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https://www.readbyqxmd.com/read/28062560/the-amyloid-phenomenon-and-its-links-with-human-disease
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/27934019/experimental-and-computational-analysis-of-protein-stabilization-by-gly-to-d-ala-substitution-a-convolution-of-native-state-and-unfolded-state-effects
#6
Junjie Zou, Benben Song, Carlos Simmerling, Daniel Raleigh
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I' and II″ β-turns...
December 7, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27833622/downregulation-of-a-udp-arabinomutase-gene-in-switchgrass-panicum-virgatum-l-results-in-increased-cell-wall-lignin-while-reducing-arabinose-glycans
#7
Jonathan D Willis, James A Smith, Mitra Mazarei, Ji-Yi Zhang, Geoffrey B Turner, Stephen R Decker, Robert W Sykes, Charleson R Poovaiah, Holly L Baxter, David G J Mann, Mark F Davis, Michael K Udvardi, Maria J Peña, Jason Backe, Maor Bar-Peled, C N Stewart
Background: Switchgrass (Panicum virgatum L.) is a C4 perennial prairie grass and a dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are inhibited by the plant cell wall's natural recalcitrance against enzymatic degradation. Plant hemicellulose polysaccharides such as arabinoxylans structurally support and cross-link other cell wall polymers. Grasses predominately have Type II cell walls that are abundant in arabinoxylan, which comprise nearly 25% of aboveground biomass...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27814576/protein-oxidation-an-overview-of-metabolism-of-sulphur-containing-amino-acid-cysteine
#8
Saheem Ahmad, Hamda Khan, Uzma Shahab, Shahnawaz Rehman, Zeeshan Rafi, Mohd Yasir Khan, Ahsanullah Ansari, Zeba Siddiqui, Jalaluddin Mohammad Ashraf, Saleh M S Abdullah, Safia Habib, Moin Uddin
The available data suggest that among cellular constituents, proteins are the major target for oxidation primarily because of their quantity and high rate of interactions with ROS. Proteins are susceptible to ROS modifications of amino acid side chains which alter protein structure. Among the amino acids, Cysteine (Cys) is more prone to oxidation by ROS because of its high nucleophilic property. The reactivity of Cys with ROS is due to the presence of thiol group. In the oxidised form, Cys forms disulfide bond, which are primary covalent cross-link found in proteins, and which stabilize the native conformation of a protein...
January 1, 2017: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/27795445/critical-contribution-of-tyr15-in-the-hiv-1-integrase-in-in-facilitating-in-assembly-and-nonenzymatic-function-through-the-in-precursor-form-with-reverse-transcriptase
#9
Tatsuro Takahata, Eri Takeda, Minoru Tobiume, Kenzo Tokunaga, Masaru Yokoyama, Yu-Lun Huang, Atsuhiko Hasegawa, Tatsuo Shioda, Hironori Sato, Mari Kannagi, Takao Masuda
: Nonenzymatic roles for HIV-1 integrase (IN) at steps prior to the enzymatic integration step have been reported. To obtain structural and functional insights into the nonenzymatic roles of IN, we performed genetic analyses of HIV-1 IN, focusing on a highly conserved Tyr15 in the N-terminal domain (NTD), which has previously been shown to regulate an equilibrium state between two NTD dimer conformations. Replacement of Tyr15 with alanine, histidine, or tryptophan prevented HIV-1 infection and caused severe impairment of reverse transcription without apparent defects in reverse transcriptase (RT) or in capsid disassembly kinetics after entry into cells...
January 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/27782635/structure-and-dynamics-of-polyelectrolyte-surfactant-mixtures-under-conditions-of-surfactant-excess
#10
Ingo Hoffmann, Miriam Simon, Bela Farago, Ralf Schweins, Peter Falus, Olaf Holderer, Michael Gradzielski
Oppositely charged polyelectrolyte (PE) surfactant mixtures can self-assemble into a large variety of mesoscopic structures, so-called polyelectrolyte surfactant complexes (PESCs). These structures directly affect the macroscopic behavior of such solutions. In this study, we investigated mixtures of the cationically charged PE JR 400 and the anionic surfactant SDS with the help of different neutron scattering and fluorescence methods. While an excess of PE charges in semi-dilute solutions causes an increase of viscosity, it has been observed that an excess of surfactant charges reduces the viscosity while precipitation is observed at charge equilibrium...
September 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27748576/gelatin-porous-scaffolds-as-delivery-systems-of-calcium-alendronate
#11
Silvia Panzavolta, Paola Torricelli, Sonia Casolari, Annapaola Parrilli, Sofia Amadori, Milena Fini, Adriana Bigi
The systemic administration of bisphosphonates (BPs) for the treatment of metabolic diseases characterized by abnormal bone loss suffers from several adverse side effects, which can be reduced by implementation of alternative modes of administration. In this work, glutaraldehyde cross-linked gelatin scaffolds are proposed as delivery systems of calcium alendronate monohydrate (CaAL•H2 O). The 3D highly porous scaffolds display a relevant interconnected porosity (>94%), independently from CaAL•H2 O content (0, 3, and 6 wt%)...
October 17, 2016: Macromolecular Bioscience
https://www.readbyqxmd.com/read/27735959/isolation-and-structural-analysis-of-the-covalent-adduct-formed-between-a-bis-amino-mitoxantrone-analogue-and-dna-a-pathway-to-major-minor-groove-cross-linked-adducts
#12
Shyam K Konda, Celine Kelso, Jelena Medan, Brad E Sleebs, Don R Phillips, Suzanne M Cutts, J Grant Collins
The major covalent adduct formed between a (13)C-labelled formaldehyde activated bis-amino mitoxantrone analogue (WEHI-150) and the hexanucleotide d(CG(5Me)CGCG)2 has been isolated by HPLC chromatography and the structure determined by NMR spectroscopy. The results indicate that WEHI-150 forms one covalent bond through a primary amine to the N-2 of the G2 residue, with the polycyclic ring structure intercalated at the (5Me)C3pG4/G10p(5Me)C9 site. Furthermore, the WEHI-150 aromatic ring system is oriented approximately parallel to the long axis of the base pairs, with one aliphatic side-chain in the major groove and the other side-chain in the minor groove...
October 13, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27714610/ribosomal-synthesis-of-thioether-bridged-bicyclic-peptides
#13
Nina Bionda, Rudi Fasan
Many biologically active peptides found in nature exhibit a bicyclic structure wherein a head-to-tail cyclic backbone is further constrained by an intramolecular linkage connecting two side chains of the peptide. Accordingly, methods to access macrocyclic peptides sharing this overall topology could be of significant value toward the discovery of new functional entities and bioactive compounds. With this goal in mind, we recently developed a strategy for enabling the biosynthesis of thioether-bridged bicyclic peptides in living bacterial cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27678386/synthesis-of-polylactide-based-core-shell-interface-cross-linked-micelles-for-anticancer-drug-delivery
#14
Chih-Kuang Chen, Wei-Jen Lin, Yu Hsia, Leu-Wei Lo
Well-defined poly(ethylene glycol)-b-allyl functional polylactide-b-polylactides (PEG-APLA-PLAs) are synthesized through sequential ring-opening polymerization. PEG-APLA-PLAs that have amphiphilic properties and reactive allyl side chains on their intermediate blocks are successfully transferred to core-shell interface cross-linked micelles (ICMs) by micellization and UV-initiated irradiation. ICMs have demonstrated enhanced colloidal stability in physiological-mimicking media. Hydrophobic molecules such as Nile Red or doxorubicin (Dox) are readily loaded into ICMs; the resulting drug-ICM formulations possess slow and sustained drug release profiles under physiological-mimicking conditions...
September 28, 2016: Macromolecular Bioscience
https://www.readbyqxmd.com/read/27672697/chemical-synthesis-of-peptides-containing-site-specific-advanced-glycation-endproducts
#15
Harveen Kaur, Meder Kamalov, Margaret A Brimble
In nature, proteins, lipids, and nucleic acids can nonenzymatically react with sugars and sugar degradation products to give rise to a diverse range of modifications, known as advanced glycation endproducts (AGEs). These AGEs typically occur at lysine and arginine residues of long-lived proteins, such as collagen, and can modify the structure and function of the native protein. AGEs accumulate during the normal aging process, and AGE formation is dramatically accelerated with diabetes. AGEs have also been implicated in a wide range of debilitating conditions including cardiovascular, renal failure, and neurodegenerative diseases...
October 18, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27621316/bypass-of-dna-protein-cross-links-conjugated-to-the-7-deazaguanine-position-of-dna-by-translesion-synthesis-polymerases
#16
Susith Wickramaratne, Shaofei Ji, Shivam Mukherjee, Yan Su, Matthew G Pence, Lee Lior-Hoffmann, Iwen Fu, Suse Broyde, F Peter Guengerich, Mark Distefano, Orlando D Schärer, Yuk Yin Sham, Natalia Tretyakova
DNA-protein cross-links (DPCs) are bulky DNA lesions that form both endogenously and following exposure to bis-electrophiles such as common antitumor agents. The structural and biological consequences of DPCs have not been fully elucidated due to the complexity of these adducts. The most common site of DPC formation in DNA following treatment with bis-electrophiles such as nitrogen mustards and cisplatin is the N7 position of guanine, but the resulting conjugates are hydrolytically labile and thus are not suitable for structural and biological studies...
November 4, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27612701/self-healable-mussel-mimetic-nanocomposite-hydrogel-based-on-catechol-containing-polyaspartamide-and-graphene-oxide
#17
Bo Wang, Young Sil Jeon, Ho Seok Park, Ji-Heung Kim
Stimuli-responsive and self-healing materials have a wide range of potential uses, and some significant research has focused on cross-linking of hydrogel materials by means of reversible coordination bonding. The resulting materials, however, tend to have poor mechanical properties with pronounced weakness and brittleness. In this work, we present a novel mussel-inspired graphene oxide(GO)-containing hydrogel based on modified polyaspartamide with γ-amino butyric acid (GABA), 3.4-dihydroxyphenethylamine (DOPA), and ethanolamine (EA), termed PolyAspAm(GABA/DOPA/EA)...
December 1, 2016: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/27551163/ph-responsive-and-oxidation-resistant-wet-adhesive-based-on-reversible-catechol-boronate-complexation
#18
Ameya R Narkar, Brett Barker, Matthew Clisch, Jingfeng Jiang, Bruce P Lee
A smart adhesive capable of binding to a wetted surface was prepared by copolymerizing dopamine methacrylamide (DMA) and 3-acrylamido phenylboronic acid (AAPBA). pH was used to control the oxidation state and the adhesive property of the catechol side chain of DMA and to trigger the catechol-boronate complexation. FTIR spectroscopy confirmed the formation of the complex at pH 9, which was not present at pH 3. The formation of the catechol-boronate complex increased the cross-linking density of the adhesive network...
August 9, 2016: Chemistry of Materials: a Publication of the American Chemical Society
https://www.readbyqxmd.com/read/27548069/reversible-deactivation-radical-polymerization-of-monomers-containing-activated-aziridine-groups
#19
David C McLeod, Nicolay V Tsarevsky
Polymers bearing activated aziridine groups are attractive precursors to α-substituted-β-amino-functionalized materials due to the enhanced reactivity of the pendant aziridine functionalities toward ring-opening by nucleophiles. Two aziridine-containing styrenic monomers, 2-(4-vinylphenyl)aziridine (VPA) and N-mesyl-2-(4-vinylphenyl)aziridine (NMVPA), were polymerized under a variety of reversible deactivation radical polymerization conditions. Low-catalyst-concentration atom transfer radical polymerization (LCC-ATRP) and reversible addition-fragmentation chain-transfer (RAFT) polymerization were ineffective at producing well-defined polymers from VPA due to side reactions between the aziridine functionalities and the agents controlling the polymerizations (catalysts or chain transfer agents)...
October 2016: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/27521457/benchmarking-of-protein-carbonylation-analysis-in-caenorhabditis-elegans-specific-considerations-and-general-advice
#20
S Pyr Dit Ruys, J-M Bonzom, S Frelon
Oxidative stress has been extensively studied due to its correlation with cellular disorders and aging. In proteins, one biomarker of oxidative stress is the presence of carbonyl groups, such as aldehyde and ketone, in specific amino acid side chains such as lysine, proline, arginine and threonine, so-called protein carbonylation (PC). PC study is now a growing field in general and medical science since PC accumulation is associated with various pathologies and disorders. At present, enzyme-linked immunosorbent assays (ELISA) seem to be the most robust method of quantifying the presence of carbonyl groups in proteins, despite having some recognised caveats...
August 10, 2016: Free Radical Biology & Medicine
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