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https://www.readbyqxmd.com/read/28733212/the-peroxyl-radical-induced-oxidation-of-escherichia-coli-ftsz-and-its-single-tryptophan-mutant-y222w-modifies-specific-side-chains-generates-protein-cross-links-and-affects-biological-function
#1
Elizabeth Escobar-Álvarez, Fabian Leinisch, Gissela Araya, Octavio Monasterio, Lasse G Lorentzen, Eduardo Silva, Michael J Davies, Camilo López-Alarcón
FtsZ (filamenting temperature-sensitive mutant Z) is a key protein in bacteria cell division. The wild-type Escherichia coli FtsZ sequence (FtsZwt) contains three tyrosine (Tyr, Y) and sixteen methionine (Met, M) residues. The Tyr at position 222 is a key residue for FtsZ polymerization. Mutation of this residue to tryptophan (Trp, W; mutant Y222W) inhibits GTPase activity resulting in an extended time in the polymerized state compared to FtsZwt. Protein oxidation has been highlighted as a determinant process for bacteria resistance and consequently oxidation of FtsZwt and the Y222W mutant, by peroxyl radicals (ROO•) generated from AAPH (2,2'-azobis(2-methylpropionamidine) dihydrochloride) was studied...
July 18, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28717933/a-novel-ms-cleavable-azo-cross-linker-for-peptide-structure-analysis-by-free-radical-initiated-peptide-sequencing-frips
#2
Claudio Iacobucci, Christoph Hage, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28690007/bioreactor-induced-mesenchymal-progenitor-cell-differentiation-and-elastic-fiber-assembly-in-engineered-vascular-tissues
#3
Shigang Lin, Kibret Mequanint
In vitro maturation of engineered vascular tissues (EVT) requires the appropriate incorporation of smooth muscle cells (SMC) and extracellular matrix (ECM) components similar to native arteries. To this end, the aim of the current study was to fabricate 4 mm inner diameter vascular tissues using mesenchymal progenitor cells seeded into tubular scaffolds. A dual-pump bioreactor operating either in perfusion or pulsatile perfusion mode was used to generate physiological-like stimuli to promote progenitor cell differentiation, extracellular elastin production, and tissue maturation...
July 6, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28654756/hydrogels-with-a-memory-dual-responsive-organometallic-poly-ionic-liquid-s-with-hysteretic-volume-phase-transition
#4
Kaihuan Zhang, Xueling Feng, Chongnan Ye, Mark A Hempenius, G Julius Vancso
We report on the synthesis and structure-property relations of a novel, dual-responsive organometallic poly(ionic liquid) (PIL), consisting of a poly(ferrocenylsilane) backbone of alternating redox-active, silane-bridged ferrocene units and tetraalkylphosphonium sulfonate moieties in the side groups. This PIL is redox responsive due to the presence of ferrocene in the backbone and also exhibits a lower critical solution temperature (LCST)-type thermal responsive behavior. The LCST phase transition originates from the interaction between water molecules and the ionic substituents and shows a concentration-dependent, tunable transition temperature in aqueous solution...
July 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28636365/sustainable-elastomers-from-renewable-biomass
#5
Zhongkai Wang, Liang Yuan, Chuanbing Tang
Sustainable elastomers have undergone explosive growth in recent years, partly due to the resurgence of biobased materials prepared from renewable natural resources. However, mounting challenges still prevail: How can the chemical compositions and macromolecular architectures of sustainable polymers be controlled and broadened? How can their processability and recyclability be enabled? How can they compete with petroleum-based counterparts in both cost and performance? Molecular-biomass-derived polymers, such as polymyrcene, polymenthide, and poly(ε-decalactone), have been employed for constructing thermoplastic elastomers (TPEs)...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28570824/protein-epitope-mimetics-from-new-antibiotics-to-supramolecular-synthetic-vaccines
#6
Katja Zerbe, Kerstin Moehle, John A Robinson
Protein epitope mimetics provide powerful tools to study biomolecular recognition in many areas of chemical biology. They may also provide access to new biologically active molecules and potentially to new classes of drug and vaccine candidates. Here we highlight approaches for the design of folded, structurally defined epitope mimetics, by incorporating backbone and side chains of hot residues onto a stable constrained scaffold. Using robust synthetic methods, the structural, biological, and physical properties of epitope mimetics can be optimized, by variation of both side chain and backbone chemistry...
June 1, 2017: Accounts of Chemical Research
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
#7
Lloyd S Robinson, Warren G Lewis, Amanda L Lewis
The gut harbors many symbiotic, commensal, and pathogenic microbes that break down and metabolize host carbohydrates. Sialic acids are prominent outermost carbohydrates on host glycoproteins called mucins and protect underlying glycan chains from enzymatic degradation. Sialidases produced by some members of the colonic microbiota can promote the expansion of several potential pathogens (e.g. Clostridium difficile, Salmonella, and Escherichia coli) that do not produce sialidases. O-Acetyl ester modifications of sialic acids help resist the action of many sialidases and are present at high levels in the mammalian colon...
July 14, 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
#8
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 the 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 the presence of desleucyl-oritavancin at subinhibitory concentration using liquid chromatography-mass spectrometry (LC-MS)...
August 1, 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
#9
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...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28448030/synthesis-of-biocompatible-liquid-crystal-elastomer-foams-as-cell-scaffolds-for-3d-spatial-cell-cultures
#10
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
#11
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 light scattering and transmission electron microscopy. The number of cholesteryl groups per physical cross-linking site was estimated using a fluorescence quenching method...
July 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
#12
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...
May 2, 2017: Biochemistry
https://www.readbyqxmd.com/read/28381672/supramolecular-polymeric-materials-containing-cyclodextrins
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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