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https://www.readbyqxmd.com/read/28526748/the-sialate-o-acetylesterase-esta-from-gut-bacteroidetes-species-enables-sialidase-mediated-cross-species-foraging-of-9-o-acetylated-sialoglycans
#1
Lloyd S Robinson, Warren G Lewis, Amanda L Lewis
The gut harbors many symbiotic, commensal, and pathogenic microbes that engage in the breakdown and metabolism of host carbohydrates. Sialic acids are prominent outermost carbohydrates on mucins and protect underlying glycan chains from enzymatic degradation. Sialidases produced by some members of the colonic microbiota have been shown to promote the expansion of several potential pathogens (e.g. Clostridium difficile, Salmonella, Escherichia coli) that do not produce sialidases. O-acetyl ester modifications of sialic acids help resist the action of many sialidases and are found at high levels in the mammalian colon...
May 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28507244/inhibition-of-staphylococcus-aureus-cell-wall-biosynthesis-by-desleucyl-oritavancin-a-quantitative-peptidoglycan-composition-analysis-by-mass-spectrometry
#2
James D Chang, Erin E Foster, Aanchal N Thadani, Alejandro J Ramirez, Sung Joon Kim
Oritavancin is a lipoglycopeptide antibiotic that exhibits potent activities against vancomycin-resistant Gram-positive pathogens. Oritavancin differs from vancomycin by a hydrophobic side chain attached to the drug disaccharide, which forms a secondary-binding site to enable oritavancin binding to the cross-linked peptidoglycan in cell wall. The mode of action of secondary-binding site was investigated by measuring the changes in the peptidoglycan composition of Staphylococcus aureus grown in presence of desleucyl-oritavancin at sub-inhibitory concentration using liquid chromatography-mass spectrometry (LC-MS)...
May 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28506526/molecular-simulation-and-biochemical-studies-support-an-elevator-type-transport-mechanism-in%C3%A2-eiic
#3
Jumin Lee, Zhenning Ren, Ming Zhou, Wonpil Im
Enzyme IIC (EIIC) is a membrane-embedded sugar transport protein that is part of the phosphoenolpyruvate-dependent phosphotransferases. Crystal structures of two members of the glucose EIIC superfamily, bcChbC in the inward-facing conformation and bcMalT in the outward-facing conformation, were previously solved. Comparing the two structures led us to the hypothesis that sugar translocation could be achieved by an elevator-type transport mechanism in which a transport domain binds to the substrate and, through rigid body motions, transports it across the membrane...
May 13, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28448030/synthesis-of-biocompatible-liquid-crystal-elastomer-foams-as-cell-scaffolds-for-3d-spatial-cell-cultures
#4
Marianne E Prévôt, Senay Ustunel, Leah E Bergquist, Richard Cukelj, Yunxiang Gao, Taizo Mori, Lindsay Pauline, Robert J Clements, Elda Hegmann
Here, we present a step-by-step preparation of a 3D, biodegradable, foam-like cell scaffold. These scaffolds were prepared by cross-linking star block co-polymers featuring cholesterol units as side-chain pendant groups, resulting in smectic-A (SmA) liquid crystal elastomers (LCEs). Foam-like scaffolds, prepared using metal templates, feature interconnected microchannels, making them suitable as 3D cell culture scaffolds. The combined properties of the regular structure of the metal foam and of the elastomer result in a 3D cell scaffold that promotes not only higher cell proliferation compared to conventional porous templated films, but also better management of mass transport (i...
April 11, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28423990/self-assembled-nanogel-of-cholesterol-bearing-xyloglucan-as-a-drug-delivery-nanocarrier
#5
Shin-Ichi Sawada, Hiroko Yukawa, Shigeo Takeda, Yoshihiro Sasaki, Kazunari Akiyoshi
Xyloglucan (XG) is a multibranched polysaccharide consisting of a main chain β-1,4-glucan with xylose and galactose side chains. In this study, cholesterol-bearing XG (CHXG) was synthesized by the reaction of XG with cholesteryl N- (6-isocyanatohexyl) carbamate. The CHXG molecules self-assembled in water to form nanogels consisting of about 100 molecules of XG, and were characterized using differential light scattering and transmission electron microscopy. The number of cholesteryl groups per physical cross-linking site was estimated using a fluorescence quenching method...
April 20, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/28409923/the-catalase-activity-of-catalase-peroxidases-is-modulated-by-changes-in-the-pka-of-the-distal-histidine
#6
Miguel Machuqueiro, Bruno Victor, Jacek Switala, Jacylyn Villanueva, Carme Rovira, Ignacio Fita, Peter C Loewen
The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu ∼7 and ∼15 Å, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected...
April 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28381672/supramolecular-polymeric-materials-containing-cyclodextrins
#7
REVIEW
Masaki Nakahata, Yoshinori Takashima, Akira Harada
Smart design of polymeric materials may lead to intelligent materials exhibiting unique functional properties. Looking at nature, living systems use specific and reversible intermolecular interactions in realizing complex functions. Hence reversible bonds based on selective molecular recognition can impart artificial materials with unique functional properties. This review mainly focuses on supramolecular polymeric materials based on cyclodextrin-based host-guest interactions. Polymeric materials using molecular recognition at polymer main chain, side chain, and termini are described...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28301130/graphene-embedded-hydrogel-nanofibers-for-detection-and-removal-of-aqueous-phase-dyes
#8
Kyungun Im, Duong Nguyen Nguyen, Saerona Kim, Hye Jeong Kong, Yukyung Kim, Chul Soon Park, Oh Seok Kwon, Hyeonseok Yoon
A facile route to graphene/polymer hydrogel nanofibers was developed. An aqueous dispersion of graphene (containing >40% bilayer graphene flakes) stabilized by a functionalized water-soluble polymer with phenyl side chains was successfully electrospun to yield nanofibers. Subsequent vapor-phase cross-linking of the nanofibers produced graphene-embedded hydrogel nanofibers (GHNFs). Interestingly, the GHNFs showed chemical sensitivity to the cationic dyes methylene blue (MB) and crystal violet (CV) in the aqueous phase...
March 29, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28299927/supramolecular-hydrogels-based-on-dna-self-assembly
#9
Yu Shao, Haoyang Jia, Tianyang Cao, Dongsheng Liu
Extracellular matrix (ECM) provides essential supports three dimensionally to the cells in living organs, including mechanical support and signal, nutrition, oxygen, and waste transportation. Thus, using hydrogels to mimic its function has attracted much attention in recent years, especially in tissue engineering, cell biology, and drug screening. However, a hydrogel system that can merit all parameters of the natural ECM is still a challenge. In the past decade, deoxyribonucleic acid (DNA) has arisen as an outstanding building material for the hydrogels, as it has unique properties compared to most synthetic or natural polymers, such as sequence designability, precise recognition, structural rigidity, and minimal toxicity...
March 16, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28252951/effects-of-xylan-side-chain-substitutions-on-xylan-cellulose-interactions-and-implications-for-thermal-pretreatment-of-cellulosic-biomass
#10
Caroline S Pereira, Rodrigo L Silveira, Paul Dupree, Munir S Skaf
Lignocellulosic biomass is mainly constituted by cellulose, hemicellulose, and lignin and represents an important resource for the sustainable production of biofuels and green chemistry materials. Xylans, a common hemicellulose, interact with cellulose and often exhibit various side chain substitutions including acetate, (4-O-methyl) glucuronic acid, and arabinose. Recent studies have shown that the distribution of xylan substitutions is not random, but follows patterns that are dependent on the plant taxonomic family and cell wall type...
March 13, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28250957/the-mechanism-behind-the-selection-of-two-different-cleavage-sites-in-nag-nam-polymers
#11
Marko Mihelič, Kristina Vlahoviček-Kahlina, Miha Renko, Stephane Mesnage, Andreja Doberšek, Ajda Taler-Verčič, Andreja Jakas, Dušan Turk
Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28199083/shape-memory-hydrogels-evolution-of-structural-principles-to-enable-shape-switching-of-hydrophilic-polymer-networks
#12
Candy Löwenberg, Maria Balk, Christian Wischke, Marc Behl, Andreas Lendlein
The ability of hydrophilic chain segments in polymer networks to strongly interact with water allows the volumetric expansion of the material and formation of a hydrogel. When polymer chain segments undergo reversible hydration depending on environmental conditions, smart hydrogels can be realized, which are able to shrink/swell and thus alter their volume on demand. In contrast, implementing the capacity of hydrogels to switch their shape rather than volume demands more sophisticated chemical approaches and structural concepts...
February 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28182517/rapid-chair-side-test-for-detection-of-porphyromonas-gingivalis
#13
N M O'Brien-Simpson, K Burgess, J C Lenzo, G C Brammar, I B Darby, E C Reynolds
Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis, and its intraoral levels have been shown to predict disease progression (activity). An accurate and sensitive chair-side (point of care) test to determine disease activity is critical for early intervention and clinical management of disease. This study aimed to develop a rapid, chair-side, saliva-based detection of P. gingivalis. Monoclonal antibodies (mAbs) to the A1-adhesin domain of the P. gingivalis RgpA-Kgp proteinase-adhesin complex were screened by enzyme-linked immunosorbent assay and microbial flow cytometry, with 2 mAbs shown to recognize all laboratory and clinical strains tested, without significantly cross-reacting with other oral bacteria tested...
February 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28170226/significance-of-individual-residues-at-the-regulatory-site-of-yeast-pyruvate-decarboxylase-for-allosteric-substrate-activation
#14
Michael Spinka, Sebastian Seiferheld, Philipp Zimmermann, Elena Bergner, Anne-Kathrin Blume, Angelika Schierhorn, Tom Reichenbach, Robert Pertermann, Christiane Ehrt, Stephan König
The catalytic activity of the allosteric enzyme pyruvate decarboxylase from yeast is strictly controlled by its own substrate pyruvate via covalent binding at a separate regulatory site. Kinetic studies, chemical modifications, cross-linking, small-angle X-ray scattering, and crystal structure analyses have led to a detailed understanding of the substrate activation mechanism at an atomic level with C221 as the core moiety of the regulatory site. To characterize the individual role of the residues adjacent to C221, we generated variants H92F, H225F, H310F, A287G, S311A, and C221A/C222A...
March 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28128940/sequence-selective-binding-of-oligopeptides-in-water-through-hydrophobic-coding
#15
Joseph K Awino, Roshan W Gunasekara, Yan Zhao
A general method for sequence-specific binding of peptides remains elusive despite decades of research. By creating an array of "hydrophobically coded dimples" on the surface of surface-core doubly cross-linked micelles, we synthesized water-soluble nanoparticle receptors to recognize peptides by the location, number, and nature of their hydrophobic side chains. Minute differences in the side chains could be distinguished, and affinities up to 20 nM were obtained for biologically active oligopeptides in water...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28062560/the-amyloid-phenomenon-and-its-links-with-human-disease
#16
Christopher M Dobson
The ability of normally soluble proteins to convert into amyloid fibrils is now recognized to be a generic phenomenon. The overall cross-β architecture of the core elements of such structures is closely similar for different amino acid sequences, as this architecture is dominated by interactions associated with the common polypeptide main chain. In contrast, the multiplicity of complex and intricate structures of the functional states of proteins is dictated by specific interactions involving the variable side chains, the sequence of which is unique to a given protein...
January 6, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28024547/metrics-of-rhamnogalacturonan-i-with-%C3%AE-1%C3%A2-4-linked-galactan-side-chains-and-structural-basis-for-its-self-aggregation
#17
Olga N Makshakova, Tatyana A Gorshkova, Polina V Mikshina, Yuriy F Zuev, Serge Perez
Within the family of plant cell wall polysaccharides rhamnogalacturonans I are the most diverse and structurally complex members. In present study we characterize the 3-dimensional structures and dynamic features of the constituents of RG-I along MD trajectories. It is demonstrated that extended threefold helical structure of the rhamnogalacturonan linear backbone is the most energetically favorable motif. Branching helps to stabilize a conformer of the backbone twisted along 1→2 glycosidic linkage triggering the orientation of long side chains without altering the extended overall backbone chain conformation...
February 20, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/27990808/self-assembly-of-thermoreversible-hydrogels-via-molecular-recognition-toward-a-spatially-organized-coculture-system
#18
Ryota Tamate, Kotomi Takahashi, Takeshi Ueki, Aya Mizutani Akimoto, Ryo Yoshida
In this study, we present the spontaneous adhesion of two thermoreversible physically cross-linked hydrogels via molecular recognition under a physiological condition. We successfully prepared two types of hydrogels generated using two kinds of well-defined ABA type triblock copolymers: CAT-ABA and PBA-ABA, which contain catechol and phenylboronic acid groups as functional side chains, respectively. Both types of ABA triblock copolymers were able to undergo sol-to-gel transition with the increase in temperature resulting from the formation of physical cross-links at a physiological temperature, which enables easy cell encapsulation in the hydrogel...
December 19, 2016: Biomacromolecules
https://www.readbyqxmd.com/read/27934919/chiral-sulfoxide-induced-single-turn-peptide-%C3%AE-helicity
#19
Qingzhou Zhang, Fan Jiang, Bingchuan Zhao, Huacan Lin, Yuan Tian, Mingsheng Xie, Guoyun Bai, Adam M Gilbert, Gilles H Goetz, Spiros Liras, Alan A Mathiowetz, David A Price, Kun Song, Meihua Tu, Yujie Wu, Tao Wang, Mark E Flanagan, Yun-Dong Wu, Zigang Li
Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide...
December 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27934152/combined-effect-of-chain-extension-and-supramolecular-interactions-on-rheological-and-adhesive-properties-of-acrylic-pressure-sensitive-adhesives
#20
Xavier Callies, Olivier Herscher, Cécile Fonteneau, Alexis Robert, Sandrine Pensec, Laurent Bouteiller, Guylaine Ducouret, Costantino Creton
A new approach for the elaboration of low molecular weight pressure-sensitive adhesives based on supramolecular chemistry is explored. The synthesis of model systems coupled with probe-tack tests and rheological experiments highlights the influence of the transient network formed by supramolecular bonds on the adhesion energy. The first step of our approach consists of synthesizing poly(butyl acrylate-co-glycidyl methacrylate) copolymers from a difunctional initiator able to self-associate by four hydrogen bonds between urea groups...
December 7, 2016: ACS Applied Materials & Interfaces
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