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Slađana Strmečki, Mojmír Trefulka, Pavlína Zatloukalová, Michal Durech, Borivoj Vojtesek, Emil Paleček
Glycosylation of proteins plays an important role in health and diseases. At present new simple and inexpensive methods of glycoprotein analysis are sought. We developed a monoclonal antibody Manost 2.1 in mice after immunization with the adduct of mannan with Os(VI)temed complex (temed is N,N,N',N'-tetramethylethylenediamine). The specificity of this antibody to different biomolecules treated with Os(VI)temed was tested using dot blot immunoassay. Manost 2.1 showed specificity toward Os(VI)temed-modified polysaccharides, glycoproteins and ribonucleotide at the 3'-end in DNA...
February 22, 2017: Analytica Chimica Acta
Ruth Röder, Tobias Preiß, Patrick Hirschle, Benjamin Steinborn, Andreas Zimpel, Miriam Hoehn, Joachim O Rädler, Thomas Bein, Ernst Wagner, Stefan Wuttke, Ulrich Lächelt
Self-assembly of individual units into multicomponent complexes is a powerful approach for the generation of functional super-structures. We present the coordinative interaction of oligohistidine-tags (His-tags) with metal-organic framework nanoparticles (MOF NPs). By this novel concept, different molecular units can be anchored on the outer surface of MOF NPs in a self-assembly process generating multifunctional nanosystems. The article focuses on two main objectives: first, the detailed investigation of the assembly process and fundamental establishment of the novel functionalization concept; and second, its subsequent use for the development of biomacromolecule (e...
January 11, 2017: Journal of the American Chemical Society
Yiping Chen, Yunlei Xianyu, Xingyu Jiang
As one of the major tools for and by chemical science, biochemical analysis is becoming increasingly important in fields like clinical diagnosis, food safety, environmental monitoring, and the development of chemistry and biochemistry. The advancement of nanotechnology boosts the development of analytical chemistry, particularly the nanoparticle (NP)-based approaches for biochemical assays. Functional NPs can greatly improve the performance of biochemical analysis because they can accelerate signal transduction, enhance the signal intensity, and enable convenient signal readout due to their unique physical and chemical properties...
January 9, 2017: Accounts of Chemical Research
Hyesoo Jeong, Soolin Kim, Jimin Lee, Jin Young Park, Wenmei Zhou, Xiyuan Liu, So Dam Kim, Yun Seon Song, Chang-Young Jang, Sei-Ryang Oh, Sangho Choi, Minsun Chang
Larrea nitida Cav. (LNC), which belongs to the family Zygophyllaceae, is widely indigenous and used in South America to treat various pathological conditions. It contains the antioxidant and antiinflammatory but toxic nordihydroguaiaretic acid (NDGA) as well as O-methylated metabolite of NDGA (MNDGA) as bioactive compounds. The hepatic metabolism-based toxicological potential of extracts of LNC (LNE), NDGA, and MNDGA has not previously been reported. The present study aimed to characterize the phase I and phase II hepatic metabolism and reactive intermediates of LNE, NDGA, and MNDGA and their effects on the major drug-metabolizing enzymes in vitro and ex vivo...
January 2017: Phytotherapy Research: PTR
Junhui Yang, Cuicui Ding, Liulian Huang, Min Zhang, Lihui Chen
γ-PGA-NHS ester, which was prepared using poly(γ-glutamic acid) (γ-PGA) and N-hydroxysuccinimide (NHS) as the raw materials, was synthesized to be a novel cross-linker of collagen. Fourier transform infrared spectra analysis suggested that the products displayed the characteristic absorption peak of ester. Results from nuclear magnetic resonance analysis indicated that the esterification degree of γ-PGA-NHS ester was increased with the increase of NHS. Modified collagen was prepared and characterized. The results of circular dichroism analysis indicated modified collagen retained the triple helix structure of natural collagen...
January 3, 2017: International Journal of Biological Macromolecules
Jan Heyda, Halil I Okur, Jana Hladílková, Kelvin B Rembert, William Hunn, Tinglu Yang, Joachim Dzubiella, Pavel Jungwirth, Paul S Cremer
A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd(+)) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation's action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd(+) was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO4(2-)...
January 5, 2017: Journal of the American Chemical Society
Nicole A Estrich, Armando Hernandez-Garcia, Renko de Vries, Thomas H LaBean
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc...
January 6, 2017: ACS Nano
Min Zheng, Jeffrey R Reimers, Mark P Waller, Pavel V Afonine
Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is twofold: firstly, the restraints have the potential to be more accurate, and secondly, the restraints can be more easily applied to new molecules such as drugs or novel cofactors. Here, a new project called Q|R aimed at developing quantum-based refinement of biomacromolecules is under active development by researchers at Shanghai University together with PHENIX developers...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
Shilei Wang, Jie Wu, Hao Yang, Xiangyu Liu, Qiaomu Huang, Zhong Lu
Dental caries is a widespread disease mainly caused by the anaerobic oral pathogen Streptococcus mutans (S. mutans). Ag/ZnO nanocomposite is an efficient antibacterial agent because of its high antibacterial activity and low cytotoxicity. In this study, rod-like Ag/ZnO nanocomposite was synthesized through a deposition-precipitation method and characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. The activity of Ag/ZnO nanocomposite against S. mutans was evaluated by determining the minimal inhibitory concentration, minimum bactericidal concentration and growth inhibition curve...
January 2017: Journal of Materials Science. Materials in Medicine
Christian Domilongo Bope, Dudu Tong, Xiuting Li, Lanyuan Lu
Elastic network models (ENMs) based on simple harmonic potential energy function have been proven over the last decade to be reliable computational models for understanding the intrinsic dynamics of biomacromolecules. In the original ENMs, the spring constants for different contact pairs are assumed to be identical, while there are a number of recent developments to determine non-uniform spring constants from atomistic force fields or experimental information. In particular, the fluctuation matching approaches in coarse-grained modeling can be applied to build more realistic heterogeneous ENMs, using information from an atomistic force field or experimental B-factors...
December 30, 2016: Progress in Biophysics and Molecular Biology
Sanaullah Khan, Johnny Birch, Pernille Harris, Marie-Rose Van Calsteren, Richard Ipsen, Günther H J Peters, Birte Svensson, Kristoffer Almdal
Molecular structures of exopolysaccharides are required to understand their functions and the relationships between the structure and physical and rheological properties. Small-angle X-ray scattering and dynamic light scattering were used in conjunction with molecular modeling to characterize solution structures of three lactic acid bacterial hetero-exopolysaccharides (HePS-1, HePS-2 and HePS-3). Values of radius of gyration RG, cross-sectional radius of gyration RXS, approximate length L and hydrodynamic diameter were not directly proportional to the molar mass and indicated the HePSs adopted a compact coil-like rather than an extended conformation...
January 2, 2017: Biomacromolecules
Lik Hang Yuen, Raphael Franzini
DNA-encoded chemical libraries (DECLs) are pools of DNA-tagged small molecules that enable facile screening and identification of biomacromolecule binders. The successful development of DECLs has leads to their increasingly important role in drug development and screening hits have entered clinical trials. In this review, we summarize the development and currently active research areas of DECLs with a focus on contributions from groups at academic institutes. We further look at opportunities and future direction of DECL research in medicinal chemistry and chemical biology based on the symbiotic relationship between academia and industry...
December 29, 2016: Chembiochem: a European Journal of Chemical Biology
Zhaohui Wang, Min Luo, Chengqiong Mao, Qi Wei, Tian Zhao, Yang Li, Gang Huang, Jinming Gao
Efficient delivery of biomacromolecules (e.g., proteins, nucleic acids) into cell cytosol remains a critical challenge for the development of macromolecular therapeutics or diagnostics. To date, most common approaches to assess cytosolic delivery rely on fluorescent labeling of macromolecules with an "always on" reporter and subcellular imaging of endolysosomal escape by confocal microscopy. This strategy is limited by poor signal-to-noise ratio and only offers low throughput, qualitative information. Herein we describe a quantitative redox-activatable sensor (qRAS) for the real-time monitoring of cytosolic delivery of macromolecules...
December 16, 2016: Angewandte Chemie
Jeffrey O'Brien, Shih-Hui Lee, Shunsuke Onogi, Kenneth J Shea
Biochemical diversity of venom extracts often occurs within a small number of shared protein families. Developing a sequestrant capable of broad-spectrum neutralization across various protein isoforms within these protein families is a necessary step in creating broad-spectrum antivenom. Using directed synthetic evolution to optimize a nanoparticle (NP) formulation capable of sequestering and neutralizing venomous phospholipase A2 (PLA2), we demonstrate that broad-spectrum neutralization and sequestration of venomous biomacromolecules is possible via a single optimized NP formulation...
December 28, 2016: Journal of the American Chemical Society
Xiaoqing Liu, Jean-Paul Chapel, Christophe Schatz
While many studies on coacervation have targeted biomacromolecules, we review in this article the key structure, thermodynamic and kinetic features of a fully synthetic coacervating system based on polyacrylic acid (PAA) and poly(diallyldimethylammonium chloride) (PDADMAC) oppositely charged polyelectrolytes at pH10, where PAA chains are fully deprotonated. Among the main points of interest, we can highlight (i) the presence of polyelectrolyte complex (PEC) nanoparticles that, unexpectedly, coexist with a certain amount of coacervate droplets in a large range of compositions, even far from stoichiometry; (ii) the fact that these PEC nanoparticles are likely precursors of the coacervation occurring at stoichiometry; (iii) the formation of soluble PECs only in a certain range of physicochemical conditions; (iv) the equilibrium properties of the system; (v) and last but not least a distinctive kinetic signature at stoichiometry evidenced by a peak in light scattering at very short times (~100ms)...
October 28, 2016: Advances in Colloid and Interface Science
Han Shih, Tanja Greene, Murray Korc, Chien-Chi Lin
Photopolymerized biomimetic hydrogels with adaptable properties have been widely used for cell and tissue engineering applications. As a widely adopted gel cross-linking method, photopolymerization provides experimenters on-demand and spatial-temporal controls in gelation kinetics. Long wavelength ultraviolet (UV) light initiated photopolymerization is among the most popular methods in the fabrication of cell-laden hydrogels owing to its rapid and relatively mild gelation conditions. The use of UV light, however, still causes concerns regarding its potential negative impacts on cells...
December 12, 2016: Biomacromolecules
Geyou Ao, Jason K Streit, Jeffrey A Fagan, Ming Zheng
New structural characteristics emerge when solid-state crystals are constructed in lower dimensions. This is exemplified by single-wall carbon nanotubes, which exhibit a degree of freedom in handedness and a multitude of helicities that give rise to three distinct types of electronic structures: metals, quasi-metals, and semiconductors. Here we report the use of intrinsically chiral single-stranded DNA to achieve simultaneous handedness and helicity control for all three types of nanotubes. We apply polymer aqueous two-phase systems to select special DNA-wrapped carbon nanotubes, each of which we argue must have an ordered DNA structure that binds to a nanotube of defined handedness and helicity and resembles a well-folded biomacromolecule with innate stereoselectivity...
December 28, 2016: Journal of the American Chemical Society
Sébastien Balme, Mathilde Lepoitevin, Ludovic F Dumée, Mikhael Bechelany, Jean-Marc Janot
The fundamental understanding of the transport mechanisms of objects across a single nanopore is one key point to develop Coulter counters at the nanoscale for macromolecule or nanoparticle detection. In this area, nanoparticles have been less investigated than biomacromolecules such as DNA or proteins due to their self-aggregation in the presence of salts. In this work, the transport of modified latex nanoparticles across solid-state nanopores was investigated. To prevent their aggregation, their surface was modified with a low molecular weight single strand DNA coating...
December 8, 2016: Soft Matter
J Jacques Jassoy, Andreas Berndhäuser, Fraser Duthie, Sebastian P Kühn, Gregor Hagelueken, Olav Schiemann
Structure determination of biomacromolecules under in-cell conditions is a relevant yet challenging task. Electron paramagnetic resonance (EPR) distance measurements in combination with site-directed spin labeling (SDSL) are a valuable tool in this endeavor but the usually used nitroxide spin labels are not well-suited for in-cell measurements. In contrast, triarylmethyl (trityl) radicals are highly persistent, exhibit a long relaxation time and a narrow spectral width. Here, the synthesis of a versatile collection of trityl spin labels and their application in in vitro and in-cell trityl-iron distance measurements on a cytochrome P450 protein are described...
January 2, 2017: Angewandte Chemie
Nigel Kirby, Nathan Cowieson, Adrian M Hawley, Stephen T Mudie, Duncan J McGillivray, Michael Kusel, Vesna Samardzic-Boban, Timothy M Ryan
Radiation damage is a major limitation to synchrotron small-angle X-ray scattering analysis of biomacromolecules. Flowing the sample during exposure helps to reduce the problem, but its effectiveness in the laminar-flow regime is limited by slow flow velocity at the walls of sample cells. To overcome this limitation, the coflow method was developed, where the sample flows through the centre of its cell surrounded by a flow of matched buffer. The method permits an order-of-magnitude increase of X-ray incident flux before sample damage, improves measurement statistics and maintains low sample concentration limits...
December 1, 2016: Acta Crystallographica. Section D, Structural Biology
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