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https://www.readbyqxmd.com/read/29295983/structural-basis-for-dna-3-end-processing-by-human-tyrosyl-dna-phosphodiesterase-1
#1
Fiona J Flett, Emilija Ruksenaite, Lee A Armstrong, Shipra Bharati, Roberta Carloni, Elizabeth R Morris, C Logan Mackay, Heidrun Interthal, Julia M Richardson
Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA...
January 2, 2018: Nature Communications
https://www.readbyqxmd.com/read/29237363/incorporation-of-an-n-methyl-amino-acid-into-a-template-peptide-alters-anisotropy-in-the-crystal-growth-of-gold-nanoparticles-synthesized-by-the-peptide-template-method
#2
Kin-Ya Tomizaki, Ryuuichi Nanbu, Makoto Kasuga, Takahito Imai
Gold nanocrystals hold promise for use as catalysts and in photonic/plasmonic devices, electronics, sensing/imaging systems, drug delivery systems, and photothermal therapies due to their unique physical, chemical, and biocompatible properties. Various organic templates have been used to control of the size, shape, structure, surface modification and topology of gold nanocrystals. The synthesis of gold nanorods currently requires a cytotoxic surfactant to control morphology. To control the shape of gold nanocrystals, we previously demonstrated the de novo design and synthesis of a b-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X = L-2-naphthylalanine, Nal)...
December 13, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29211485/surface-characterization-and-platelet-adhesion-on-thin-hydrogel-films-of-poly-vinyl-ether
#3
Nozomi Itagaki, Yukari Oda, Toyoaki Hirata, Hung Kim Nguyen, Daisuke Kawaguchi, Hisao Matsuno, Keiji Tanaka
Poly(vinyl ether), with short oxyethylene side chains which possess a simple and relatively polar structure, should be a unique candidate for a bioinert material thanks to its solubility in water. On the basis of living cationic copolymerization and subsequent ultraviolet light irradiation, thin films of poly(2-methoxyethyl vinyl ether) with different cross-linking densities were prepared on solid substrates. The films were thickened in water, and the extent was dependent on the cross-linking density. Although the surface chemistry and aggregation states were almost identical to one another, the stiffness, or the softness, of the outermost region in the film was strongly dependent on the cross-linking density...
December 6, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29211462/the-eponymous-cofactors-in-cytochrome-p460s-from-ammonia-oxidizing-bacteria-are-iron-porphyrinoids-whose-macrocycles-are-dibasic
#4
Meghan A Smith, Kyle M Lancaster
The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear...
December 6, 2017: Biochemistry
https://www.readbyqxmd.com/read/29206106/effect-of-chain-stiffness-on-the-structure-of-single-chain-polymer-nanoparticles
#5
Angel J Moreno, Petra Bacova, Federica Lo Verso, Arantxa Arbe, Juan Colmenero, Jose A Pomposo
Polymeric single-chain nanoparticles (SCNPs) are soft nano-objects synthesized by purely intramolecular cross-linking of single polymer chains. By means of computer simulations, we investigate the conformational properties of SCNPs as a function of the bending stiffness of their linear polymer precursors. We investigate a broad range of characteristic ratios from the fully flexible case to those typical of bulky synthetic polymers. Increasing stiffness hinders bonding of groups separated by short contour distances and increases looping over longer distances, leading to more compact nanoparticles with a structure of highly interconnected loops...
December 5, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29174286/structural-basis-of-activation-of-mammalian-heme-peroxidases
#6
REVIEW
Prashant K Singh, Naseer Iqbal, Harsh V Sirohi, Hridoy R Bairagya, Punit Kaur, Sujata Sharma, Tej P Singh
The mammalian heme peroxidases including lactoperoxidase (LPO), myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO) contain a covalently linked heme moiety. Initially, it was believed that the heme group was fully cross-linked to protein molecule through at least two ester linkages involving conserved glutamate and aspartate residues with 1-methyl and 5-methyl groups of pyrrole rings A and C respectively. In MPO, an additional sulfonium ion linkage was present between 2-vinyl group of pyrrole ring A of the heme moiety and a methionine residue of the protein...
November 21, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29156637/synthesis-and-improved-cross-linking-properties-of-c5-modified-furan-bearing-pnas
#7
Joke Elskens, Alex Manicardi, Valentina Costi, Annemieke Madder, Roberto Corradini
Over the past decades, peptide nucleic acid/DNA (PNA:DNA) duplex stability has been improved via backbone modification, often achieved via introducing an amino acid side chain at the α- or γ-position in the PNA sequence. It was previously shown that interstrand cross-linking can further enhance the binding event. In this work, we combined both strategies to fine-tune PNA crosslinking towards single stranded DNA sequences using a furan oxidation-based crosslinking method; for this purpose, γ-l-lysine and γ-l-arginine furan-PNA monomers were synthesized and incorporated in PNA sequences via solid phase synthesis...
November 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29134996/photo-cross-linked-perylene-diimide-derivative-materials-as-efficient-electron-transporting-layers-in-inverted-polymer-solar-cells
#8
Yong-Jin Noh, Yu-Jin Choi, Ji-Ho Jeong, Seok-Soon Kim, Kwang-Un Jeong, Seok-In Na
We present an efficient and stable interfacial material based on a water-soluble perylene diimide derivative functionalized with ionic and methacrylate groups (abbreviated as PDIM), which can be stabilized by the photo-polymerization of diacrylate groups at both ends of the side chain in the PDIM. The characteristics of the photo-cross-linked PDIM films were examined using absorption spectra, cyclic voltammetry, work function, and surface morphology. The feasibility of the photo-cross-linked PDIM films as a novel electron transporting layer (ETL) in polymer solar cells (PSCs) was also investigated...
November 23, 2017: Nanoscale
https://www.readbyqxmd.com/read/29105983/radical-copolymerization-of-vinyl-ethers-and-cyclic-ketene-acetals-as-a-versatile-platform-to-design-functional-polyesters
#9
Antoine Tardy, Jean-Claude Honoré, Johanna Tran, Didier Siri, Vianney Delplace, Isabelle Bataille, Didier Letourneur, Josette Perrier, Cendrine Nicoletti, Marc Maresca, Catherine Lefay, Didier Gigmes, Julien Nicolas, Yohann Guillaneuf
For the first time, the free-radical copolymerization of cyclic ketene acetals (CKAs) and vinyl ethers (VEs) was investigated as an efficient, yet simple approach for the preparation of functional aliphatic polyesters. The copolymerization of CKA and VE was first predicted to be quasi-ideal by DFT calculations. The theoretical prediction was experimentally confirmed by the copolymerization of 2-methylene-1,3-dioxepane (MDO) and butyl vinyl ether (BVE), leading to rMDO = 0.73 and rBVE = 1.61. We then illustrated the versatility of this approach by preparing different functional polyesters: (i) copolymers functionalized by fluorescent probes; (ii) amphiphilic copolymers grafted with poly(ethylene glycol) (PEG) side chains able to self-assemble into PEGylated nanoparticles; (iii) antibacterial films active against Gram+ and Gram- bacteria (including a multiresistant strain) and (iv) cross-linked bioelastomers with suitable properties for tissue engineering applications...
November 5, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29031897/smart-electrical-bi-layers-lipopeptides-novel-peptidic-chains-like-zigzag-map-esterified-with-phospho-glyceride-as-mono-layer-moieties-capable-in-forming-a-meso-sphere-envelop-with-scaffold-ability-to-cellular-impurities
#10
REVIEW
Sami Saadi, Nazamid Saari, Abdulkarim Sabo Mohammed, Hasanah Mohd Ghazali, Farooq Anwar
Cell impurities are an emerging nucleating molecular barriers having the capability in disordering the metabolic chain reactions of proteolysis, glycolysis and lipolysis. Their massive effects induced by copolymer crystal growth in compaction with metal and mineral transients are extended as well as in damaging DNA and mRNA structure motif and other molecular assembly e.g. histones structure unites. Their polycrystalline packing modes, polydispersity and their tendency to surface and interface adhesion prompted us in structuring scaffold biomaterials enriched with biopeptides, layered by phospho-glycerides ester-forms...
October 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28990530/isoform-separation-by-a-mixed-mode-resin-toyopearl-mx-trp-650m
#11
Tsutomu Arakawa
TOYOPEARL particles are cross-linked hydroxylated methacrylic polymers available in different pore and particle sizes. They are conjugated with different ligands to generate ion-exchange, hydrophobic interaction and affinity resins. They have excellent physical and chemical properties. A mixed-mode resin, TOYOPEARL MX-Trp-650M, is made of this particle with tryptophan conjugated via N-terminal amino group and hence has both hydrophobic/aromatic side chain and carboxyl group. In this review, I will summarize the properties of the TOYOPEARL particles and MX-Trp-650M resin and application of this resin for purification of proteins and in some detail the separation of disulfide (SS)-scrambled oligomers of insulin-like growth factor-1 (IGF-1)...
October 9, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28962874/formation-and-detection-of-oxidant-generated-tryptophan-dimers-in-peptides-and-proteins
#12
Luke Carroll, David I Pattison, Justin B Davies, Robert F Anderson, Camilo Lopez-Alarcon, Michael J Davies
Free radicals are produced during physiological processes including metabolism and the immune response, as well as on exposure to multiple external stimuli. Many radicals react rapidly with proteins resulting in side-chain modification, backbone fragmentation, aggregation, and changes in structure and function. Due to its low oxidation potential, the indole ring of tryptophan (Trp) is a major target, with this resulting in the formation of indolyl radicals (Trp(•)). These undergo multiple reactions including ring opening and dimerization which can result in protein aggregation...
September 28, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28898504/reversible-dna-protein-cross-linking-at-epigenetic-dna-marks
#13
Shaofei Ji, Hongzhao Shao, Qiyuan Han, Christopher L Seiler, Natalia Y Tretyakova
5-Formylcytosine (5fC) is an endogenous DNA modification frequently found within regulatory elements of mammalian genes. Although 5fC is an oxidation product of 5-methylcytosine (5mC), the two epigenetic marks show distinct genome-wide distributions and protein affinities, suggesting that they perform different functions in epigenetic signaling. A unique feature of 5fC is the presence of a potentially reactive aldehyde group in its structure. Herein, we show that 5fC bases in DNA readily form Schiff-base conjugates with Lys side chains of nuclear proteins in vitro and in vivo...
September 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28876055/supramolecular-assembly-of-peptide-amphiphiles
#14
Mark P Hendricks, Kohei Sato, Liam C Palmer, Samuel I Stupp
Peptide amphiphiles (PAs) are small molecules that contain hydrophobic components covalently conjugated to peptides. In this Account, we describe recent advances involving PAs that consist of a short peptide sequence linked to an aliphatic tail. The peptide sequence can be designed to form β-sheets among the amino acids near the alkyl tail, while the residues farthest from the tail are charged to promote solubility and in some cases contain a bioactive sequence. In water, β-sheet formation and hydrophobic collapse of the aliphatic tails induce assembly of the molecules into supramolecular one-dimensional nanostructures, commonly high-aspect-ratio cylindrical or ribbonlike nanofibers...
October 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28837839/genetic-and-structural-elucidation-of-capsular-polysaccharides-from-streptococcus-pneumoniae-serotype-23a-and-23b-and-comparison-to-serotype-23f
#15
Neil Ravenscroft, Aneesa Omar, Jason Hlozek, Cesarina Edmonds-Smith, Rainer Follador, Fabio Serventi, Gerd Lipowsky, Michelle M Kuttel, Paola Cescutti, Amirreza Faridmoayer
Streptococcus pneumoniae is a globally important encapsulated human pathogen with approximately 100 different serotypes recognized. Serogroup 23 consists of serotype 23F, present in licensed vaccines, and emerging serotypes 23A and 23B. Here, we report the previously unknown structures of the pneumococcal capsular polysaccharides serotype 23A and 23B determined using genetic analysis, NMR spectroscopy, composition and linkage analysis and Smith degradation (of polysaccharide 23A). The structure of the serotype 23A capsular polysaccharide is: →4)-β-D-Glcp-(1→3)-[[α-L-Rhap-(1→2)]-[Gro-(2→P→3)]-β-D-Galp-(1→4)]-β-L-Rhap-(1→...
August 18, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28813684/mimicking-mechanical-response-of-natural-tissues-strain-hardening-induced-by-transient-reticulation-in-lactose-modified-chitosan-chitlac
#16
Michela Cok, Pasquale Sacco, Davide Porrelli, Andrea Travan, Massimiliano Borgogna, Eleonora Marsich, Sergio Paoletti, Ivan Donati
The effect of transient cross-links has been explored on a lactose-modified chitosan, which previously had shown interesting biological features. The presence of galactose side chains and of the polyol spacer resulted particularly appealing for the reticulation by borate ions. The interaction between chitlac and borax was investigated by means of (11)B-NMR while rheology pointed to a marked non-linear behavior depending on the amount of borax added to the system. The presence of limited amount of cross-linking ion led to dilatant behavior when the steady flow curve was measured...
August 13, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28772607/preparation-and-characterization-of-polyurethanes-with-cross-linked-siloxane-in-the-side-chain-by-sol-gel-reactions
#17
Hui Zhao, Tong-Hui Hao, Guo-Hua Hu, Dean Shi, Da Huang, Tao Jiang, Qun-Chao Zhang
A series of novel polyurethanes containing cross-linked siloxane in the side chain (SPU) were successfully synthesized through a sol-gel process. The SPU was composed of 0%-20% N-(n-butyl)-3-aminopropyltriethoxysilane (HDI-T) modified hexamethylene diisocynate homopolymer. The effects of HDI-T content on both the structure and properties of SPU were investigated by Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), mechanical properties tests, gel content test, water contact angle measurement and water absorption test...
February 28, 2017: Materials
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
#18
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
#19
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...
October 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
#20
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 4mm 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...
September 1, 2017: Acta Biomaterialia
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