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Structural Studies on ι-Carrageenan Derived Oligosaccharides and Its Application  [PDF]
Annabelle V. Briones, Toshinori Sato
Advances in Chemical Engineering and Science (ACES) , 2014, DOI: 10.4236/aces.2014.41003
Abstract:

Mild hydrochloric acid hydrolysis of i-carrageenan from Eucheuma spinosum yielded two oligosaccharides of sulfated tetrasaccharide structure. These were characterized by Fourier Transform Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR) and Electrospray Ionization Mass Spectrometry (ESIMS). Both oligosaccharides have structure of b-D-galactopyranose(Galp)4S-(14)-α-D-AnGalp2S-(13)-b-D-galactopyranose Galp)4S-(14)-α-D-AnGalp2S-(13). Application of the resulting oligosaccharides on protein delivery system in terms of encapsulation efficiency was performed.

Structural-functional studies of peptides derived from a long-chain snake neurotoxin Naja naja oxiana  [cached]
Adak Nasiripourdori,Bijan Ranjbar,Hossein Naderi-manesh,Faramarz Mehrnejad
Physiology and Pharmacology , 2008,
Abstract: Introduction: The design and structural characterization of mini-proteins with a compact, folded structure provide insight into the complex architecture of proteins today and has long been a challenging issue in structural- functional studies. Alpha neurotoxins from snake venom have a distinct folded structure comprised of a disulphide core and three loops or “fingers”; each of these loops are considered as a separate functional domain. Because of selectivity and specificity of snake alpha neurotoxins, they are ideal candidates for structural-functional studies. Method: With the assumption that each "loop" in the structure of alpha neurotoxin is able to fold as a structurally independent unit and could possibly have functional properties, we have minimized the structure of a long-chain alpha neurotoxin into 18 and 31 amino acid peptides using solid-phase synthesis and cloning methods, respectively. The molecules are structurally studied using circular dichroism spectroscopy and also in vitro using organ bath apparatus and chick biventer cervicis muscle (CBCM). Results: The 18 and 31-mer peptides form predominant beta structures ( -turn and -sheet/alpha helix) in aqueous solutions which vary with solvent ionic strength. Data from in vitro and in silico studies indicate that these minimized structures block the twitches in chick biventer cervices muscle with concentrations higher than 0.5 M; and this effect is absolutely dose dependent. On the other hand, the long-chain alpha neurotoxin completely and irreversibly blocks the CBCM even at 50 nanomolar concentration and both effects are post synaptic. Conclusion: These data support the primary assumption that the peptides derived from the second loop of snake alpha neurotoxin can have a distinct folded structure and furthermore, exist as an independent biological unit.
Structural Studies and Investigation on the Activity of Imidazole-Derived Thiosemicarbazones and Hydrazones against Crop-Related Fungi  [PDF]
Débora C. Reis,Angel A. Recio Despaigne,Jeferson G. Da Silva,Nayane F. Silva,Camila F. Vilela,Isolda C. Mendes,Jacqueline A. Takahashi,Heloisa Beraldo
Molecules , 2013, DOI: 10.3390/molecules181012645
Abstract: New imidazole derived thiosemicarbazones and hydrazones were prepared by condensation of 4(5)-imidazole carboxaldehyde, 4-(1 H-imidazole-1-yl)benzaldehyde and 4-(1 H-imidazole-1-yl)acetophenone with a thiosemicarbazide or hydrazide. All compounds were characterized by quantitative elemental analysis, IR and NMR techniques. Eight structures were determined by single crystal X-ray diffraction. The antifungal activities of the compounds were evaluated. None of the compounds exhibited significant activity against Aspergillus flavus and Candida albicans, while 4(5)-imidazolecarboxaldehyde thiosemicarbazone (ImT) and 4-(1 H-imidazole-1-yl)benzaldehyde thiosemicabazone (4ImBzT) were highly and selectively active against Cladosporium cladosporioides. 4(5)-Imidazolecarboxaldehyde benzoyl hydrazone (4(5)ImPh), 4(5)-imidazolecarboxaldehyde- para-chlorobenzoyl hydrazone (4(5)Im pClPh), 4(5)-imidazolecarboxaldehyde- para-nitrobenzoyl hydrazone (4(5)Im pNO 2Ph), 4-(imidazole-1-yl)acetophenone- para-chloro-benzoyl hydrazone (4ImAc pClPh) and 4-(imidazole-1-yl)acetophenone- para-nitro-benzoylhydrazone (4ImAc pNO 2Ph) were highly active against Candida glabrata. 4(5)Im pClPh and 4(5)Im pNO 2Ph were very effective against C. cladosporioides. In many cases, activity was superior to that of the reference compound nystatin.
Structural confirmation of oligosaccharides newly isolated from sugar beet molasses
Tatsuya Abe, Kenichi Horiuchi, Hiroto Kikuchi, Tsutomu Aritsuka, Yusuke Takata, Eri Fukushi, Yukiharu Fukushi, Jun Kawabata, Keiji Ueno, Shuichi Onodera, Norio Shiomi
Chemistry Central Journal , 2012, DOI: 10.1186/1752-153x-6-89
Abstract: Four oligosaccharides were newly isolated from sugar beet molasses using high-performance liquid chromatography (HPLC) and carbon-Celite column chromatography. Structural confirmation of the saccharides was provided by methylation analysis, matrix-assisted laser desorption/ionaization time of flight mass spectrometry (MALDI-TOF-MS), and nuclear magnetic resonance (NMR) measurements.The following oligosaccharides were identified in sugar beet molasses: β-D-galactopyranosyl-(1- > 6)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named β-planteose), α-D-galactopyranosyl-(1- > 1)-β-D-fructofuranosyl-(2 <-> 1)-α-D-glucopyranoside (named1-planteose), α-D-glucopyranosyl-(1- > 6)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (theanderose), and β-D-glucopyranosyl-(1- > 3)-α-D-glucopyranosyl-(1 <-> 2)-β-D-fructofuranoside (laminaribiofructose). 1-planteose and laminaribiofructose were isolated from natural sources for the first time.Several oligosaccharides have been reported in the field of cane and beet sugar processing. For example, in addition to sucrose itself, isokestose (1-kestose) [1,2], kestose (6-kestose) [1,2], and neokestose [2,3] are present in cane and beet refinery molasses, while theanderose [4] has been reported in cane molasses. These oligosaccharides are composed of sucrose and D-fructose or D-glucose.On the other hand, raffinose is present in sugar beet [5] and its molasses [6]. Raffinose is a trisaccharide formed by the addition of D-galactose to the D-glucose moiety of sucrose via an alpha-(1- > 6) linkage. Raffinose is not decomposed during refining. Instead, it accumulates in beet molasses because it is chemically stable under the processing conditions, and it can therefore be manufactured from beet molasses. Raffinose forms non-hygroscopic crystals or powder. This property makes raffinose useful for processing into a stable powder or granule pellet-type products [7] for use in food materials. Moreover, raffinose has the characteristics of a pr
Seaweed Polysaccharides and Derived Oligosaccharides Stimulate Defense Responses and Protection Against Pathogens in Plants  [PDF]
Jeannette Vera,Jorge Castro,Alberto Gonzalez,Alejandra Moenne
Marine Drugs , 2011, DOI: 10.3390/md9122514
Abstract: Plants interact with the environment by sensing “non-self” molecules called elicitors derived from pathogens or other sources. These molecules bind to specific receptors located in the plasma membrane and trigger defense responses leading to protection against pathogens. In particular, it has been shown that cell wall and storage polysaccharides from green, brown and red seaweeds (marine macroalgae) corresponding to ulvans, alginates, fucans, laminarin and carrageenans can trigger defense responses in plants enhancing protection against pathogens. In addition, oligosaccharides obtained by depolymerization of seaweed polysaccharides also induce protection against viral, fungal and bacterial infections in plants. In particular, most seaweed polysaccharides and derived oligosaccharides trigger an initial oxidative burst at local level and the activation of salicylic (SA), jasmonic acid (JA) and/or ethylene signaling pathways at systemic level. The activation of these signaling pathways leads to an increased expression of genes encoding: (i) Pathogenesis-Related (PR) proteins with antifungal and antibacterial activities; (ii) defense enzymes such as pheylalanine ammonia lyase (PAL) and lipoxygenase (LOX) which determine accumulation of phenylpropanoid compounds (PPCs) and oxylipins with antiviral, antifugal and antibacterial activities and iii) enzymes involved in synthesis of terpenes, terpenoids and/or alkaloids having antimicrobial activities. Thus, seaweed polysaccharides and their derived oligosaccharides induced the accumulation of proteins and compounds with antimicrobial activities that determine, at least in part, the enhanced protection against pathogens in plants.
Combinatorial Enzyme Approach to Produce Oligosaccharides of Diverse Structures for Functional Screen  [PDF]
Dominic W. S. Wong, Doris Feng, Sarah Batt, William Orts
Advances in Enzyme Research (AER) , 2018, DOI: 10.4236/aer.2018.62002
Abstract: Combinatorial chemistry has been a focus of research activity in modern drug discovery and biotechnology. It is a concept by which a vast library of molecular diversity is synthesized and screened for target properties. This report is to illustrate the application of enzyme technology using the concept of combinatorial chemistry as a novel approach for the bioconversion of plant fibers. Citrus pectin was subjected to combinatorial enzyme digestion to create libraries of pectic oligosaccharides with diverse structural variants. Repeated cycles of fractionation and screening resulted in the isolation and identification of an active oligoGalA species with antimicrobial activity.
Structural Characterisation by ESI-MS of Feruloylated Arabino-oligosaccharides Synthesised by Chemoenzymatic Esterification  [PDF]
Christina Vafiadi,Evangelos Topakas,Edwin J Bakx,Henk A Schols,Paul Christakopoulos
Molecules , 2007, DOI: 10.3390/12071367
Abstract: The chemoenzymatic synthesis of feruloylated arabino-oligosaccharides has been achieved, using a feruloyl esterase type C from Sporotrichum thermophile (StFaeC).The structure of the feruloylated products was confirmed by ESI-MSn.
Molecular fishing: marine oligosaccharides  [PDF]
Antonio Trincone
Frontiers in Marine Science , 2014, DOI: 10.3389/fmars.2014.00026
Abstract: It is difficult to overvalue the importance of polysaccharides for the great number of applicative fields in which they appeared. Oligosaccharides are relatively short compounds that are prepared from the longer polysaccharides or could also be found as such in nature. The potential in bioactivity of marine polysaccharides is still considered under-exploited and these molecules, including the derived oligosaccharides, are an extraordinary source of chemical diversity. Sustainable ways to access marine oligosaccharides are particularly important in view of the huge list of the effects they play in cell events; enzymatic tools, on which these sustainable ways are based, and modern techniques for purification and for the investigation of chemical structures, will be shortly discussed indicating the most important recent literature.
Structural alphabets derived from attractors in conformational space
Alessandro Pandini, Arianna Fornili, Jens Kleinjung
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-97
Abstract: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.Most proteins have arisen by natural selection to adopt a hierarchical three-dimensional fold, where regularly shaped structural motifs are packed together and form a hydrophobic core. The first description of two of these motifs introduced the concept of secondary structures (α-helix and β-sheet) and demonstrated that some local structures have a repetitive nature [1]. Later it was discovered that almost all regions of a protein backbone can be rebuilt by few substructures common to different proteins [2]. With increasing availability of high quality structures, it also became clear that some of the adopted conformations are realised much more frequently than others and more recently a detailed analysis of the Ramachandran space [3] for structures of different crystallographic resolution showed clustering of both secondary structure types and random coil conformations at distinct conformational attractors [4]. These attractors can be labelled as conformational 'states' and the protein structure can be considered as a sequence of conformational states. Indeed, classical secondary structur
Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison  [PDF]
Liaqat Ali,Diarmuid T. Kenny,Catherine A. Hayes,Niclas G. Karlsson
Metabolites , 2012, DOI: 10.3390/metabo2040648
Abstract: The availability of specific exoglycosidases alongside a spectral library of O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides a pathway to make the elucidation of O-linked oligosaccharides more efficient. Here, we advise an approach of exoglycosidase-digestion of O-linked oligosaccharide mixtures, for structures that do not provide confirmative spectra. The combination of specific exoglycosidase digestion and MS 2 matching of the exoglycosidase products with structures from UniCarb-DB, allowed the assignment of unknown structures. This approach was illustrated by treating sialylated core 2 O-linked oligosaccharides, released from the human synovial glycoprotein (lubricin), with a α2–3 specific sialidase. This methodology demonstrated the exclusive 3 linked nature of the sialylation of core 2 oligosaccharides on lubricin.?When specific exoglycosidases were not available, MS 3 spectral matching using standards was used. This allowed the unusual 4-linked terminal GlcNAc epitope in a porcine stomach to be identified in the GlcNAc1-4Galb1–3(GlcNAcb1-6)GalNAcol structure, indicating the antibacterial epitope GlcNAca1–4. In total, 13 structures were identified using exoglycosidase and MS n, alongside UniCarb-DB fragment spectra comparison. UniCarb-DB could also be used to identify the specificity of unknown exoglycosidases in human saliva. Endogenous salivary exoglycosidase activity on mucin oligosaccharides could be monitored by comparing the generated tandem MS spectra with those present in UniCarb-DB, showing that oral exoglycosidases were dominated by sialidases with a higher activity towards 3-linked sialic acid rather than 6-linked sialic acid.
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