EMS or waxy corn starch as control (CON) for 10 days. The enzymatic modification led to twice as many α-1,6-glycosidic bonds (~8%) in the amylopectin fraction in the EMS in comparison with the non-modified native waxy corn starch (4% α-1,6-glycosidic bonds). Linear discriminant analysis revealed distinct clustering of mucosal gene expression for EMS and CON diets in jejunum. Compared with the CON diet, the EMS intake up-regulated jejunal expression of sodium-coupled monocarboxylate transporter (SMCT), glucagon-like peptide-1 (GLP1) and gastric inhibitory polypeptide (GIP) (P<0.05) and intestinal alkaline phosphatase (ALPI) (P=0.08), which may be related to greater luminal SCFA availability, whereas cecal gene expression was unaffected by diet. Hepatic peroxisome proliferator-activated receptor γ (PPARγ) expression tended (P=0.07) to be down-regulated in pigs fed the EMS diet compared with pigs fed the CON diet, which may explain the trend (P=0.08) of 30% decrease in serum triglycerides in pigs fed the EMS diet. Furthermore, pigs fed the EMS diet had a 50% higher (P=0.03) serum urea concentration than pigs fed the CON diet potentially indicating an increased use of glucogenic amino acids for energy acquisition in these pigs. Present findings suggested the jejunum as the target site to influence the intestinal epithelium and altered lipid and carbohydrate metabolism by EMS feeding.

Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide

PubMed Central

Zhao, Binwu

2017-01-01

The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack. PMID:28329017
Role of Disulfide Bridges in the Activity and Stability of a Cold-Active α-Amylase

PubMed Central

Siddiqui, Khawar Sohail; Poljak, Anne; Guilhaus, Michael; Feller, Georges; D'Amico, Salvino; Gerday, Charles; Cavicchioli, Ricardo

2005-01-01

The cold-adapted α-amylase from Pseudoalteromonas haloplanktis unfolds reversibly and cooperatively according to a two-state mechanism at 30°C and unfolds reversibly and sequentially with two transitions at temperatures below 12°C. To examine the role of the four disulfide bridges in activity and conformational stability of the enzyme, the eight cysteine residues were reduced with β-mercaptoethanol or chemically modified using iodoacetamide or iodoacetic acid. Matrix-assisted laser desorption-time of flight mass spectrometry analysis confirmed that all of the cysteines were modified. The iodoacetamide-modified enzyme reversibly folded/unfolded and retained approximately one-third of its activity. Removal of all disulfide bonds resulted in stabilization of the least stable region of the enzyme (including the active site), with a concomitant decrease in activity (increase in activation enthalpy). Disulfide bond removal had a greater impact on enzyme activity than on stability (particularly the active-site region). The functional role of the disulfide bridges appears to be to prevent the active site from developing ionic interactions. Overall, the study demonstrated that none of the four disulfide bonds are important in stabilizing the native structure of enzyme, and instead, they appear to promote a localized destabilization to preserve activity. PMID:16109962
Probing the determinants of protein stability: comparison of class A beta-lactamases.

PubMed Central

Vanhove, M; Houba, S; b1motte-Brasseur, J; Frère, J M

1995-01-01

Five class A beta-lactamases produced by various mesophilic bacterial species have been compared. Although closely related in primary and overall structures, these enzymes exhibit very different stabilities. In order to investigate the factors responsible for these differences, several features deduced from the amino acid composition and three-dimensional structures were studied for the five proteins. This analysis revealed that higher stability appeared to correlate with increased numbers of intramolecular hydrogen bonds and of salt bridges. By contrast, the global hydrophobicity of the protein seemed to play a relatively minor role. A strongly unfavourable balance between charged residues and the presence of a cis-peptide bond preceding a non-proline residue might also contribute to the particularly low stability of two of the enzymes. PMID:8948443
Average bond energies between boron and elements of the fourth, fifth, sixth, and seventh groups of the periodic table

NASA Technical Reports Server (NTRS)

Altshuller, Aubrey P

1955-01-01

The average bond energies D(gm)(B-Z) for boron-containing molecules have been calculated by the Pauling geometric-mean equation. These calculated bond energies are compared with the average bond energies D(exp)(B-Z) obtained from experimental data. The higher values of D(exp)(B-Z) in comparison with D(gm)(B-Z) when Z is an element in the fifth, sixth, or seventh periodic group may be attributed to resonance stabilization or double-bond character.
Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity.

PubMed

Pal, Kuntal; Kumar, Shiva; Sharma, Shikha; Garg, Saurabh Kumar; Alam, Mohammad Suhail; Xu, H Eric; Agrawal, Pushpa; Swaminathan, Kunchithapadam

2010-07-02

The open reading frame Rv1326c of Mycobacterium tuberculosis (Mtb) H37Rv encodes for an alpha-1,4-glucan branching enzyme (MtbGlgB, EC 2.4.1.18, Uniprot entry Q10625). This enzyme belongs to glycoside hydrolase (GH) family 13 and catalyzes the branching of a linear glucose chain during glycogenesis by cleaving a 1-->4 bond and making a new 1-->6 bond. Here, we show the crystal structure of full-length MtbGlgB (MtbGlgBWT) at 2.33-A resolution. MtbGlgBWT contains four domains: N1 beta-sandwich, N2 beta-sandwich, a central (beta/alpha)(8) domain that houses the catalytic site, and a C-terminal beta-sandwich. We have assayed the amylase activity with amylose and starch as substrates and the glycogen branching activity using amylose as a substrate for MtbGlgBWT and the N1 domain-deleted (the first 108 residues deleted) MtbDelta108GlgB protein. The N1 beta-sandwich, which is formed by the first 105 amino acids and superimposes well with the N2 beta-sandwich, is shown to have an influence in substrate binding in the amylase assay. Also, we have checked and shown that several GH13 family inhibitors are ineffective against MtbGlgBWT and MtbDelta108GlgB. We propose a two-step reaction mechanism, for the amylase activity (1-->4 bond breakage) and isomerization (1-->6 bond formation), which occurs in the same catalytic pocket. The structural and functional properties of MtbGlgB and MtbDelta108GlgB are compared with those of the N-terminal 112-amino acid-deleted Escherichia coli GlgB (ECDelta112GlgB).
Hydrogen-Bonding Catalysis and Inhibition by Simple Solvents in the Stereoselective Kinetic Epoxide-Opening Spirocyclization of Glycal Epoxides to Form Spiroketals

PubMed Central

Wurst, Jacqueline M.; Liu, Guodong; Tan, Derek S.

2011-01-01

Mechanistic investigations of a MeOH-induced kinetic epoxide-opening spirocyclization of glycal epoxides have revealed dramatic, specific roles for simple solvents in hydrogen-bonding catalysis of this reaction to form spiroketal products stereoselectively with inversion of configuration at the anomeric carbon. A series of electronically-tuned C1-aryl glycal epoxides was used to study the mechanism of this reaction based on differential reaction rates and inherent preferences for SN2 versus SN1 reaction manifolds. Hammett analysis of reaction kinetics with these substrates is consistent with an SN2 or SN2-like mechanism (ρ = −1.3 vs. ρ = −5.1 for corresponding SN1 reactions of these substrates). Notably, the spirocyclization reaction is second-order dependent on MeOH and the glycal ring oxygen is required for second-order MeOH catalysis. However, acetone cosolvent is a first-order inhibitor of the reaction. A transition state consistent with the experimental data is proposed in which one equivalent of MeOH activates the epoxide electrophile via a hydrogen bond while a second equivalent of MeOH chelates the sidechain nucleophile and glycal ring oxygen. A paradoxical previous observation that decreased MeOH concentration leads to increased competing intermolecular methyl glycoside formation is resolved by the finding that this side reaction is only first-order dependent on MeOH. This study highlights the unusual abilities of simple solvents to act as hydrogen-bonding catalysts and inhibitors in epoxide-opening reactions, providing both stereoselectivity and discrimination between competing reaction manifolds. This spirocyclization reaction provides efficient, stereocontrolled access to spiroketals that are key structural motifs in natural products. PMID:21539313
Influence of architecture on the kinetic stability of molecular assemblies.

PubMed

Patel, Amesh B; Allen, Stephanie; Davies, Martyn C; Roberts, Clive J; Tendler, Saul J B; Williams, Philip M

2004-02-11

The strength of a multimolecular system depends on the number of interactions that hold it together. Using dynamic force spectroscopy, we show how the kinetic stability of a system decreases as the number of molecular bonds is increased, as predicted by theory. The data raise important considerations for experimental tests of bond strength and, as a paradigm, suggest both routes to and pitfalls in methods for computational simulation of molecular transitions, such as ligand binding and protein folding.
Effect of harvest timing on leaf production and yield of diterpene glycosides in Stevia rebaudiana Bert: a specialty perennial crop for Mississippi

USDA-ARS?s Scientific Manuscript database

Stevia rebaundiana (Bertoni), a perennial shrub of the Asteraceae, is one of the most important sources of non-caloric natural sweeteners. Stevia’s plant extracts and glycosides have been used for several years in Paraguay and Brazil. Several studies suggest that Stevia and its glycosides exert ben...
Phenolic glycosides from sugar maple (Acer saccharum) bark.

PubMed

Yuan, Tao; Wan, Chunpeng; González-Sarrías, Antonio; Kandhi, Vamsikrishna; Cech, Nadja B; Seeram, Navindra P

2011-11-28

Four new phenolic glycosides, saccharumosides A-D (1-4), along with eight known phenolic glycosides, were isolated from the bark of sugar maple (Acer saccharum). The structures of 1-4 were elucidated on the basis of spectroscopic data analysis. All compounds isolated were evaluated for cytotoxicity effects against human colon tumorigenic (HCT-116 and Caco-2) and nontumorigenic (CCD-18Co) cell lines.
A new cinnamic acid glycoside from roots of Heracleum dissectum.

PubMed

Wang, Zhi-Gang; Mi, Jie; Wang, Xin-Rui; Huo, Ya-Yu; Peng, Ya-Jie; Zhang, Hai-Min; Gao, Yang; Zhang, Hai-Long

2018-01-01

From the roots of Heracleum dissectum Lebb., one new cinnamic acid glycoside derivative named dissectumoside (1), together with eight known compounds including three phenolics, three phenolic glycosides and two phenylpropanoic glycoside were isolated using various chromatographic methods. Among them compound 2-9 was isolated from the plant for the first time. Their structures were elucidated and identified on the basis of their physicochemical properties and by extensive analyses of NMR spectroscopy and high-resolution mass spectrometry. The results of triglyceride accumulation screening in 3T3-L1 cells showed that compounds 1, 5 and 9 exhibited significantly accelerating activities of adipogenesis in adipocytes.
Characterization of an anti-tuberculosis resin glycoside from the prairie medicinal plant Ipomoea leptophylla.

PubMed

Barnes, Curtis C; Smalley, Mary K; Manfredi, Kirk P; Kindscher, Kelly; Loring, Hillary; Sheeley, Douglas M

2003-11-01

The organic soluble extract from the leaves of the native North American prairie plant Ipomoea leptophylla (big root morning glory) showed in vitro activity against M. tuberculosis. Bioassay-guided fractionation of this extract resulted in the identification of two new resin glycosides (6, 7). Base-catalyzed hydrolysis of these glycosides gave operculinic acid (1) as the glycosidic acid component as well as trans-cinnamic acid, propanoic acid, and lauric acid. The complete structure elucidation was accomplished through derivatization, 1D and 2D NMR spectroscopy (TOCSY, ROESY, HSQC, HMBC), and MS/MS experiments on 6 and 7 as well as the permethylated derivative 8.
Phytosterol glycosides reduce cholesterol absorption in humans

PubMed Central

Lin, Xiaobo; Ma, Lina; Racette, Susan B.; Anderson Spearie, Catherine L.; Ostlund, Richard E.

2009-01-01

Dietary phytosterols inhibit intestinal cholesterol absorption and regulate whole body cholesterol excretion and balance. However, they are biochemically heterogeneous and a portion is glycosylated in some foods with unknown effects on biological activity. We tested the hypothesis that phytosterol glycosides reduce cholesterol absorption in humans. Phytosterol glycosides were extracted and purified from soy lecithin in a novel two-step process. Cholesterol absorption was measured in a series of three single-meal tests given at intervals of 2 wk to each of 11 healthy subjects. In a randomized crossover design, participants received ∼300 mg of added phytosterols in the form of phytosterol glycosides or phytosterol esters, or placebo in a test breakfast also containing 30 mg cholesterol-d7. Cholesterol absorption was estimated by mass spectrometry of plasma cholesterol-d7 enrichment 4–5 days after each test. Compared with the placebo test, phytosterol glycosides reduced cholesterol absorption by 37.6 ± 4.8% (P < 0.0001) and phytosterol esters 30.6 ± 3.9% (P = 0.0001). These results suggest that natural phytosterol glycosides purified from lecithin are bioactive in humans and should be included in methods of phytosterol analysis and tables of food phytosterol content. PMID:19246636
Overview: the history, technical function and safety of rebaudioside A, a naturally occurring steviol glycoside, for use in food and beverages.

PubMed

Carakostas, M C; Curry, L L; Boileau, A C; Brusick, D J

2008-07-01

Rebaudioside A is a sweet tasting steviol glycoside extracted and purified from Stevia rebaudiana (Bertoni). Steviol glycosides can currently be used as a food ingredient in only a handful of countries. Questions on specifications, safety and special population effects have prevented steviol glycosides from obtaining a legal status permitting their use as a sweetener in most countries. A set of papers reporting results of research studies and reviews has been compiled in this Supplement to definitively answer unresolved questions. Specifically, recently completed studies on the general and reproductive toxicity of rebaudioside A corroborate studies carried out with purified steviol glycosides demonstrating safety at high dietary intake levels. Comparative metabolism studies provide further affirmation of the common metabolic pathway for all steviol glycosides and the common metabolism between rats and humans. Finally, clinical studies provide further evidence that purified rebaudioside A has no effect on either blood pressure or glucose homeostasis. This paper summarizes the information used to conclude that high purity rebaudioside A (rebiana) produced to food-grade specifications and according to Good Manufacturing Practices is safe for human consumption under its intended conditions of use as a general purpose sweetener.
Development and application of a quantitative method based on LC-QqQ MS/MS for determination of steviol glycosides in Stevia leaves.

PubMed

Molina-Calle, M; Sánchez de Medina, V; Delgado de la Torre, M P; Priego-Capote, F; Luque de Castro, M D

2016-07-01

Stevia is a currently well-known plant thanks to the presence of steviol glycosides, which are considered as sweeteners obtained from a natural source. In this research, a method based on LC-MS/MS by using a triple quadrupole detector was developed for quantitation of 8 steviol glycosides in extracts from Stevia leaves. The ionization and fragmentation parameters for selected reaction monitoring were optimized. Detection and quantitation limits ranging from 0.1 to 0.5ng/mL and from 0.5 to 1ng/mL, respectively, were achieved: the lowest attained so far. The steviol glycosides were quantified in extracts from leaves of seven varieties of Stevia cultivated in laboratory, greenhouse and field. Plants cultivated in field presented higher concentration of steviol glycosides than those cultivated in greenhouse. Thus, the way of cultivation clearly influences the concentration of these compounds. The inclusion of branches together with leaves as raw material was also evaluated, showing that this inclusion modifies, either positively or negatively, the concentration of steviol glycosides. Copyright © 2016 Elsevier B.V. All rights reserved.
Characterization of phenolic compounds and antinociceptive activity of Sempervivum tectorum L. leaf juice.

PubMed

Alberti, Ágnes; Béni, Szabolcs; Lackó, Erzsébet; Riba, Pál; Al-Khrasani, Mahmoud; Kéry, Ágnes

2012-11-01

Sempervivum tectorum L. (houseleek) leaf juice has been known as a traditional herbal remedy. The aim of the present study was the chemical characterization of its phenolic compounds and to develop quantitation methods for its main flavonol glycoside, as well as to evaluate its antinociceptive activity. Lyophilized houseleek leaf juice was studied by HPLC-DAD coupled to electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to identify flavonol glycosides, hydroxy-benzoic and hydroxy-cinnamic acids. Ten flavonol glycosides and sixteen phenolic acid compounds were identified or tentatively characterized. Structure of the main flavonol compound was identified by nuclear magnetic resonance spectroscopy. Three characteristic kaempferol glycosides were isolated and determined by LC-ESI-MS/MS with external calibration method, using the isolated compounds as standard. The main flavonol glycoside was also determined by HPLC-DAD. Validated HPLC-DAD and LC-ESI-MS/MS methods were developed to quantify kaempferol-3-O-rhamnosyl-glucoside-7-O-rhamnoside and two other kaempferol glycosides. Antinociceptive activity of houseleek leaf juice was investigated by writhing test of mice. Sempervivum extract significantly reduced pain in the mouse writhing test. Copyright © 2012 Elsevier B.V. All rights reserved.
Effectiveness and stability of silane coupling agent incorporated in 'universal' adhesives.

PubMed

Yoshihara, Kumiko; Nagaoka, Noriyuki; Sonoda, Akinari; Maruo, Yukinori; Makita, Yoji; Okihara, Takumi; Irie, Masao; Yoshida, Yasuhiro; Van Meerbeek, Bart

2016-10-01

For bonding indirect restorations, some 'universal' adhesives incorporate a silane coupling agent to chemically bond to glass-rich ceramics so that a separate ceramic primer is claimed to be no longer needed. With this work, we investigated the effectiveness/stability of the silane coupling function of the silanecontaining experimentally prepared adhesives and Scotchbond Universal (3MESPE). Experimental adhesives consisted of Scotchbond Universal and the silane-free Clearfil S3 ND Quick (Kuraray Noritake) mixed with Clearfil Porcelain Bond Activator (Kuraray Noritake) and the two adhesives to which γ-methacryloxypropyltrimethoxysilane (γ-MPTS) was added. Shear bond strength was measured onto silica-glass plates; the adhesive formulations were analyzed using fourier transform infrared spectroscopy (FTIR) and 13C nuclear magnetic resonance (NMR). In addition, shear bond strength onto CAD-CAM composite blocks was measured without and after thermo-cycling ageing. A significantly higher bond strength was recorded when Clearfil Porcelain Bond Activator was freshly mixed with the adhesive. Likewise, the experimental adhesives, to which γ-MPTS was added, revealed a significantly higher bond strength, but only when the adhesive was applied immediately after mixing; delayed application resulted in a significantly lower bond strength. FTIR and (13)C NMR revealed hydrolysis and dehydration condensation to progress with the time after γ-MPTS was mixed with the two adhesives. After thermo-cycling, the bond strength onto CAD-CAM composite blocks remained stable only for the two adhesives with which Clearfil Porcelain Bond Activator was mixed. Only the silane coupling effect of freshly prepared silanecontaining adhesives was effective. Clinically, the use of a separate silane primer or silane freshly mixed with the adhesive remains recommended to bond glass-rich ceramics. Copyright © 2016 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.
Cocrystals of 6-propyl-2-thiouracil: N-H···O versus N-H···S hydrogen bonds.

PubMed

Tutughamiarso, Maya; Egert, Ernst

2011-11-01

In order to investigate the relative stability of N-H···O and N-H···S hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C(4)H(5)N(3)·2C(7)H(10)N(2)OS, (I), the `base pair' is connected by one N-H···S and one N-H···N hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-H···S hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C(9)H(11)N(3)O(2)·2C(7)H(10)N(2)OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C(7)H(10)N(2)OS, (III), is stabilized by pairwise N-H···O and N-H···S hydrogen bonds. In all three structures, N-H···S hydrogen bonds occur only within R(2)(2)(8) patterns, whereas N-H···O hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.
Intramolecular hydrogen bonding in malonaldehyde and its radical analogues.

PubMed

Lin, Chen; Kumar, Manoj; Finney, Brian A; Francisco, Joseph S

2017-09-28

High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA RS , and cis-MA RA , both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA RA , in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA RS , in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ * orbital of acceptor O-H bond (n → σ * OH ). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA RS .
Role of halogen and hydrogen bonds for stabilization of antithyroid drugs with hypohalous acids (HOX, X = I, Br, and Cl) adducts

NASA Astrophysics Data System (ADS)

El-Sheshtawy, Hamdy S.; El-Mehasseb, Ibrahim

2017-11-01

The mechanism for the inhibition of thyroid hormones by the thioamide-like antithyroid drug is a key process in the thyroid gland function. Therefore, in this study theoretical investigation of the molecular interaction between two antithyroid drugs, namely methimazol (MMI) and thiazoline-2-thione (T2T), with the hypohalous acids (HOX, X = I, Br, and Cl), which act as heme-linked halogenated species to tyrosine residue was discussed. The calculations were performed by M06-2X and MP2 using aug-cc-pVDZ level of theory. In addition, wB97xd/6-31G* level of theory was used in order to account for the dispersion forces. The results show the possible formation of three adducts, which is stabilized by halogen bond (I), both halogen and hydrogen bonds (II), two hydrogen bonds (III). The binding energies of the complexes reveals stabilization in the order III > II > I. The binding energies of the complexes was increased with increasing the electron affinity and polarizability of halogen atom, the dipole moment of the complexes (I and II), the electrostatic potential on halogen atom (Vmax:i.e σ-hole), and the charge-transfer process through the halogen bond in I. On the other hand, the binding energies of the complexes decreased with increasing the halogen atom electronegativity and the dipole moment of complex III. Natural bond orbital (NBO) analysis was used to investigate the molecular orbital interactions and the charge transfer process upon complexation.
Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study.

PubMed

Brovarets', Ol'ha O; Yurenko, Yevgen P; Hovorun, Dmytro M

2014-01-01

This study aims to cast light on the physico-chemical nature and energetic of the non-conventional CH···O/N H-bonds in the biologically important natural nucleobase pairs using a comprehensive quantum-chemical approach. As a whole, the 36 biologically important pairs, involving canonical and rare tautomers of nucleobases, were studied by means of all available up-to-date state-of-the-art quantum-chemical techniques along with quantum theory "Atoms in molecules" (QTAIM), Natural Bond Orbital (NBO) analysis, Grunenberg's compliance constants theory, geometrical and vibrational analyses to identify the CH···O/N interactions, reveal their physico-chemical nature and estimate their strengths as well as contribution to the overall base-pairs stability. It was shown that all the 38 CH···O/N contacts (25 CH···O and 13 CH···N H-bonds) completely satisfy all classical geometrical, electron-topological, in particular Bader's and "two-molecule" Koch and Popelier's, and vibrational criteria of H-bonding. The positive values of Grunenberg's compliance constants prove that the CH···O/N contacts in nucleobase pairs are stabilizing interactions unlike electrostatic repulsion and anti-H-bonds. NBO analysis indicates the electron density transfer from the lone electron pair of the acceptor atom (O/N) to the antibonding orbital corresponding to the donor group σ(∗)(CH). Moreover, significant increase in the frequency of the out-of-plane deformation modes γ (CH) under the formation of the CH···O (by 17.2÷81.3/10.8÷84.7 cm(-1)) and CH···N (by 32.7÷85.9/9.0÷77.9 cm(-1)) H-bonds at the density functional theory (DFT)/second-order Møller-Plesset (MP2) levels of theory, respectively, and concomitant changes of their intensities can be considered as reliable indicators of H-bonding. The strengths of the CH···O/N interactions, evaluated by means of Espinosa-Molins-Lecomte formula, lie within the range 0.45÷3.89/0.62÷4.10 kcal/mol for the CH···O H-bonds and 1.45÷3.17/1.70÷3.43 kcal/mol for the CH···N H-bonds at the DFT/MP2 levels of theory, respectively. We revealed high linear mutual correlations between the H-bond energy and different physico-chemical parameters of the CH···O/N H-bonds. Based on these observations, the authors asserted that the most reliable descriptors of the H-bonding are the electron density ρ at the СН···О/N H-bond critical points and the NBO calculated stabilization energy E((2)). The linear dependence of the H-bond energy ECH···O/N (in kcal/mol) on the electron density ρ (in atomic units) was established (DFT/MP2): ECH···O = 248.501[Formula: see text]ρ-0.367/260.518[Formula: see text]ρ-0.373 and ECH···N = 218.125[Formula: see text]ρ-0.339/243.599[Formula: see text]ρ-0.441. Red-shifted and blue-shifted CH···O/N H-bonds behave in a similar way and can be described with the same fit parameters. It was found that the A-U HH2 and U-U3 nucleobase pairs are stabilized solely by the CH···O/N H-bonds. At the same time, in the A-U HH1, A-U HH2, A-Asyn 1, A-Asyn 2, A-Asyn 3, A-A4, A-G1, A-G2, G-U1, G-U2, G-U3, G-C HH1, U-U1, U-U2, U-U3 and A-C nucleobase pairs the CH···O/N H-bonds play a prominent role (>30%) in their stabilization. We suppose that unconventional CH···O/N H-bond plays the role of the third "fulcrum", ensuring structurally dynamic similarity of the isomorphic base pairs of different origin, which are incorporated equally well into the structure of the DNA double helix.

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

PubMed

Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Bjørn Olav

2016-04-12

Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity.
Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

PubMed

Bandyopadhyay, D; Bhattacharyya, D

2006-10-15

It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.
Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.
Pregnane Glycosides Interfere With Steroidogenic Enzymes to Down-Regulate Corticosteroid Production in Human Adrenocortical H295R Cells

PubMed Central

KOMARNYTSKY, SLAVKO; ESPOSITO, DEBORA; POULEV, ALEXANDER; RASKIN, ILYA

2013-01-01

A group of bioactive steroidal glycosides (pregnanes) with anorectic activity in animals was isolated from several genera of milkweeds including Hoodia and Asclepias. In this study, we investigated the effects, structure-activity relationships, and mechanism of action of pregnane glycosides on steroidogenesis in human adrenocortical H295R cells. Administration of pregnane glycosides for 24 h suppressed the basal and forskolin-stimulated release of androstenedione, corticosterone, and cortisone from H295R cells. The conversion of progesterone to 11-deoxycorticosterone and 17-hydroxyprogesterone to either androstenedione or 11-deoxycortisol was most strongly affected, with 12-cinnamoyl-, benzoyl-, and tigloyl-containing pregnanes showing the highest activity. Incubation of pregnane glycosides for 24 h had no effect on mRNA transcripts of CYP11A1, CYP21A1, CYP11B1 cytochrome enzymes and steroidogenic acute regulatory protein (StaR) protein, yet resulted in twofold decrease in HSD3B1 mRNA levels. At the same time, pregnane glycosides had no effect on the CYP1, 2, or 3 drug and steroid metabolism enzymes and showed weak Na+/K+ ATPase and glucocorticoid receptor binding. Taken together, these data suggest that pregnane glycosides specifically suppress steroidogenesis through strong inhibition of 11β-hydroxylase and steroid 17-alpha-monooxygenase, and weak inhibition of cytochrome P450 side chain cleavage enzyme and 21β-hydroxylase, but not 3β-hydroxysteroid dehydrogenase/isomerase. PMID:23065845
Induction of apoptosis in colon cancer cells treated with isorhamnetin glycosides from Opuntia ficus-indica pads.

PubMed

Antunes-Ricardo, Marilena; Moreno-García, Beatriz E; Gutiérrez-Uribe, Janet A; Aráiz-Hernández, Diana; Alvarez, Mario M; Serna-Saldivar, Sergio O

2014-12-01

(OFI) contains health-promoting compounds like flavonoids, being the isorhamnetin glycosides the most abundant. We evaluated the effect of OFI extracts with different isorhamnetin glycosides against two different human colon cancer cells (HT-29 and Caco2). The extracts were obtained by alkaline hydrolysis with NaOH at 40 °C during 15, 30 or 60 min. Tri and diglycosides were the most abundant isorhamnetin glycosides, therefore these compounds were isolated to compare their cytotoxic effect with the obtained from the extracts. The OFI extracts and purified isorhamnetin glycosides were more cytotoxic against HT-29 cells than Caco2 cells. OFI-30 exhibited the lowest IC50 value against HT-29 (4.9 ± 0.5 μg/mL) and against Caco2 (8.2 ± 0.3 μg/mL). Isorhamnetin diglycosides IG5 and IG6 were more cytotoxic than pure isorhamnetin aglycone or triglycosides when they were tested in HT-29 cells. Bioluminescent analysis revealed increased activity of caspase 3/7 in OFI extracts-treated cells, particularly for the extract with the highest concentration of isorhamnetin triglycosides. Flow cytometry analysis confirmed that OFI extract and isorhamnetin glycosides induced a higher percentage of apoptosis in HT-29 than in Caco2, while isorhamnetin was more apoptotic in Caco2. This research demonstrated that glycosilation affected antiproliferative effect of pure isorhamnetin glycosides or when they are mixed with other phytochemicals in an extract obtained from OFI.
Mild extraction methods using aqueous glucose solution for the analysis of natural dyes in textile artefacts dyed with Dyer's madder (Rubia tinctorum L.).

PubMed

Ford, Lauren; Henderson, Robert L; Rayner, Christopher M; Blackburn, Richard S

2017-03-03

Madder (Rubia tinctorum L.) has been widely used as a red dye throughout history. Acid-sensitive colorants present in madder, such as glycosides (lucidin primeveroside, ruberythric acid, galiosin) and sensitive aglycons (lucidin), are degraded in the textile back extraction process; in previous literature these sensitive molecules are either absent or present in only low concentrations due to the use of acid in typical textile back extraction processes. Anthraquinone aglycons alizarin and purpurin are usually identified in analysis following harsh back extraction methods, such those using solvent mixtures with concentrated hydrochloric acid at high temperatures. Use of softer extraction techniques potentially allows for dye components present in madder to be extracted without degradation, which can potentially provide more information about the original dye profile, which varies significantly between madder varieties, species and dyeing technique. Herein, a softer extraction method involving aqueous glucose solution was developed and compared to other back extraction techniques on wool dyed with root extract from different varieties of Rubia tinctorum. Efficiencies of the extraction methods were analysed by HPLC coupled with diode array detection. Acidic literature methods were evaluated and they generally caused hydrolysis and degradation of the dye components, with alizarin, lucidin, and purpurin being the main compounds extracted. In contrast, extraction in aqueous glucose solution provides a highly effective method for extraction of madder dyed wool and is shown to efficiently extract lucidin primeveroside and ruberythric acid without causing hydrolysis and also extract aglycons that are present due to hydrolysis during processing of the plant material. Glucose solution is a favourable extraction medium due to its ability to form extensive hydrogen bonding with glycosides present in madder, and displace them from the fibre. This new glucose method offers an efficient process that preserves these sensitive molecules and is a step-change in analysis of madder dyed textiles as it can provide further information about historical dye preparation and dyeing processes that current methods cannot. The method also efficiently extracts glycosides in artificially aged samples, making it applicable for museum textile artefacts. Copyright © 2017 Elsevier B.V. All rights reserved.
Insight into destabilization mechanism of Mg-based hydrides interstitially co-doped with nonmetals: a DFT study

NASA Astrophysics Data System (ADS)

Wu, Zhen; Zhu, Luying; Yang, Fusheng; Zhang, Zaoxiao; Nyamsi, Serge N.

2018-04-01

Mg-based metal hydride is one of the most promising materials for hydrogen energy storage. However, the high thermal stability due to strong bonding effects between the atoms limits its practical application. In order to reduce the thermal stability, a method of doping double nonmetals into Mg-based system was proposed in this study. The density functional theory (DFT) calculation results showed that the thermal stabilities of both the B-N co-doped Mg-based alloy and its hydride are reduced compared with pure Mg-based system. The relative formation enthalpies of the alloy and its hydride are 0.323 and 0.595 eV atom-1, respectively. The values are much higher than those for either singly B- or N-doped Mg-based system. The more significant destabilization by doping double nonmetal elements than single element is mainly attributed to a dual effect in weakening Mg-Ni/NiH4 bonds, caused by criss-cross interactions between B-Ni and N-Mg bonds.
Formation of Supported Graphene Oxide: Evidence for Enolate Species.

PubMed

Novotny, Zbynek; Nguyen, Manh-Thuong; Netzer, Falko P; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Dohnálek, Zdenek

2018-04-18

Graphene oxides are promising materials for novel electronic devices or anchoring of the active sites for catalytic applications. Here we focus on understanding the atomic oxygen (AO) binding and mobility on different regions of graphene (Gr) on Ru(0001). Differences in the Gr/Ru lattices result in the superstructure, which offers an array of distinct adsorption sites. We employ scanning tunneling microscopy and density functional theory to map out the chemical identity and stability of prepared AO functionalities in different Gr regions. The AO diffusion is utilized to establish that in the regions that are close to the metal substrate the terminally bonded enolate groups are strongly preferred over bridge-bonded epoxy groups. No oxygen species are observed on the graphene regions that are far from the underlying Ru, indicating their low relative stability. This study provides a clear fundamental basis for understanding the local structural, electronic factors and C-Ru bond strengthening/weakening processes that affect the stability of enolate and epoxy species.
5-Nitrosalicylic Acid as a Novel Matrix for In-Source Decay in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

PubMed Central

Asakawa, Daiki

2013-01-01

The matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) of peptides and glycans was studied using an oxidizing chemical, 5-nitrosalicylic acid (5-NSA) as the matrix. The use of 5-NSA for the MALDI-ISD of peptides and glycans promoted fragmentation pathways involving “hydrogen-deficient” radical precursors. Hydrogen abstraction from peptides resulted in the production of a “hydrogen-deficient” peptide radical that contained a radical site on the amide nitrogen in the peptide backbone with subsequent radical-induced cleavage at the Cα–C bonds. Cleavage at the Cα–C bond leads to the production of an a•/x fragment pair and the radical a• ions then undergo further hydrogen abstraction to form a ions after Cα–C bond cleavage. Since the Pro residue does not contain a nitrogen-centered radical site, Cα–C bond cleavage does not occur at this site. Alternatively, the specific cleavage of CO−N bonds leads to a b•/y fragment pair at Xxx−Pro which occurs via hydrogen abstraction from the Cα−H in the Pro residue. In contrast, “hydrogen-deficient” glycan radicals were generated by hydrogen abstraction from hydroxyl groups in glycans. Both glycosidic and cross-ring cleavages occurred as the result of the degradation of “hydrogen-deficient” glycan radicals. Cross-ring cleavage ions are potentially useful in linkage analysis, one of the most critical steps in the characterization of glycans. Moreover, isobaric glycans could be distinguished by structure specific ISD ions, and the molar ratio of glycan isomers in a mixture can be estimated from their fragment ions abundance ratios. MALDI-ISD with 5-NSA could be a useful method for the sequencing of peptides including the location of post-translational modifications, identification and semi-quantitative analysis of mixtures of glycan isomers. PMID:24860709
Frequency References for Gravitational Wave Missions

NASA Technical Reports Server (NTRS)

Preston, Alix; Thrope, J. I.; Donelan, D.; Miner, L.

2012-01-01

The mitigation of laser frequency noise is an important aspect of interferometry for LISA-like missions. One portion of the baseline mitigation strategy in LISA is active stabilization utilizing opto-mechanical frequency references. The LISA optical bench is an attractive place to implement such frequency references due to its environmental stability and its access to primary and redundant laser systems. We have made an initial investigation of frequency references constructed using the techniques developed for the LISA and LISA Pathfinder optical benches. Both a Mach-Zehnder interferometer and triangular Fabry-Perot cavity have been successfully bonded to a Zerodur baseplate using the hydroxide bonding method. We will describe the construction of the bench along with preliminary stability results.
Dietary flavonoid aglycones and their glycosides: Which show better biological significance?

PubMed

Xiao, Jianbo

2017-06-13

The dietary flavonoids, especially their glycosides, are the most vital phytochemicals in diets and are of great general interest due to their diverse bioactivity. The natural flavonoids almost all exist as their O-glycoside or C-glycoside forms in plants. In this review, we summarized the existing knowledge on the different biological benefits and pharmacokinetic behaviors between flavonoid aglycones and their glycosides. Due to various conclusions from different flavonoid types and health/disease conditions, it is very difficult to draw general or universally applicable comments regarding the impact of glycosylation on the biological benefits of flavonoids. It seems as though O-glycosylation generally reduces the bioactivity of these compounds - this has been observed for diverse properties including antioxidant activity, antidiabetes activity, anti-inflammation activity, antibacterial, antifungal activity, antitumor activity, anticoagulant activity, antiplatelet activity, antidegranulating activity, antitrypanosomal activity, influenza virus neuraminidase inhibition, aldehyde oxidase inhibition, immunomodulatory, and antitubercular activity. However, O-glycosylation can enhance certain types of biological benefits including anti-HIV activity, tyrosinase inhibition, antirotavirus activity, antistress activity, antiobesity activity, anticholinesterase potential, antiadipogenic activity, and antiallergic activity. However, there is a lack of data for most flavonoids, and their structures vary widely. There is also a profound lack of data on the impact of C-glycosylation on flavonoid biological benefits, although it has been demonstrated that in at least some cases C-glycosylation has positive effects on properties that may be useful in human healthcare such as antioxidant and antidiabetes activity. Furthermore, there is a lack of in vivo data that would make it possible to make broad generalizations concerning the influence of glycosylation on the benefits of flavonoids for human health. It is possible that the effects of glycosylation on flavonoid bioactivity in vitro may differ from that seen in vivo. With in vivo (oral) treatment, flavonoid glycosides showed similar or even higher antidiabetes, anti-inflammatory, antidegranulating, antistress, and antiallergic activity than their flavonoid aglycones. Flavonoid glycosides keep higher plasma levels and have a longer mean residence time than those of aglycones. We should pay more attention to in vivo benefits of flavonoid glycosides, especially C-glycosides.
Bond angles in transition metal tetracarbonyl compounds: A further test of the theory of hybrid bond orbitals*

PubMed Central

Pauling, Linus

1978-01-01

An equation for the bond angles OC—M—CO for tetracarbonyl groups in which the transition metal atom M is enneacovalent, derived from the simple theory of hybrid sp3d5 bond orbitals, is tested by comparison of the calculated values of the angles with the experimental values reported for many compounds containing M(CO)4 groups, especially those with M = Fe, Mn, Re, Cr, or Mo. The importance of the energy of resonance of single bonds and double bonds in stabilizing octahedral complexes of chromium and manganese with carbonyl, phosphine, arsine, and thio groups is also discussed. PMID:16592490
Experimental studies on the nature of bonding of DNA/bipyridyl-(ethylenediamine)platinum(II) and DNA/netropsin complexes in solution and oriented wet-spun films

NASA Astrophysics Data System (ADS)

Marlowe, R. L.; Szabo, A.; Lee, S. A.; Rupprecht, A.

2002-03-01

The stability of complexes of NaDNA with bipyridyl-(ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)]) and with netropsin has been studied using two techniques: (i) ultraviolet melting experiments were done on NaDNA/[(bipy)Pt(en)], showing that the [(bipy)Pt(en)] ligand stabilizes the DNA double helix structure; and (ii) swelling measurements (via optical microscopy) as a function of relative humidity were done on wet-spun oriented films of NaDNA/[(bipy)Pt(en)] and of NaDNA/netropsin. The swelling data shows that an irreversible transition of the films occurs at high relative humidity, first for the NaDNA/netropsin, then for pure NaDNA, and lastly for the NaDNA/[(bipy)Pt(en)]. These results are indicative that the [(bipy)Pt(en)] complex stabilizes the intermolecular bonds which mediate the film swelling characteristics. A model is suggested for the binding of [(bipy)Pt(en)] to DNA to explain why the swelling experiments show this ligand as increasing the intermolecular bond strength between the DNA double helices, while netropsin decreases this degree of stabilization.
Engineered disulfide bonds increase active-site local stability and reduce catalytic activity of a cold-adapted alkaline phosphatase.

PubMed

Asgeirsson, Bjarni; Adalbjörnsson, Björn Vidar; Gylfason, Gudjón Andri

2007-06-01

Alkaline phosphatase is an extracellular enzyme that is membrane-bound in eukaryotes but resides in the periplasmic space of bacteria. It normally carries four cysteine residues that form two disulfide bonds, for instance in the APs of Escherichia coli and vertebrates. An AP variant from a Vibrio sp. has only one cysteine residue. This cysteine is second next to the nucleophilic serine in the active site. We have individually modified seven residues to cysteine that are on two loops predicted to be within a 5 A radius. Four of them formed a disulfide bond to the endogenous cysteine. Thermal stability was monitored by circular dichroism and activity measurements. Global stability was similar to the wild-type enzyme. However, a significant increase in heat-stability was observed for the disulfide-containing variants using activity as a measure, together with a large reduction in catalytic rates (k(cat)) and a general decrease in Km values. The results suggest that a high degree of mobility near the active site and in the helix carrying the endogenous cysteine is essential for full catalytic efficiency in the cold-adapted AP.
Hydrogen-bond symmetrization breakdown and dehydrogenation mechanism in FeO2H at high pressure

NASA Astrophysics Data System (ADS)

Hu, Q.; Zhu, S.; Mao, H. K.; Mao, W. L.; Sheng, H.

2017-12-01

The cycling of hydrogen plays an important role in the geochemical evolution of our planet. In Earth's interiors, hydrogen cycling is mainly carried out by hydrous minerals. Under high-pressure conditions, asymmetric hydroxyl bonds in hydrous minerals tend to form a symmetric O-H-O configuration that improves their thermal stability. Therefore it is possible to transport water into the deeper part of the Earth's lower mantle. Here, we employ first-principles free-energy landscape sampling methods based on a recently developed stochastic surface walking algorithm to reveal the transition mechanism of a water-bearing mineral, FeO2H, at deep mantle conditions. By resolving the lowest-energy transition pathway from ɛ-FeO2H to the high-pressure Py-phase, we demonstrate that half of the O-H bonds in the mineral rupture during the structural transition, leading toward the breakdown of symmetrized hydrogen bonds and eventual dehydrogenation. Our study sheds new light on the stability of symmetric hydrogen bonds in hydrous minerals during structural transitions and suggests a dehydrogenation mechanism from water in the deep mantle.
Spectroscopic Identification of the Au-C Bond Formation upon Electroreduction of an Aryl Diazonium Salt on Gold.

PubMed

Guo, Limin; Ma, Lipo; Zhang, Yelong; Cheng, Xun; Xu, Ye; Wang, Jin; Wang, Erkang; Peng, Zhangquan

2016-11-08

Electroreduction of aryl diazonium salts on gold can produce organic films that are more robust than their analogous self-assembled monolayers formed from chemical adsorption of organic thiols on gold. However, whether the enhanced stability is due to the Au-C bond formation remains debated. In this work, we report the electroreduction of an aryl diazonium salt of 4,4'-disulfanediyldibenzenediazonium on gold forming a multilayer of Au-(Ar-S-S-Ar) n , which can be further degraded to a monolayer of Au-Ar-S - by electrochemical cleavage of the S-S moieties within the multilayer. By conducting an in situ surface-enhanced Raman spectroscopic study of both the multilayer formation/degradation and the monolayer reduction/oxidation processes, coupled to density functional theory calculations, we provide compelling evidence that an Au-C bond does form upon electroreduction of aryl diazonium salts on gold and that the enhanced stability of the electrografted organic films is due to the Au-C bond being intrinsically stronger than the Au-S bond for a given phenylthiolate compound by ca. 0.4 eV.
Synthesis and evaluation of di- and trimeric hydroxylamine-based β-(1→3)-glucan mimetics.

PubMed

Ferry, Angélique; Malik, Gaëlle; Guinchard, Xavier; Vĕtvička, Václav; Crich, David

2014-10-22

Di- and trimeric hydroxylamine-based mimetics of β-(1→3)-glucans have been accessed by an asymmetric synthesis route featuring an iterative double ring-closing reductive amination reaction. These oligomeric hydroxylamines are demonstrated to inhibit the staining of human neutrophils and of mouse macrophages by fluorescent anti-CR3 and anti-dectin-1 antibodies, respectively, and to stimulate phagocytosis, all in a linkage-dependent manner suggestive of binding to the lectin domains of complement receptor 3 (CR3) and dectin-1. The ability of these relatively short mimetics to bind to CR3 and dectin-1, as compared to the greater degree of polymerization required in β-(1→3)-glucans, is discussed in terms of the increased hydrophobicity of the α-face on replacement of the glycosidic bond by the hydroxylamine linkage.
The amylase inhibitor montbretin A reveals a new glycosidase inhibition motif.

PubMed

Williams, Leslie K; Zhang, Xiaohua; Caner, Sami; Tysoe, Christina; Nguyen, Nham T; Wicki, Jacqueline; Williams, David E; Coleman, John; McNeill, John H; Yuen, Violet; Andersen, Raymond J; Withers, Stephen G; Brayer, Gary D

2015-09-01

The complex plant flavonol glycoside montbretin A is a potent (Ki = 8 nM) and specific inhibitor of human pancreatic α-amylase with potential as a therapeutic for diabetes and obesity. Controlled degradation studies on montbretin A, coupled with inhibition analyses, identified an essential high-affinity core structure comprising the myricetin and caffeic acid moieties linked via a disaccharide. X-ray structural analyses of the montbretin A-human α-amylase complex confirmed the importance of this core structure and revealed a novel mode of glycosidase inhibition wherein internal π-stacking interactions between the myricetin and caffeic acid organize their ring hydroxyls for optimal hydrogen bonding to the α-amylase catalytic residues D197 and E233. This novel inhibitory motif can be reproduced in a greatly simplified analog, offering potential for new strategies for glycosidase inhibition and therapeutic development.
Constraints on Biogenic Emplacement of Crystalline Calcium Carbonate and Dolomite

NASA Astrophysics Data System (ADS)

Colas, B.; Clark, S. M.; Jacob, D. E.

2015-12-01

Amorphous calcium carbonate (ACC) is a biogenic precursor of calcium carbonates forming shells and skeletons of marine organisms, which are key components of the whole marine environment. Understanding carbonate formation is an essential prerequisite to quantify the effect climate change and pollution have on marine population. Water is a critical component of the structure of ACC and the key component controlling the stability of the amorphous state. Addition of small amounts of magnesium (1-5% of the calcium content) is known to promote the stability of ACC presumably through stabilization of the hydrogen bonding network. Understanding the hydrogen bonding network in ACC is fundamental to understand the stability of ACC. Our approach is to use Monte-Carlo simulations constrained by X-ray and neutron scattering data to determine hydrogen bonding networks in ACC as a function of magnesium doping. We have already successfully developed a synthesis protocol to make ACC, and have collected X-ray data, which is suitable for determining Ca, Mg and O correlations, and have collected neutron data, which gives information on the hydrogen/deuterium (as the interaction of X-rays with hydrogen is too low for us to be able to constrain hydrogen atom positions with only X-rays). The X-ray and neutron data are used to constrain reverse Monte-Carlo modelling of the ACC structure using the Empirical Potential Structure Refinement program, in order to yield a complete structural model for ACC including water molecule positions. We will present details of our sample synthesis and characterization methods, X-ray and neutron scattering data, and reverse Monte-Carlo simulations results, together with a discussion of the role of hydrogen bonding in ACC stability.
Noncovalent Organocatalysis Based on Hydrogen Bonding: Elucidation of Reaction Paths by Computational Methods

NASA Astrophysics Data System (ADS)

Etzenbach-Effers, Kerstin; Berkessel, Albrecht

In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

Relative stabilities of IgG1 and IgG4 Fab domains: Influence of the light–heavy interchain disulfide bond architecture

PubMed Central

Heads, James T; Adams, Ralph; D'Hooghe, Lena E; Page, Matt J T; Humphreys, David P; Popplewell, Andrew G; Lawson, Alastair D; Henry, Alistair J

2012-01-01

The stability of therapeutic antibodies is a prime pharmaceutical concern. In this work we examined thermal stability differences between human IgG1 and IgG4 Fab domains containing the same variable regions using the thermofluor assay. It was found that the IgG1 Fab domain is up to 11°C more stable than the IgG4 Fab domain containing the same variable region. We investigated the cause of this difference with the aim of developing a molecule with the enhanced stability of the IgG1 Fab and the biological properties of an IgG4 Fc. We found that replacing the seven residues, which differ between IgG1 CH1 and IgG4 CH1 domains, while retaining the native IgG1 light-heavy interchain disulfide (L–H) bond, did not affect thermal stability. Introducing the IgG1 type L–H interchain disulfide bond (DSB) into the IgG4 Fab resulted in an increase in thermal stability to levels observed in the IgG1 Fab with the same variable region. Conversely, replacement of the IgG1 L–H interchain DSB with the IgG4 type L–H interchain DSB reduced the thermal stability. We utilized the increased stability of the IgG1 Fab and designed a hybrid antibody with an IgG1 CH1 linked to an IgG4 Fc via an IgG1 hinge. This construct has the expected biophysical properties of both the IgG4 Fc and IgG1 Fab domains and may therefore be a pharmaceutically relevant format. PMID:22761163
Accumulation of Flavonoid Glycosides and UFGT Gene Expression in Mulberry Leaves (Morus alba L.) before and after Frost.

PubMed

Yu, Xiaofeng; Zhu, Yiling; Fan, Jingyi; Wang, Dujun; Gong, Xiaohui; Ouyang, Zhen

2017-08-01

In order to determine the molecular mechanism underlying the influence of frost on chemical changes in mulberry leaves, the UFGT activity, expression level, and accumulation of flavonoid glycosides in mulberry leaves (Morus alba L.) were studied. The expression of UFGT gene was investigated by quantitative real-time PCR (qRT-PCR) and the UFGT activity, accumulation of flavonoid glycosides was studied by high performance liquid chromatography. Then, the correlation between the expression level of UFGT, the UFGT activity, and the flavonoid glycosides accumulation with temperature was explored. The accumulation of isoquercitrin and astragalin is significantly positively correlated with UFGT gene expression and UFGT activity. On the contrary, the average temperature was significantly negatively correlated with the level of UFGT gene expression and UFGT activity. The results show that after frost, low temperature can induce the expression of UFGT gene in mulberry leaves, resulting in the accumulation of flavonoid glycosides. © 2017 Wiley-VHCA AG, Zurich, Switzerland.
Fabrication of a biofuel cell improved by the π-conjugated electron pathway effect induced from a new enzyme catalyst employing terephthalaldehyde

NASA Astrophysics Data System (ADS)

Chung, Yongjin; Hyun, Kyu Hwan; Kwon, Yongchai

2015-12-01

A model explaining the π-conjugated electron pathway effect induced by a novel cross-linker adopted enzyme catalyst is suggested and the performance and stability of an enzymatic biofuel cell (EBC) adopting the new catalyst are evaluated. For this purpose, new terephthalaldehyde (TPA) and conventional glutaraldehyde (GA) cross-linkers are adopted on a glucose oxidase (GOx), polyethyleneimine (PEI) and carbon nanotube (CNT)(GOx/PEI/CNT) structure. GOx/PEI/CNT cross-linked by TPA (TPA/[GOx/PEI/CNT]) results in a superior EBC performance and stability to other catalysts. It is attributed to the π bonds conjugated between the aldehyde of TPA and amine of the GOx/PEI molecules. By π conjugation, electrons bonded with carbon and nitrogen are delocalized, promoting the electron transfer and catalytic activity with an excellent EBC performance. The maximum power density (MPD) of an EBC adopting TPA/[GOx/PEI/CNT] (0.66 mW cm-2) is far better than that of the other EBCs (the MPD of EBC adopting GOx/PEI/CNT is 0.40 mW cm-2). Regarding stability, the covalent bonding formed between TPA and GOx/PEI plays a critical role in preventing the denaturation of GOx molecules, leading to an excellent stability. By repeated measurements of the catalytic activity, TPA/[GOx/PEI/CNT] maintains its activity to 92% of its initial value even after five weeks.A model explaining the π-conjugated electron pathway effect induced by a novel cross-linker adopted enzyme catalyst is suggested and the performance and stability of an enzymatic biofuel cell (EBC) adopting the new catalyst are evaluated. For this purpose, new terephthalaldehyde (TPA) and conventional glutaraldehyde (GA) cross-linkers are adopted on a glucose oxidase (GOx), polyethyleneimine (PEI) and carbon nanotube (CNT)(GOx/PEI/CNT) structure. GOx/PEI/CNT cross-linked by TPA (TPA/[GOx/PEI/CNT]) results in a superior EBC performance and stability to other catalysts. It is attributed to the π bonds conjugated between the aldehyde of TPA and amine of the GOx/PEI molecules. By π conjugation, electrons bonded with carbon and nitrogen are delocalized, promoting the electron transfer and catalytic activity with an excellent EBC performance. The maximum power density (MPD) of an EBC adopting TPA/[GOx/PEI/CNT] (0.66 mW cm-2) is far better than that of the other EBCs (the MPD of EBC adopting GOx/PEI/CNT is 0.40 mW cm-2). Regarding stability, the covalent bonding formed between TPA and GOx/PEI plays a critical role in preventing the denaturation of GOx molecules, leading to an excellent stability. By repeated measurements of the catalytic activity, TPA/[GOx/PEI/CNT] maintains its activity to 92% of its initial value even after five weeks. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06703k
Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.
Simultaneous quantitative assessment of nine glycosides in tobacco by liquid chromatography-tandem mass spectrometry.

PubMed

Yuan, Yue; Zhou, Rong; Li, Dongliang; Luo, Cheng; Li, Guoyou

2018-03-01

A simple and efficient method combining ultrasound-assisted extraction, the conditions of which were optimized by response surface methodology, with liquid chromatography and tandem mass spectrometry was established and validated for the absolute quantification of nine non-volatile neutral glycosides originating from tobacco (Nicotiana tobaccum L.) leaves, comprising three phenolic glycosides, one benzanoid glycoside, and five sesquiterpene glycosides within three isomers, originating from tobacco leaves. Factors of extraction time, sample quantity, extraction solvent, liquid chromatographic conditions, and electrospray ionization parameters were carefully investigated to ensure the selectivity and sensitivity of the method. All calibration curves showed excellent coefficients of determination ranging from 0.9940 to 0.9996, within the range of tested concentrations. The limits of detection and quantification were 2.33-25.9 and 7.06-78.5 ng/mL, respectively. Satisfactory values of accuracy were between 80.1 to 107.9% among different sample matrixes. The relative standard deviations of intra- and inter-day analysis were less than 13.7 and 13.0% respectively. The developed method was successfully applied in a pilot study to determine the amounts of the nine endogenous glycosides in real flue-cured tobacco samples obtained from different habitats in China. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Investigation of different concentrations of MS media effects on gene expression and steviol glycosides accumulation in Stevia rebaudiana Bertoni.

PubMed

Kahrizi, Danial; Ghaheri, Matin; Yari, Zahra; Yari, Khirollah; Bahraminejad, Sohbat

2018-02-10

Stevia rebaudiana Bertoni is one of two species that contains steviol glycosides. Among steviol glycosides that extracted from leaves, stevioside and rebaudioside A are the two major and the sweetest glycosides that are about 200-300 times sweeter than sucrose with zero calories. The best method for stevia propagation is tissue culture. So, for investigation of nutrients in medium, we studied the effect of different concentrations of MS media (MS, 0.5 MS, 0.25 MS, 0 MS) on morphological traits, UGT74G1 and UGT76G1 genes expression and accumulation of steviol glycosides in stevia leaves. The best growth rate (0.472 mm/d) has occurred in plants grown in MS media. Also, the highest gene expression of UGT74G1 gene (1.000 Total lab unit) was seen under MS treatment. However, the highest expression level of UGT76G1 gene (1.701 Total lab unit) was observed at plants grown in 0 MS. The highest amount of both Stevioside and Rebaudioside A (14.23 and 8.12, respectively) were accumulated in plants under MS treatment. Obviously, dilution of MS media associated with decreasing in both expression of the intended genes and accumulation of steviol glycosides.
HPLC-DAD-ESI/MS(n) profiling of phenolic compounds from Lathyrus cicera L. seeds.

PubMed

Ferreres, F; Magalhães, S C Q; Gil-Izquierdo, A; Valentão, P; Cabrita, A R J; Fonseca, A J M; Andrade, P B

2017-01-01

Lathyrus cicera L. seeds are of interest for food and feed purposes. Despite the recognized antioxidant activity of the seeds, arising from the phenolic fraction, their phenolic compounds have not been studied in depth yet. Therefore, to determine the phenolics profile of these seeds, a target analysis was performed using high-performance liquid chromatography coupled to photodiode-array detection and electrospray ionization/ion trap mass spectrometry (HPLC-DAD-ESI/MS(n)). Thirty-seven glycosylated flavonoids were identified for the first time in the seeds of this species and, according to their MS fragmentation, clustered in flavonol-3-O-di-/tri-glycosides-7-O-rhamnosides and other flavonol-glycosides, and flavonol-3-O-(cinnamoyl)glycoside-7-O-rhamnosides, flavonol-3-O-(dihydrophaseoyl, cinnamoyl)glycoside-7-O-rhamnosides and flavonol-3-O-(malonyl)glycoside-7-O-rhamnosides. Glycosides of kaempferol were the main flavonoids found (10 non-acylated and 21 acylated), followed by those of quercetin (3) and those of isorhamnetin, apigenin and luteolin (1). The most abundant flavonols were identified as kaempferol-3-O-(2-hexosyl)hexoside-7-O-rhamnosides. The methodology used allowed to increase the knowledge on a relevant phytochemical class of seeds from L. cicera. Copyright © 2016 Elsevier Ltd. All rights reserved.
Flavonol glycosides of sea buckthorn (Hippophaë rhamnoides ssp. sinensis) and lingonberry (Vaccinium vitis-idaea) are bioavailable in humans and monoglucuronidated for excretion.

PubMed

Lehtonen, Henna-Maria; Lehtinen, Outi; Suomela, Jukka-Pekka; Viitanen, Matti; Kallio, Heikki

2010-01-13

Glucuronidation and excretion of sea buckthorn and lingonberry flavonols were investigated in a postprandial trial by analyzing the intact forms of flavonol glycosides as well as glucuronides in plasma, urine, and feces. Four study subjects consumed sea buckthorn (study day 1) and lingonberry (study day 2) breakfasts, and blood, urine, and fecal samples were collected for 8, 24, and 48 h, respectively. Both glycosides and glucuronides of the flavonol quercetin as well as kaempferol glucuronides were detected in urine and plasma samples after the consumption of lingonberries; 14% of flavonols in urine were glycosides, and 86% were glucuronidated forms (wt %). After the consumption of sea buckthorn, 5% of flavonols excreted in urine were detected intact, and 95% as the glucuronides (wt %). Solely glucuronides of flavonols isorhamnetin and quercetin were found in plasma after the consumption of sea buckthorn berries. Only glycosides were detected in the feces after each berry trial. Flavonol glycosides and glucuronides remained in blood and urine quite long, and the peak concentrations appeared slightly later than previously described. The berries seemed to serve as a good flavonol supply, providing steady flavonol input for the body for a relatively long time.
Simultaneous analysis of steviol and steviol glycosides by liquid chromatography with ultraviolet detection on a mixed-mode column: application to Stevia plant material and Stevia-containing dietary supplements.

PubMed

Jaworska, Karolina; Krynitsky, Alexander J; Rader, Jeanne I

2012-01-01

Simultaneous separation of steviol and steviol glycosides is challenging because of differences in their polarity and chemical structure. In this study, simultaneous analysis of steviol and steviol glycosides was achieved by LC with UV detection using a mixed-mode RP weak anion exchange chromatography column. Steviol and seven steviol glycosides were analyzed on an Acclaim Mixed-Mode Wax-1 (Dionex) column with a linear gradient of deionized water adjusted to pH 3.00 with phosphoric acid and acetonitrile. The extraction was performed by sonicating dry plant material at 40 degreesC in acetonitrile-water (30 + 70, v/v). LOQ values (mg/g dry weight of plant material) were rebaudioside B, 0.50; steviol, 0.70, dulcoside A, 1.0; steviolbioside, 1.2; stevioside and rebaudioside C, 2.0; rebaudioside D, 3.3; and rebaudioside A, 5.0. The method demonstrated suitable performance for all analytes tested with respect to accuracy (mean recoveries 95-99%), intraday and interday precision for retention times (0.070-0.28% and 0.33-1.0% RSD, respectively), and linearity. The method was used to authenticate steviol glycosides in several samples of Stevia plant material as well as to quantitate steviol glycosides in dietary supplements containing Stevia.
Bioavailability Challenges Associated with Development of Anti-Cancer Phenolics

PubMed Central

Gao, Song; Hu, Ming

2010-01-01

Phenolics including many polyphenols and flavonoids have the potentials to become chemoprevention and chemotherapy agents. However, poor bioavailability limits their biological effects in vivo. This paper reviews the factors that affect phenolics absorption and their bioavailabilities from the points of view of their physicochemical properties and disposition in the gastrointestinal tract. The up-to-date research data suggested that solubility and metabolism are the primary reasons that limit phenolic aglycones’ bioavailability although stability and poor permeation may also contribute to the poor bioavailabilities of the glycosides. Future investigations should further optimize phenolics’ bioavailabilities and realize their chemopreventive and chemotherapeutic effects in vivo. PMID:20370701
Influence of Hemostatic Solution on Bond Strength and Physicochemical Properties of Resin Cement.

PubMed

Araújo, Isabela Sousa de; Prado, Célio Jesus do; Raposo, Luís Henrique Araújo; Soares, Carlos José; Zanatta, Rayssa Ferreira; Torres, Carlos Rocha Gomes; Ruggiero, Reinaldo; Silva, Gisele Rodrigues da

2017-01-01

The aim of this study was to evaluate the degree of conversion, color stability, chemical composition, and bond strength of a light-cured resin cement contaminated with three different hemostatic solutions. Specimens were prepared for the control (uncontaminated resin cement) and experimental groups (resin cement contaminated with one of the hemostatic solutions) according to the tests. For degree of conversion, DC (n = 5) and color analyses (n = 10), specimens (3 mm in diameter and 2 mm thick) were evaluated by Fourier transform infrared spectroscopy (FTIR) and CIELAB spectrophotometry (L*, a*, b*), respectively. For elemental chemical analysis (n = 1), specimens (2 mm thick and 6 mm in diameter) were evaluated by x-ray energy-dispersive spectroscopy (EDS). The bond strengths of the groups were assessed by the microshear test (n = 20) in a leucite-reinforced glass ceramic substrate, followed by failure mode analysis by scanning electron microscopy (SEM). The mean values, except for the elemental chemical evaluation and failure mode, were evaluated by ANOVA and Tukey's HSD test. The color stability was influenced by storage time (p<0.001) and interaction between contamination and storage time (p<0.001). Hemostop and Viscostat Clear contamination did not affect the DC, however Viscostat increased the DC. Bond strength of the resin cement to ceramic was negatively affected by the contaminants (p<0.001). Contamination by hemostatic agents affected the bond strength, degree of conversion, and color stability of the light-cured resin cement tested.
Phenolic Glycosides in Populus tremuloides and their Effects on Long-Term Ungulate Browsing.

PubMed

Lastra, R A; Kenkel, N C; Daayf, F

2017-10-01

In the aspen-grassland ecotone of Riding Mountain, Manitoba, lightly browsed vigorous clones of trembling aspen (Populus tremuloides Michx.) occur in close proximity to heavily browsed dieback clones. This study examines whether intraspecific variation in the production of phenolic glycosides is correlated with this strong dichotomy in clonal vigor. Individual clones were sampled over four years at three sites located along a gradient of increasing soil moisture stress. At each site, eight aspen clones of similar size and age were sampled: four vigorous and four dieback clones (total of 24 individual clones). The severity of wapiti (elk) browsing was assessed as the ratio of browse-damaged to total branches per aspen ramet. Statistically significant differences in foliar concentrations of the phenolic glycosides salicortin and tremulacin were observed between vigorous and dieback clones: a mean of 14.8% dry mass for lightly browsed (vigorous) clones, versus just 7.0% for heavily browsed (dieback) clones. Mean concentrations of foliar phenolics were also significantly greater in more moisture-stressed sites. These results demonstrate that the strong dichotomy in clonal vigor (vigorous versus dieback clones) is associated with large differences in phenolic glycoside production. Vigorous clone ramets produce high amounts of phenolic glycosides and have low levels of herbivore browsing and low mortality rates, whereas dieback clone ramets have low amounts of phenolic glycosides and much higher herbivore browsing and mortality rates. This suggests that intraspecific variation in phenolic glycosides in trembling aspen is an important predisposing factor leading to ramet mortality, and by extension to the decline of aspen clones.
Inhibiting Na+/K+ ATPase can impair mitochondrial energetics and induce abnormal Ca2+ cycling and automaticity in guinea pig cardiomyocytes.

PubMed

Li, Qince; Pogwizd, Steven M; Prabhu, Sumanth D; Zhou, Lufang

2014-01-01

Cardiac glycosides have been used for the treatment of heart failure because of their capabilities of inhibiting Na+/K+ ATPase (NKA), which raises [Na+]i and attenuates Ca2+ extrusion via the Na+/Ca2+ exchanger (NCX), causing [Ca2+]i elevation. The resulting [Ca2+]i accumulation further enhances Ca2+-induced Ca2+ release, generating the positive inotropic effect. However, cardiac glycosides have some toxic and side effects such as arrhythmogenesis, confining their extensive clinical applications. The mechanisms underlying the proarrhythmic effect of glycosides are not fully understood. Here we investigated the mechanisms by which glycosides could cause cardiac arrhythmias via impairing mitochondrial energetics using an integrative computational cardiomyocyte model. In the simulations, the effect of glycosides was mimicked by blocking NKA activity. Results showed that inhibiting NKA not only impaired mitochondrial Ca2+ retention (thus suppressed reactive oxygen species (ROS) scavenging) but also enhanced oxidative phosphorylation (thus increased ROS production) during the transition of increasing workload, causing oxidative stress. Moreover, concurrent blocking of mitochondrial Na+/Ca2+ exchanger, but not enhancing of Ca2+ uniporter, alleviated the adverse effects of NKA inhibition. Intriguingly, NKA inhibition elicited Ca2+ transient and action potential alternans under more stressed conditions such as severe ATP depletion, augmenting its proarrhythmic effect. This computational study provides new insights into the mechanisms underlying cardiac glycoside-induced arrhythmogenesis. The findings suggest that targeting both ion handling and mitochondria could be a very promising strategy to develop new glycoside-based therapies in the treatment of heart failure.
MOLECULAR BONDING SYSTEM - INNOVATIVE TECHNOLOGY EVALUATION REPORT

EPA Science Inventory

This document presents an evaluation of the Molecular Bonding System (MBS) and its ability to chemically stabilize three metals-contaminated wstes/soils during a SITe demo. The MBS process treated approximately 500 tons each of soil/Fill, Slag, and Miscellaneous Smelter Waste wit...
Nectar chemistry mediates the behavior of parasitized bees: consequences for plant fitness.

PubMed

Richardson, Leif L; Bowers, M Deane; Irwin, Rebecca E

2016-02-01

Plants produce an array of secondary metabolites that play important ecological roles as anti-herbivore and anti-pathogen defenses. Many herbivores experience physiological costs when they consume secondary metabolites, yet some also benefit, for example when these chemicals confer resistance to parasites and predators. Secondary metabolites are often present in nectar and pollen, which is paradoxical given that floral rewards are important in the attraction of mutualists rather than deterrence of antagonists. Motivated by studies of interactions among plants, herbivores, and parasites, as well as research showing that secondary metabolites can reduce bee disease, we characterized the occurrence of two iridoid glycosides, aucubin and catalpol, in floral rewards and other tissues of the bee pollinated plant, Chelone glabra. We then experimentally investigated effects of nectar iridoid glycoside concentrations on the foraging behavior of bumble bee pollinators naturally afflicted by a parasitoid fly and a protozoan intestinal parasite, and subsequent effects on an estimate of plant reproduction. We found that floral nectar had lower iridoid glycoside concentrations than leaves, pollen, and corollas, and that, compared to those plant parts, the relative ratio of the two primary iridoid glycosides, aucubin and catalpol, was reversed in nectar. Whether bees carried parasitoid fly larvae did not affect their response to nectar chemistry; however, there was a significant interaction between protozoan parasite infection and nectar treatment, with infected bees foraging longer at flowers with high compared to low nectar iridoid glycoside concentrations. Parasitized bees were also more likely to return to inflorescences with high iridoid glycoside nectar. Consequently, flowers in the high iridoid glycoside nectar treatment donated significantly more pollen to conspecific stigmas than did flowers in the low iridoid glycoside treatment, suggesting an increase in male plant fitness. Taken together, these results demonstrate that nectar secondary metabolites can mediate the behavior of pollinators with subsequent benefits for estimates of plant reproduction.
The influence of stevia glycosides on the growth of Lactobacillus reuteri strains.

PubMed

Deniņa, I; Semjonovs, P; Fomina, A; Treimane, R; Linde, R

2014-03-01

Use of stevia-derived sweeteners was recently officially approved by the European Commission, and their application in the food industry has increased, especially in functional foods. However, there are scarce data about the influence of stevia on probiotic bacteria, which are important both as an inhabitant of the human gut and as a functional food additive. Taking into consideration the broad application of Lactobacillus reuteri in functional foods, the aim of the research was to evaluate the influence of stevia glycosides on its growth. Six Lact. reuteri strains were tested for their ability to grow in the presence of stevioside and rebaudioside A (0·2-2·6 g l(-1) ). The effect of stevia glycosides on biomass concentration, cell count, pH and lactic and acetic acid synthesis was analysed. Both glycosides impaired the growth of analysed strains. However, the inhibitory effect was strain specific, and the concentration-dependent effect was not observed for all parameters. The most pronounced concentration-dependent effect was on lactic and acetic acid production. Taking into account the observed strain-specific inhibitory effect of stevia glycosides, it could be suggested to evaluate the influence of them on each strain employed before their simultaneous application in functional foods. The study showed that the growth of Lactobacillus reuteri strains was inhibited in the presence of stevia sweeteners stevioside and rebaudioside A. Probiotics, for example Lact. reuteri strains, are often used as functional additives in health foods and are an important natural inhabitant of the human gastrointestinal tract. Stevia glycosides application in food is increasing; yet, there are no data about the influence of stevia glycosides on Lact. reuteri growth and very few data on growth of other lactobacilli, either in probiotic foods or in the gastrointestinal tract. This research shows that it is necessary to evaluate the influence of stevia glycosides on other groups of micro-organisms in further research. © 2013 The Society for Applied Microbiology.
Apoptotic activities of cardenolide glycosides from Asclepias subulata.

PubMed

Rascón-Valenzuela, L A; Velázquez, C; Garibay-Escobar, A; Vilegas, W; Medina-Juárez, L A; Gámez-Meza, N; Robles-Zepeda, R E

2016-12-04

Asclepias subulata Decne. (Apocynaceae) is a shrub occurring in Sonora-Arizona desert. The ethnic groups of Sonora, Mexico, Seris and Pimas, use this plant for the treatment of sore eyes, gastrointestinal disorders and cancer. To determine the cell death pathways that the cardenolide glycosides with antiproliferative activity found in the methanol extract of A. subulata are able to activate. The effect of cardenolide glycosides isolated of A. subulata on induction of apoptosis in cancer cells was evaluated through the measuring of several key events of apoptosis. A549 cells were treated for 12h with doses of 3.0, 0.2, 3.0 and 1.0µM of 12, 16-dihydroxicalotropin, calotropin, corotoxigenin 3-O-glucopyranoside and desglucouzarin, respectively. Apoptotic and necrotic cell levels were measured by double staining with annexin V-FITC/PI. Mitochondrial membrane depolarization was examined through JC-1 staining. Apoptosis cell death and the apoptosis pathways activated by cardenolide glycosides isolated of A. subulata were further characterized by the measurement of caspase-3, caspase-8 and caspase-9 activity. Apoptotic assays showed that the four cardenolide glycosides isolated of A. subulata induced apoptosis in A549 cells, which was evidencing by phosphatidylserine externalization in 18.2%, 17.0%, 23.9% and 22.0% for 12, 16-dihydroxicalotropin, calotropin, corotoxigenin 3-O-glucopyranoside and desglucouzarin, respectively, compared with 4.6% of control cells. Cell death was also associated with a decrease in mitochondrial membrane potential, which was more than 75% in the treated cultures respect to control. The activation of caspase-3 was observed in all cardenolide glycosides-treated cancer cells indicating the caspase-dependent apoptosis of A549 cells. Extrinsic and intrinsic apoptosis pathways were activated by cardenolide glycosides treatment at the doses tested. In this study was found that cardenolide glycosides, 12, 16-dihydroxicalotropin, calotropin, corotoxigenin 3-O-glucopyranoside and desglucouzarin, isolated from A. subulata induced the cell death trough caspase-dependent apoptosis, which was activated, preferably, by extrinsic pathway. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Monoterpenyl Glycosyltransferases Differentially Contribute to Production of Monoterpenyl Glycosides in Two Aromatic Vitis vinifera Varieties

PubMed Central

Li, Xiang-Yi; Wen, Ya-Qin; Meng, Nan; Qian, Xu; Pan, Qiu-Hong

2017-01-01

HIGHLIGHTS A similar trend on accumulation of glycosidically bound monoterpenes was observed in both varietiesTwo VvGT7 alleles mutations occurred at key sites in Muscat blanc à PetitVvGT14 exerted a major role in production of monoterpenyl glycosides in both varieties Terpenoids are the major aroma components and generally exist as both free and glycosidically-bound forms, of which nonvolatile glycosides account for a large fraction in grape berries. Our previous study has indicated that differential accumulation of monoterpenyl glycosides in Vitis vinifera “Muscat blanc à Petit” between two regions is closely correlated to monoterpenyl glucosyltransferase (VvGT14, XM_002285734.2) transcript abundance. However, it has not been determined yet whether this correlation also exists in other Vitis vinifera varieties. This study investigated the evolution of free and glycosidically bound monoterpenes in two Vitis vinifera variety “Muscat blanc à Petit” and “Gewurztraminer” under two vintages, and further assessed the relation between the accumulation of bound monoterpenes and two monoterpenyl glycosyltransferase transcript levels. Results showed that free monoterpenes exhibited three evolution patterns in both varieties during berry development of two vintages, whereas glycosidically bound monoterpenes showed a concentration elevation with berry maturation. The Cis-rose oxide and geraniol were major components contributing to the aroma odors of “Gewürztraminer” grapes while linalool was major aroma contributor to the “Muscat blanc à Petit grain” grapes. The accumulation of glycosidically bound monoterpenes in both varieties was accompanied with the high expression of VvGT7 (XM_002276510.2) and VvGT14. Only one allele of VvGT7 was found in the variety “Gewürztraminer” and no mutation was observed in its enzyme active sites. XB-VvGT7-4 and XB-VvGT7-5 were two alleles of VvGT7 detected in “Muscat blanc à Petit grain.” The mutation on its enzyme active site inhibited the activity of XB-VvGT7-4, whereas VvGT7-5 exhibited an alteration on enzyme activity due to the insertion mutation at the position 443. Only one VvGT14 allele was found in both varieties, and the VvGT14 allele in both varieties showed the similarity on amino acid sequence. No mutation occurred in active sites of VvGT14 allele. These indicated that VvGT7 and VvGT14 differentially contributed to the production of monoterpenyl glycosides in these Vitis Vinifera varieties. PMID:28751905
Monoterpenyl Glycosyltransferases Differentially Contribute to Production of Monoterpenyl Glycosides in Two Aromatic Vitis vinifera Varieties.

PubMed

Li, Xiang-Yi; Wen, Ya-Qin; Meng, Nan; Qian, Xu; Pan, Qiu-Hong

2017-01-01

HIGHLIGHTS A similar trend on accumulation of glycosidically bound monoterpenes was observed in both varietiesTwo VvGT7 alleles mutations occurred at key sites in Muscat blanc à Petit VvGT14 exerted a major role in production of monoterpenyl glycosides in both varieties Terpenoids are the major aroma components and generally exist as both free and glycosidically-bound forms, of which nonvolatile glycosides account for a large fraction in grape berries. Our previous study has indicated that differential accumulation of monoterpenyl glycosides in Vitis vinifera "Muscat blanc à Petit" between two regions is closely correlated to monoterpenyl glucosyltransferase ( VvGT14 , XM_002285734.2) transcript abundance. However, it has not been determined yet whether this correlation also exists in other Vitis vinifera varieties. This study investigated the evolution of free and glycosidically bound monoterpenes in two Vitis vinifera variety "Muscat blanc à Petit" and "Gewurztraminer" under two vintages, and further assessed the relation between the accumulation of bound monoterpenes and two monoterpenyl glycosyltransferase transcript levels. Results showed that free monoterpenes exhibited three evolution patterns in both varieties during berry development of two vintages, whereas glycosidically bound monoterpenes showed a concentration elevation with berry maturation. The Cis -rose oxide and geraniol were major components contributing to the aroma odors of "Gewürztraminer" grapes while linalool was major aroma contributor to the "Muscat blanc à Petit grain" grapes. The accumulation of glycosidically bound monoterpenes in both varieties was accompanied with the high expression of VvGT7 (XM_002276510.2) and VvGT14 . Only one allele of VvGT7 was found in the variety "Gewürztraminer" and no mutation was observed in its enzyme active sites. XB-VvGT7-4 and XB-VvGT7-5 were two alleles of VvGT7 detected in "Muscat blanc à Petit grain." The mutation on its enzyme active site inhibited the activity of XB-VvGT7-4 , whereas VvGT7-5 exhibited an alteration on enzyme activity due to the insertion mutation at the position 443. Only one VvGT14 allele was found in both varieties, and the VvGT14 allele in both varieties showed the similarity on amino acid sequence. No mutation occurred in active sites of VvGT14 allele. These indicated that VvGT7 and VvGT14 differentially contributed to the production of monoterpenyl glycosides in these Vitis Vinifera varieties.
β-sheet-like hydrogen bonds interlock the helical turns of a photoswitchable foldamer to enhance the binding and release of chloride.

PubMed

Lee, Semin; Hua, Yuran; Flood, Amar H

2014-09-05

Inspired by halorhodopsin's use of photoisomerization to regulate chloride, aryltriazole-based foldamers have been created to "catch and release" chloride ions upon light irradiation of end-appended azobenzenes. The proposed mode of stabilization exploits a β-sheet-like hydrogen-bonding array to cooperatively interlock the ends of a foldamer together with its helical core. We find that the hydrogen-bonding array has a greater influence on stabilizing the helix than the π-stacked seam under the conditions examined (50:50 MeCN/THF). Thus, we show how it is possible to enhance the difference between Cl(-) binding and release using light-dependent control over the foldamer's degree of helix stabilization. Making and breaking three π-π contacts with light caused an 8-fold change in chloride affinity (40 300 M(-1) ⇄ 5000 M(-1)), five π-π contacts produced a 17-fold change (126 000 M(-1) ⇄ 7400 M(-1)), and strategically located hydrogen-bonding units enabled a greater 84-fold differential (970 000 M(-1) ⇄ 11 600 M(-1)). The improved performances were attributed to stepwise increases in the preorganization of the binding pocket that catches chloride while leaving the cis states with just one π-π contact relatively unchanged.

[UPLC-MS/MS determination of content of three iridoids of xingnaojing oral preparation in rat brains and study on their brain pharmacokinetics].

PubMed

Xu, Pan; Du, Shou-Ying; Lu, Yang; Bai, Jie; Liu, Hui-Min; Du, Qiu; Chen, Zhen-Zhen; Wang, Zhen

2014-06-01

To establish a UPLC-MS/MS method for the simultaneous determination of geniposide, genipin 1-O-beta-D-gentiobioside and geniposidic acid in rat brains and study the brain pharmacokinetics of the three iridoid glycosides in stroke rat after the oral administration of Xingnaojing. In this experiment, brain samples were precipitated with protein for twice. Acquity BEH C18 column was adopted, with acetonitrile-0.1% formic acid-water as the mobile phase for gradient elution. ESI source was adopted for mass spectra; multiple reaction monitoring (MRM) was conducted to detect negative ions. The time for sample analysis was 3.5 min. the results showed good linear relations among the three iridoid glycosides, with the extraction recovery between 99.6% and 114.3%, good intra- and inter-day precisions and accuracies and stability in line with the requirements. The t1/2 and MRT in the three components were similar in brains of stroke rats. Geniposide and genipin 1-O-beta-D-gentiobioside showed double peaks; where as geniposidic acid showed a single peak. In conclusion, the method is so specific, sensitive, accurate and reliable that it can be used to study the brain pharmacokinetics of Xingnaojing oral preparation.
Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.
Stability and Solid Solutions of Hydrous Alumino-Silicates in the Earth's Mantle

NASA Astrophysics Data System (ADS)

Panero, W. R.; Caracas, R.

2017-12-01

The degree to which the Earth's mantle stores and cycles water in excess of the storage capacity of nominally anhydrous minerals is dependent upon the stability of hydrous phases under mantle-relevant pressures, temperatures, and compositions. Two hydrous phases, phase D and phase H are stable to the pressures and temperatures of the Earth's lower mantle, suggesting that the Earth's lower mantle may participate in the cycling of water. Each phase has a wide solid solution series between MgSi2O6H2-Al2SiO6H2 and MgSiO4H2-2δAlOOH-SiO2, respectively, yet most work addresses end-member compositions for analysis of stability and elastic properties. We present the results of density functional theory calculations on the stability, structure, bonding, partitioning, and elasticity of hydrous phases D and H in the Al2O3-SiO2-MgO-H2O system, addressing the solid solution series through a statistical sampling of site occupancy and calculation of the partition function from the grand canonical ensemble. We find that the addition of Al to the endmember compositions stabilizes each phase to higher temperatures through additional configurational entropy. We further find that solid solutions tend not to undergo hydrogen-bond symmetrization as is found in the end member compositions as a result of non-symmetric bonding environments.
Mechanism for Si–Si Bond Rupture in Single Molecule Junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Haixing; Kim, Nathaniel T.; Su, Timothy A.

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si–Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si–Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si–Si bond is ruptured using an applied voltage. We investigate this voltage induced Si–Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation ofmore » molecular vibrational modes by tunneling electrons leads to homolytic Si–Si bond rupture.« less
Mechanism for Si-Si Bond Rupture in Single Molecule Junctions.

PubMed

Li, Haixing; Kim, Nathaniel T; Su, Timothy A; Steigerwald, Michael L; Nuckolls, Colin; Darancet, Pierre; Leighton, James L; Venkataraman, Latha

2016-12-14

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si-Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si-Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si-Si bond is ruptured using an applied voltage. We investigate this voltage induced Si-Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation of molecular vibrational modes by tunneling electrons leads to homolytic Si-Si bond rupture.
A novel engineered interchain disulfide bond in the constant region enhances the thermostability of adalimumab Fab.

PubMed

Nakamura, Hitomi; Oda-Ueda, Naoko; Ueda, Tadashi; Ohkuri, Takatoshi

2018-01-01

We constructed a system for expressing the Fab of the therapeutic human monoclonal antibody adalimumab at a yield of 20 mg/L in the methylotrophic yeast Pichia pastoris. To examine the contribution of interchain disulfide bonds to conformational stability, we prepared adalimumab Fab from which the interchain disulfide bond at the C-terminal region at both the CH 1 and CL domains was deleted by substitution of Cys with Ala (Fab ΔSS ). DSC measurements showed that the Tm values of Fab ΔSS were approximately 5 °C lower than those of wild-type Fab, suggesting that the interchain disulfide bond contributes to conformational thermostability. Using computer simulations, we designed a novel interchain disulfide bond outside the C-terminal region to increase the stability of Fab ΔSS . The resulting Fab (mutSS Fab ΔSS ) had the mutations H:V177C and L:Q160C in Fab ΔSS , confirming the formation of the disulfide bond between CH 1 and CL. The thermostability of mutSS Fab ΔSS was approximately 5 °C higher than that of Fab ΔSS . Therefore, the introduction of the designed interchain disulfide bond enhanced the thermostability of Fab ΔSS and mitigated the destabilization caused by partial reduction of the interchain disulfide bond at the C-terminal region, which occurs in site-specific modification such as PEGylation. Copyright © 2017 Elsevier Inc. All rights reserved.
Preparation and Evaluation at the Delta Opioid Receptor of a Series of Linear Leu-Enkephalin Analogues Obtained by Systematic Replacement of the Amides

PubMed Central

2013-01-01

Leu-enkephalin analogues, in which the amide bonds were sequentially and systematically replaced either by ester or N-methyl amide bonds, were prepared using classical organic chemistry as well as solid phase peptide synthesis (SPPS). The peptidomimetics were characterized using competition binding, ERK1/2 phosphorylation, receptor internalization, and contractility assays to evaluate their pharmacological profile over the delta opioid receptor (DOPr). The lipophilicity (LogD7.4) and plasma stability of the active analogues were also measured. Our results revealed that the last amide bond can be successfully replaced by either an ester or an N-methyl amide bond without significantly decreasing the biological activity of the corresponding analogues when compared to Leu-enkephalin. The peptidomimetics with an N-methyl amide function between residues Phe and Leu were found to be more lipophilic and more stable than Leu-enkephalin. Findings from the present study further revealed that the hydrogen-bond donor properties of the fourth amide of Leu-enkephalin are not important for its biological activity on DOPr. Our results show that the systematic replacement of amide bonds by isosteric functions represents an efficient way to design and synthesize novel peptide analogues with enhanced stability. Our findings further suggest that such a strategy can also be useful to study the biological roles of amide bonds. PMID:23650868
Demonstration of Subscale Cermet Fuel Specimen Fabrication Approach Using Spark Plasma Sintering and Diffusion Bonding

NASA Technical Reports Server (NTRS)

Barnes, Marvin W.; Tucker, Dennis S.; Benensky, Kelsa M.

2018-01-01

Nuclear thermal propulsion (NTP) has the potential to expand the limits of human space exploration by enabling crewed missions to Mars and beyond. The viability of NTP hinges on the development of a robust nuclear fuel material that can perform in the harsh operating environment (> or = 2500K, reactive hydrogen) of a nuclear thermal rocket (NTR) engine. Efforts are ongoing to develop fuel material and to assemble fuel elements that will be stable during the service life of an NTR. Ceramic-metal (cermet) fuels are being actively pursued by NASA Marshall Space Flight Center (MSFC) due to their demonstrated high-temperature stability and hydrogen compatibility. Building on past cermet fuel development research, experiments were conducted to investigate a modern fabrication approach for cermet fuel elements. The experiments used consolidated tungsten (W)-60vol%zirconia (ZrO2) compacts that were formed via spark plasma sintering (SPS). The consolidated compacts were stacked and diffusion bonded to assess the integrity of the bond lines and internal cooling channel cladding. The assessment included hot hydrogen testing of the manufactured surrogate fuel and pure W for 45 minutes at 2500 K in the compact fuel element environmental test (CFEET) system. Performance of bonded W-ZrO2 rods was compared to bonded pure W rods to access bond line integrity and composite stability. Bonded surrogate fuels retained structural integrity throughout testing and incurred minimal mass loss.
Can 1% chlorhexidine diacetate and ethanol stabilize resin-dentin bonds?

PubMed Central

Manso, Adriana Pigozzo; Grande, Rosa Helena Miranda; Bedran-Russo, Ana Karina; Reis, Alessandra; Loguercio, Alessandro D.; Pashley, David Henry; Carvalho, Ricardo Marins

2014-01-01

Objectives To examine the effects of the combined use of chlorhexidine and ethanol on the durability of resin-dentin bonds. Methods Forty-eight flat dentin surfaces were etched (32% phosphoric acid), rinsed (15 s) and kept wet until bonding procedures. Dentin surfaces were blot-dried with absorbent paper and re-wetted with water (Water, control), 1% chlorhexidine diacetate in water (CHD/Water), 100% ethanol (Ethanol), or 1% chlorhexidine diacetate in ethanol (CHD/Ethanol) solutions for 30 s. They were then bonded with All Bond 3 (AB3, Bisco) or Excite (EX, Ivoclar-Vivadent) using a smooth, continuous rubbing application (10 s), followed by 15 s gentle air stream to evaporate solvents. The adhesives were light-cured (20 s) and resin composite build-ups constructed for the microtensile method. Bonded beams were obtained and tested after 24-hours, 6-months and 15-months of water storage at 37°C. Storage water was changed every month. Effects of treatment and testing periods were analyzed (ANOVA, Holm-Sidak, p<0.05) for each adhesive. Results There were no interactions between factors for both etch-and-rinse adhesives. AB3 was significantly affected only by storage (p = 0.003). Excite was significantly affected only by treatments (p = 0.048). AB3 treated either with ethanol or CHD/ethanol resulted in reduced bond strengths after 15 months. The use of CHD/ethanol resulted in higher bond strengths values for Excite. Conclusions Combined use of ethanol/1% chlorhexidine diacetate did not stabilize bond strengths after 15 months. PMID:24815823
Chiral exciton coupling of merocyanine dyes within a well defined hydrogen-bonded assembly

PubMed Central

Prins, Leonard J.; Thalacker, Christoph; Würthner, Frank; Timmerman, Peter; Reinhoudt, David N.

2001-01-01

Multichromophoric hydrogen-bonded assemblies 13⋅(BAR)6 are studied that bear a remarkably close resemblance to commelinin, a naturally occurring assembly responsible for an intense blue color of flowers. The incorporated chromophores exhibit a hypsochromic shift in the UV/visible (Vis) absorption maximum (Δ λmax = 14 nm) compared with the free chromophores. In addition, the chiroptical properties of incorporated chromophores can be rationally controlled by changing the supramolecular chirality of the assembly. These properties have been used to study the stability of this type of assembly with UV and CD spectroscopy at concentrations far below the NMR sensitivity threshold (10−4 M). The determined C50% values of 2–3 μM in benzene show the extremely high stability of these hydrogen-bonded assemblies. PMID:11526228
Diterpenoid glycosides from the bitter fern Gleichenia quadripartita.

PubMed

Socolsky, Cecilia; Asakawa, Yoshinori; Bardón, Alicia

2007-12-01

Fifteen new diterpenoid glycosides (1a-n, 2) were isolated from an Argentine collection of the bitter fern Gleichenia quadripartita along with the known flavonoid glycoside afzelin. Structure elucidation was accomplished by 1D and 2D NMR spectroscopy and by high-resolution MS analyses. In addition, X-ray crystallographic analysis of a monocrystal of 1a as well as chemical derivatization of 1h and 1m were performed to confirm their structures.
8,14-Secopregnane glycosides from the aerial parts of Asclepias tuberosa.

PubMed

Warashina, Tsutomu; Noro, Tadataka

2009-07-01

Twenty pregnane glycosides, tuberoside A(1)-L(5), were isolated from the diethyl ether-soluble fraction of the MeOH extract from the aerial parts of Asclepias tuberosa (Asclepiadaceae). The pregnane glycosides were composed of 8,12;8,20-diepoxy-8,14-secopregnane as aglycon, and D-cymarose, D-oleandrose, D-digitoxose and/or D-glucose as the component sugars. Their structures were established using NMR spectroscopic analysis and chemical methodologies.
Glycosides of naphthohydroquinones and anthraquinones isolated from the aerial parts of Morinda parvifolia Bartl. ex DC (Rubiaceae) increase p53 mRNA expression in A2780 cells.

PubMed

Su, Xianming; Zhang, Jian; Li, Changkang; Li, Fenghua; Wang, Hongqing; Gu, Haifeng; Li, Baoming; Chen, Ruoyun; Kang, Jie

2018-05-11

Eight previously undescribed naphthohydroquinone glycosides, namely morindaparvins H-O, together with four known anthraquinone glycosides were isolated from the n-BuOH extract of the aerial parts of Morinda parvifolia Bartl. ex DC (Rubiaceae). The structures of morindaparvins H-O were elucidated on the basis of spectroscopic analysis. To our knowledge, this is the first isolation of quinone glycosides from the plant M. parvifolia. The results showed that all 12 compounds at the concentration of 50 μM significantly increased p53 mRNA expression in A2780 cells compared with the blank control group. Copyright © 2018 Elsevier Ltd. All rights reserved.
The dynamics of solvation dictates the conformation of polyethylene oxide in aqueous, isobutyric acid and binary solutions.

PubMed

Dahal, Udaya R; Dormidontova, Elena E

2017-04-12

Polymers hydrogen-bonding with solvent represent an important broad class of polymers, properties of which depend on solvation. Using atomistic molecular dynamics simulations with the OPLS/AA force field we investigate the effect of hydrogen bonding on PEO conformation and chain mobility by comparing its behavior in isobutyric acid and aqueous solutions. In agreement with experimental data, we found that in isobutyric acid PEO forms a rather rigid extended helical structure, while in water it assumes a highly flexible coil conformation. We show that the difference in PEO conformation and flexibility is the result of the hydrogen bond stability and overall solvent dynamics near PEO. Isobutyric acid forms up to one hydrogen bond per repeat unit of PEO and interacts with PEO for a prolonged period of time, thereby stabilizing the helical structure of the polymer and reducing its segmental mobility. In contrast, water forms on average 1.2 hydrogen bonds per repeat unit of PEO (with 60% of water forming a single hydrogen bond and 40% of water forming two hydrogen bonds) and resides near PEO for a noticeably shorter time than isobutyric acid, leading to the well-documented high segmental mobility of PEO in water. We also analyze PEO conformation, hydrogen bonding and segmental mobility in binary water/isobutyric acid solutions and find that in the phase separated region PEO resides in the isobutyric-rich phase forming about 25% of its hydrogen bonds with isobutyric acid and 75% with water. We show that the dynamics of solvation affects the equilibrium properties of macromolecules, such as conformation, and by mixing of hydrogen bond-donating solvents one can significantly alter both polymer conformation and its local dynamics.
Avoiding Thiol Compound Interference: A Nanoplatform Based on High-Fidelity Au-Se Bonds for Biological Applications.

PubMed

Hu, Bo; Kong, Fanpeng; Gao, Xiaonan; Jiang, Lulu; Li, Xiaofeng; Gao, Wen; Xu, Kehua; Tang, Bo

2018-05-04

Gold nanoparticles (Au NPs) assembled through Au-S covalent bonds have been widely used in biomolecule-sensing technologies. However, during the process, detection distortions caused by high levels of thiol compounds can still significantly influence the result and this problem has not really been solved. Based on the higher stability of Au-Se bonds compared to Au-S bonds, we prepared selenol-modified Au NPs as an Au-Se nanoplatform (NPF). Compared with the Au-S NPF, the Au-Se NPF exhibits excellent anti-interference properties in the presence of millimolar levels of glutathione (GSH). Such an Au-Se NPF that can effectively avoid detection distortions caused by high levels of thiols thus offers a new perspective in future nanomaterial design, as well as a novel platform with higher stability and selectivity for the in vivo application of chemical sensing and clinical therapies. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation

PubMed Central

Fitzpatrick, Anthony W.; Knowles, Tuomas P. J.; Waudby, Christopher A.; Vendruscolo, Michele; Dobson, Christopher M.

2011-01-01

Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions. PMID:22022239
Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way.

PubMed

Wang, Jia; Chen, Jingfei; Li, Jingwen; An, Liaoyuan; Wang, Yefei; Huang, Qingshan; Yao, Lishan

2018-06-01

A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone-backbone h-bonds (i→i-4 and i-3→i-7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i→i-4 and i-3→i-7 h-bonds, respectively. This cooperativity is supported by a protein α-helices h-bond survey in the pdb databank where stacking shortens the corresponding h-bond distances. © 2018 Wiley Periodicals, Inc.
Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides

NASA Astrophysics Data System (ADS)

Madhan, B.; Thanikaivelan, P.; Subramanian, V.; Raghava Rao, J.; Unni Nair, Balachandran; Ramasami, T.

2001-10-01

Molecular modelling approaches have been used to understand the interaction of collagen-like peptides with gallic acid, which mimic vegetable tanning processes involved in protein stabilization. Several interaction sites have been identified and the binding energies of the complexes have been calculated. The calculated binding energies for various geometries are in the range 6-13 kcal/mol. It is found that some complexes exhibit hydrogen bonding, and electrostatic interaction plays a dominant role in the stabilization of the peptide by gallic acid. The π-OH type of interaction is also observed in the peptide stabilization. Molecular dynamics (MD) simulation for 600 ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.
Covalent Coupling of Nanoparticles with Low-Density Functional Ligands to Surfaces via Click Chemistry

PubMed Central

Rianasari, Ina; de Jong, Michel P.; Huskens, Jurriaan; van der Wiel, Wilfred G.

2013-01-01

We demonstrate the application of the 1,3-dipolar cycloaddition (“click” reaction) to couple gold nanoparticles (Au NPs) functionalized with low densities of functional ligands. The ligand coverage on the citrate-stabilized Au NPs was adjusted by the ligand:Au surface atom ratio, while maintaining the colloidal stability of the Au NPs in aqueous solution. A procedure was developed to determine the driving forces governing the selectivity and reactivity of citrate-stabilized and ligand-functionalized Au NPs on patterned self-assembled monolayers. We observed selective and remarkably stable chemical bonding of the Au NPs to the complimentarily functionalized substrate areas, even when estimating that only 1–2 chemical bonds are formed between the particles and the substrate. PMID:23434666
Covalent bonding: the fundamental role of the kinetic energy.

PubMed

Bacskay, George B; Nordholm, Sture

2013-08-22

This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.

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