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https://www.readbyqxmd.com/read/28345933/structure-energy-relationships-of-halogen-bonds-in-proteins
#1
Matthew R Scholfield, Melissa Coates Ford, Anna-Carin Cecilia Carlsson, Hawera Butta, Ryan A Mehl, Pui Shing Ho
The structures and stabilities of proteins are defined by a series of weak non-covalent electrostatic, van der Waals, and hydrogen bond (HB) interactions. In this study, we have designed and engineered halogen bonds (XBs) site-specifically in order to study their structure-energy relationship in a model protein, T4 lysozyme. The evidence for XBs is the displacement of the aromatic side chain towards an oxygen acceptor, at distances that are at or less than the sums of their respective van der Waals radii, when the hydroxyl substituent of the wildtype tyrosine is replaced by an iodine...
March 27, 2017: Biochemistry
https://www.readbyqxmd.com/read/28344357/quantum-dot-surface-engineering-toward-inert-fluorophores-with-compact-size-and-bright-stable-emission
#2
Sung Jun Lim, Liang Ma, André Schleife, Andrew M Smith
The surfaces of colloidal nanocrystals are complex interfaces between solid crystals, coordinating ligands, and liquid solutions. For fluorescent quantum dots, the properties of the surface vastly influence the efficiency of light emission, stability, and physical interactions, and thus determine their sensitivity and specificity when they are used to detect and image biological molecules. But after more than 30 years of study, the surfaces of quantum dots remain poorly understood and continue to be an important subject of both experimental and theoretical research...
August 1, 2016: Coordination Chemistry Reviews
https://www.readbyqxmd.com/read/28343105/photoluminescence-light-up-detection-of-zinc-ion-and-imaging-in-living-cells-based-on-the-aggregation-induced-emission-enhancement-of-glutathione-capped-copper-nanoclusters
#3
Liyun Lin, Yuefang Hu, Liangliang Zhang, Yong Huang, Shulin Zhao
In this work, we prepared glutathione (GSH)-capped copper nanoclusters (Cu NCs) with red emission by simply adjusting the pH of GSH/Cu(2+) mixture at room temperature. A photoluminescence light-up method for detecting Zn(2+) was then developed based on the aggregation induced emission enhancement of GSH-capped Cu NCs. Zn(2+) could trigger the aggregation of Cu NCs, inducing the enhancement of luminescence and the increase of absolute quantum yield from 1.3% to 6.2%. GSH-capped Cu NCs and the formed aggregates were characterized, and the possible mechanism was also discussed...
March 19, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28341704/structural-landscape-of-base-pairs-containing-post-transcriptional-modifications-in-rna
#4
Preethi P Seelam, Purshotam Sharma, Abhijit Mitra
Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures, and most commonly involve guanine or uridine modifications...
March 24, 2017: RNA
https://www.readbyqxmd.com/read/28338625/-r-aloesaponol-iii-8-methyl-ether-from-eremurus-persicus-a-novel-compound-against-leishmaniosis
#5
Daniela Rossi, Karzan Mahmood Ahmed, Raffaella Gaggeri, Serena Della Volpe, Lauretta Maggi, Giuseppe Mazzeo, Giovanna Longhi, Sergio Abbate, Federica Corana, Emanuela Martino, Marisa Machado, Raquel Varandas, Maria do Céu Sousa, Simona Collina
Leishmaniosis is a neglected tropical disease which affects several millions of people worldwide. The current drug therapies are expensive and often lack efficacy, mainly due to the development of parasite resistance. Hence, there is an urgent need for new drugs effective against Leishmania infections. As a part of our ongoing study on the phytochemical characterization and biological investigation of plants used in the traditional medicine of western and central Asia, in the present study, we focused on Eremurus persicus root extract in order to evaluate its potential in the treatment of leishmaniosis...
March 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335327/targeting-at-the-nanoscale-a-novel-s-layer-fusion-protein-enabling-controlled-immobilization-of-biotinylated-molecules
#6
Melinda Varga
With the aim of constructing an S-layer fusion protein that combines both excellent self-assembly and specific ligand i.e., biotin binding ability, streptavidin (aa 16-133) was fused to the S-layer protein of Sporosarcina ureae ATCC 13881 (SslA) devoid of its N-terminal 341 and C-terminal 172 amino acids. The genetically engineered chimeric protein could be successfully produced in E. coli, isolated, and purified via Ni affinity chromatography. In vitro recrystallisation experiments performed with the purified chimeric protein in solution and on a silicon wafer have demonstrated that fusion of the streptavidin domain does not interfere with the self-assembling properties of the S-layer part...
November 4, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28331316/in-vivo-biodistribution-and-behavior-of-cdte-zns-quantum-dots
#7
Yan Zhao, Yue Zhang, Gaofeng Qin, Jinjun Cheng, Wenhao Zeng, Shuchen Liu, Hui Kong, Xueqian Wang, Qingguo Wang, Huihua Qu
The unique features of quantum dots (QDs) make them desirable fluorescent tags for cell and developmental biology applications that require long-term, multitarget, and highly sensitive imaging. In this work, we imaged fluorescent cadmium telluride/zinc sulfide (CdTe/ZnS) QDs in organs, tissues, and cells, and analyzed the mechanism of their lymphatic uptake and cellular distribution. We observed that the fluorescent CdTe/ZnS QDs were internalized by lymph nodes in four cell lines from different tissue sources...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28327567/quantum-locality-in-game-strategy
#8
Carlos A Melo-Luna, Cristian E Susa, Andrés F Ducuara, Astrid Barreiro, John H Reina
Game theory is a well established branch of mathematics whose formalism has a vast range of applications from the social sciences, biology, to economics. Motivated by quantum information science, there has been a leap in the formulation of novel game strategies that lead to new (quantum Nash) equilibrium points whereby players in some classical games are always outperformed if sharing and processing joint information ruled by the laws of quantum physics is allowed. We show that, for a bipartite non zero-sum game, input local quantum correlations, and separable states in particular, suffice to achieve an advantage over any strategy that uses classical resources, thus dispensing with quantum nonlocality, entanglement, or even discord between the players' input states...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325225/-unconventional-experiments-in-biology-and-medicine-with-optimized-design-based-on-quantum-like-correlations
#9
Francis Beauvais
In previous articles, a description of 'unconventional' experiments (e.g. in vitro or clinical studies based on high dilutions, 'memory of water' or homeopathy) using quantum-like probability was proposed. Because the mathematical formulations of quantum logic are frequently an obstacle for physicians and biologists, a modified modeling that rests on classical probability is described in the present article. This modeling is inspired from a relational interpretation of quantum physics that applies not only to microscopic objects, but also to macroscopic structures, including experimental devices and observers...
February 2017: Homeopathy: the Journal of the Faculty of Homeopathy
https://www.readbyqxmd.com/read/28324655/tracking-the-energy-flow-on-nanoscale-via-sample-transmitted-excitation-photoluminescence-spectroscopy
#10
Pavel Moroz, Natalia Razgoniaeva, Yufan He, Gregory Jensen, Holly Eckard, H Peter Lu, Mikhail Zamkov
Tracking the energy flow in nanoscale materials is an important yet challenging goal. Experimental methods for probing the intermolecular energy transfer (ET) are often burdened by the spectral crosstalk between donor and acceptor species, which complicates unraveling their individual contributions. This issue is particularly prominent in inorganic nanoparticles and biological macromolecules featuring broad absorbing profiles. Here, we demonstrate a general spectroscopic strategy for measuring the ET efficiency between nanostructured or molecular dyes exhibiting a significant donor-acceptor spectral overlap...
March 23, 2017: ACS Nano
https://www.readbyqxmd.com/read/28321598/preparation-of-highly-biocompatible-znse-quantum-dots-using-a-new-source-of-acetyl-cysteine-as-capping-agent
#11
Ehsan Soheyli, Reza Sahraei, Gholamreza Nabiyouni
In this paper, we describe a facile method for preparation of ZnSe quantum dots (QDs) using an inexpensive and biocompatible source of acetyl cysteine in aqueous media. The structural properties of the ZnSe QDs have been characterized using XRD, FT-IR, and TEM techniques. The optical properties of the as-prepared QDs were found to be size-dependent, due to the strong confinement regime at relatively low refluxing time. Effect of solution pH and refluxing temperature on absorption and emission characteristics of the ZnSe QDs was studied...
March 20, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28320905/insights-into-the-deactivation-of-5-bromouracil-after-ultraviolet-excitation
#12
Francesca Peccati, Sebastian Mai, Leticia González
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28317922/optical-imaging-of-localized-chemical-events-using-programmable-diamond-quantum-nanosensors
#13
Torsten Rendler, Jitka Neburkova, Ondrej Zemek, Jan Kotek, Andrea Zappe, Zhiqin Chu, Petr Cigler, Jörg Wrachtrup
Development of multifunctional nanoscale sensors working under physiological conditions enables monitoring of intracellular processes that are important for various biological and medical applications. By attaching paramagnetic gadolinium complexes to nanodiamonds (NDs) with nitrogen-vacancy (NV) centres through surface engineering, we developed a hybrid nanoscale sensor that can be adjusted to directly monitor physiological species through a proposed sensing scheme based on NV spin relaxometry. We adopt a single-step method to measure spin relaxation rates enabling time-dependent measurements on changes in pH or redox potential at a submicrometre-length scale in a microfluidic channel that mimics cellular environments...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28315437/homology-modeling-molecular-docking-and-molecular-dynamics-studies-of-the-catalytic-domain-of-chitin-deacetylase-from-cryptococcus-laurentii-strain-ry1
#14
Soumyadev Sarkar, Suchetana Gupta, Writachit Chakraborty, Sanjib Senapati, Ratan Gachhui
This study provides structural insights into chitin deacetylase, over-expressing under nitrogen limiting condition in Cryptococcus laurentii strain RY1. The enzyme converts chitin, the second most abundant natural biopolymer, to chitosan, which offers tremendous applications in diverse fields. To elucidate the structure-function relationship of this biologically and industrially important enzyme, a homology model of the catalytic domain was constructed. The stability of the structure was assessed by molecular dynamics simulation studies...
March 14, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28314269/quantitative-structure-cytotoxicity-relationship-of-chalcones
#15
Hiroshi Sakagami, Yoshiko Masuda, Mineko Tomomura, Satoshi Yokose, Yoshihiro Uesawa, Naruhiko Ikezoe, Daiki Asahara, Koichi Takao, Taisei Kanamoto, Shigemi Terakubo, Hajime Kagaya, Hideki Nakashima, Yoshiaki Sugita
BACKGROUND: Fifteen chalcones were subjected to quantitative structure-activity relationship (QSAR) analysis based on their cytotoxicity and tumor specificity, in order to find their new biological activities. MATERIALS AND METHODS: Cytotoxicity against four human oral squamous cell carcinoma cell lines and three oral mesenchymal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor specificity (TS) was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal cells to that against tumor cell lines...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28306551/master-equations-and-the-theory-of-stochastic-path-integrals
#16
Markus F Weber, Erwin Frey
This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations...
April 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28299903/multifunctional-nanoparticle-composites-progress-in-the-use-of-soft-and-hard-nanoparticles-for-drug-delivery-and-imaging
#17
REVIEW
Ajmeeta Sangtani, Okhil K Nag, Lauren D Field, Joyce C Breger, James B Delehanty
With continued advancements in nanoparticle (NP) synthesis and in the interfacing of NPs with biological systems has come the exponential growth in the use of NPs for therapeutic drug delivery and imaging applications. In recent years, the advent of NP multifunctionality-the ability to perform multiple, disparate functions on a single NP platform-has garnered much excitement for the potential realization of highly functional NP-mediated drug delivery for use in the clinical setting. This Overview will survey the current state of the art (reports published within the last 5 years) of multifunctional NPs for therapeutic drug delivery, imaging or a combination thereof...
March 16, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28297997/quantum-information-processing-in-the-radical-pair-mechanism-haberkorn-s-theory-violates-the-ozawa-entropy-bound
#18
K Mouloudakis, I K Kominis
Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation so far constituting the theoretical foundation of spin chemistry violates fundamental bounds for the entropy of quantum systems, in particular the Ozawa bound. In contrast, a recently developed theory based on quantum measurements, quantum coherence measures, and quantum retrodiction, thus exemplifying the paradigm of quantum biology, satisfies the Ozawa bound as well as the Lanford-Robinson bound on information extraction...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28296892/blue-light-induced-accumulation-of-reactive-oxygen-species-is-a-consequence-of-the-drosophila-cryptochrome-photocycle
#19
Louis-David Arthaut, Nathalie Jourdan, Ali Mteyrek, Maria Procopio, Mohamed El-Esawi, Alain d'Harlingue, Pierre-Etienne Bouchet, Jacques Witczak, Thorsten Ritz, André Klarsfeld, Serge Birman, Robert J Usselman, Ute Hoecker, Carlos F Martino, Margaret Ahmad
Cryptochromes are evolutionarily conserved blue-light absorbing flavoproteins which participate in many important cellular processes including in entrainment of the circadian clock in plants, Drosophila and humans. Drosophila melanogaster cryptochrome (DmCry) absorbs light through a flavin (FAD) cofactor that undergoes photoreduction to the anionic radical (FAD•-) redox state both in vitro and in vivo. However, recent efforts to link this photoconversion to the initiation of a biological response have remained controversial...
2017: PloS One
https://www.readbyqxmd.com/read/28294217/competition-between-stacked-and-hydrogen-bonded-structures-of-cytosine-aggregates
#20
Jorge González, Imanol Usabiaga, Pedro F Arnaiz, Iker León, Rodrigo Martínez, Judith Millán, José A Fernández
The four bases of DNA constitute what is known as the "alphabet of life". Their combination of proton-donor and acceptor groups and aromatic rings allows them to form stacking structures and at the same time establish hydrogen bonds with their counterparts, resulting in the formation of the well-known double-helix structure of DNA. Here we explore the aggregation preferences of cytosine in supersonic expansions, using a combination of laser spectroscopic techniques and computations. The data obtained from the experiments carried out in the cold and isolated environment of the expansion allowed us to establish which are the leading interactions behind aggregation of cytosine molecules...
March 15, 2017: Physical Chemistry Chemical Physics: PCCP
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