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Gabriela Bitencourt-Ferreira, Walter Filgueira de Azevedo
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions is still an open problem in the simulation of biological systems, and the development of a new generation machine-learning model is an active research field. In this work, we propose a novel scoring function to predict Gibbs free energy of binding (ΔG) based on the crystallographic structure of complexes involving a protein and an active ligand...
June 7, 2018: Biophysical Chemistry
María Leiza Vitale, R-Marc Pelletier
The anterior pituitary regulates endocrine organs and physiological activities in the body. Environmental pollutants and drugs deleterious to the endocrine system may affect anterior pituitary activity through direct action on anterior pituitary cells. Within the gland, endocrine and folliculostellate cells are organized into and function as individual tridimensional networks, each network regulating its activity by coordinating the connected cells' responses to physiological or pathological cues. The gap junctions connecting endocrine cells and/or folliculostellate cells allow transmission of information among cells that is necessary for adequate network function...
June 12, 2018: Reproductive Toxicology
Shan Chen, Jonatan C Campillo-Brocal, Per Berglund, Maria Svedendahl Humble
The amine transaminase from Vibrio fluvialis (Vf-ATA) is an attractive enzyme with applications within Biocatalysis for the preparation of chiral amines. Various catalytic properties of Vf-ATA have been investigated, but a biophysical characterization of its stability has been lacking. Today, the industrial application of Vf-ATA is limited by its low operational stability. In order to enhance the knowledge regarding the structural stability of ATAs, general characterizations of different ATAs are required. In this work, the stability of Vf-ATA was explored...
June 12, 2018: Journal of Biotechnology
Raquel Valdes Angues, Austen Suits, Valerie S Palmer, Caesar Okot, Robert A Okot, Concy Atonywalo, Suzanne K Gazda, David L Kitara, Moka Lantum, Spencer S Peter
BACKGROUND: Disease surveillance in rural regions of many countries is poor, such that prolonged delays (months) may intervene between appearance of disease and its recognition by public health authorities. For infectious disorders, delayed recognition and intervention enables uncontrolled disease spread. We tested the feasibility in northern Uganda of developing real-time, village-based health surveillance of an epidemic of Nodding syndrome (NS) using software-programmed smartphones operated by minimally trained lay mHealth reporters...
June 15, 2018: PLoS Neglected Tropical Diseases
Maria Fernanda Laranjeira-Silva, Wanpeng Wang, Tamika K Samuel, Fernando Y Maeda, Vladimir Michailowsky, Iqbal Hamza, Zhongchi Liu, Norma W Andrews
Iron is essential for many cellular processes, but can generate highly toxic hydroxyl radicals in the presence of oxygen. Therefore, intracellular iron accumulation must be tightly regulated, by balancing uptake with storage or export. Iron uptake in Leishmania is mediated by the coordinated action of two plasma membrane proteins, the ferric iron reductase LFR1 and the ferrous iron transporter LIT1. However, how these parasites regulate their cytosolic iron concentration to prevent toxicity remains unknown...
June 15, 2018: PLoS Pathogens
Ruth E Timme, Hugh Rand, Maria Sanchez Leon, Maria Hoffmann, Errol Strain, Marc Allard, Dwayne Roberson, Joseph D Baugher
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions...
June 15, 2018: Microbial Genomics
Sheue-Fen Tzeng, Chin-Hsien Tsai, Tai-Kuang Chao, Yu-Ching Chou, Yu-Chih Yang, Mong-Hsun Tsai, Tai-Lung Cha, Pei-Wen Hsiao
Disseminated castration-resistant prostate cancer (CRPC) is a common disease in men that is characterized by limited survival and resistance to androgen-deprivation therapy. The increase in human epidermal growth factor receptor 2 (HER2) signaling contributes to androgen receptor activity in a subset of patients with CRPC; however, enigmatically, HER2-targeted therapies have demonstrated a lack of efficacy in patients with CRPC. Aberrant glycosylation is a hallmark of cancer and involves key processes that support cancer progression...
June 15, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Janis Timoshenko, Andris Anspoks, Arturs Cintins, Alexei Kuzmin, Juris Purans, Anatoly I Frenkel
The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra...
June 1, 2018: Physical Review Letters
Chen Wei, Boxun Sun, Zelun Cai, Zifeng Zhao, Yu Tan, Weibo Yan, Huibo Wei, Zhiwei Liu, Zuqiang Bian, Chunhui Huang
Four tridentate europium(III) complexes containing a diphenylphosphoryl group are prepared with strong bonding between the ligands and centered ion, convinced by crystal structures. Compared to their parent bidentate complexes, the tridentate complexes display improved and exceptionally high photoluminescence quantum yields (PLQYs) in powder (all over 80%, best 91%), as well as in a CH2 Cl2 solution and poly(methyl methacrylate) films, benefiting from compact, stable, and saturated coordination.
June 15, 2018: Inorganic Chemistry
Jie Chen, Yoshitaka Matsushita, Taras Kolodiazhnyi, Alexei A Belik, Yoshihiro Tsujimoto, Yoshio Katsuya, Masahiko Tanaka, Yu Su, Youguo Shi, Kazunari Yamaura
The crystal structure of HgPbO3 was studied using single-crystal X-ray diffraction and powder synchrotron X-ray diffraction. The structure was well characterized as a centrosymmetric model with a space group of R-3 m [hexagonal setting: a = 5.74413(6) Å and c = 7.25464(8) Å] rather than as a noncentrosymmetric model as was expected. It was found that Pb4+ is octahedrally coordinated by six oxygen atoms as usual, while Hg2+ is coordinated by three oxygen atoms in a planar manner, this being a very rare coordination of Hg in a solid-state material...
June 15, 2018: Inorganic Chemistry
Panwang Zhou, Keli Han
As one of the most fundamental processes, excited-state proton transfer (ESPT) plays a major role in both chemical and biological systems. In the past several decades, experimental and theoretical studies on ESPT systems have attracted considerable attention because of their tremendous potential in fluorescent probes, biological imaging, white-light-emitting materials, and organic optoelectronic materials. ESPT is related to fluorescence properties and usually occurs on an ultrafast time scale at or below 100 fs...
June 15, 2018: Accounts of Chemical Research
Nan Cao, Kemin Tan, Thirunavukkarasu Annamalai, Andrzej Joachimiak, Yuk-Ching Tse-Dinh
We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle...
June 14, 2018: Nucleic Acids Research
Takahide Tohmonda, Akiko Kamiya, Akira Ishiguro, Takashi Iwaki, Takahiko J Fujimi, Minoru Hatayama, Jun Aruga
Zic family genes encode C2H2-type zinc finger proteins that act as critical toolkit proteins in the metazoan body plan establishment. In this study, we searched evolutionarily conserved domains among 121 Zic protein sequences from 22 animal phyla and 40 classes, and addressed their evolutionary significance. The collected sequences included those from poriferans and orthonectids. We discovered seven new conserved domains (CDs), CD0-CD6, (in order from the N- to C-terminus) using the most conserved Zic protein sequences from Deuterostomia (Hemichordata, Cephalochordata), Lophotrochozoa (Cephalopoda and Brachiopoda), and Ecdysozoa (Chelicerata, Priapulida)...
June 14, 2018: Molecular Biology and Evolution
Joanna I Sulkowska, Szymon Niewieczerzal, Aleksandra I Jarmolinska, Jonathan T Siebert, Peter Virnau, Wanda Niemyska
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial...
June 14, 2018: Nucleic Acids Research
Jacqueline S Stevens, Mary C Gray, Christophe Morisseau, Alison K Criss
Background: Infection with Neisseria gonorrhoeae (Ngo) is characterized by robust neutrophil influx that is insufficient to clear the bacteria. Sustained neutrophilic inflammation contributes to serious clinical sequelae that particularly affect women, including pelvic inflammatory disease and infertility. Methods: We established a three-component system using Ngo, End1 polarized human endocervical cells, and primary human neutrophils to investigate neutrophil transepithelial migration following infection...
June 13, 2018: Journal of Infectious Diseases
Konstantina Karathanou, Ana-Nicoleta Bondar
The Sec protein secretion machinery includes proteins whose reaction coordinates involve large-scale conformational changes. Dynamic hydrogen-bond networks can provide structural plasticity required by the SecA protein motor and the SecY protein translocon. Here we discuss hydrogen-bond networks of these two Sec proteins from crystal structures and molecular simulations, and the usefulness of molecular simulations approaches to studying dynamic hydrogen bonds and their role in bacterial protein secretion.
July 1, 2018: FEMS Microbiology Letters
Hao Sun, Yaoke Duan, Xiaocui Qi, Liyang Zhang, Heqiang Huo, Haijun Gong
Background and Aims: Silicon has been proven to exert beneficial effects on plant growth and stress tolerance, and silicon accumulation varies among different plant species. Cucumber (Cucumis sativus) is a widely used dicot model for silicon accumulation, but little is known about the molecular mechanism of its silicon uptake. Previously, we isolated and characterized CsLsi1, a silicon influx transporter gene from cucumber. In this study, we cloned a putative silicon efflux transporter gene, CsLsi2, from cucumber and investigated its role in silicon uptake...
June 14, 2018: Annals of Botany
P W Stroman, G Ioachim, J M Powers, R Staud, C Pukall
Descending regulation of spinal cord responses to nociceptive signaling has a strong influence on pain perception. Prior studies using functional magnetic resonance imaging (fMRI) have indicated that in addition to reactive responses to nociceptive signals there is a continuous component to regulation, and that it may vary with differences in pain sensitivity. We hypothesize that this continuous regulation component occurs routinely in fMRI studies prior to noxious stimulation, as well as during, and following stimulation...
June 12, 2018: Pain
Daniel Niederer, Tobias Engeroff, Franziska Wallner, Ulrike Plaumann, Winfried Banzer
OBJECTIVE: To compare the exercise loads and cognitive effects of a classical workplace program from that for a motor-cognitive coordination workplace intervention. METHODS: Twenty-eight (28) employed adults (women 19, men 9) participated in a motor-cognitive coordination and a classical workplace health promotion exercise intervention. Effects on attention and cognition (trail making test [TMT]) as well as exercise load (heart rate and rates of perceived exhaustion [RPE]) were assessed...
June 13, 2018: Journal of Occupational and Environmental Medicine
Wei Li, Jing Jin, Xiaoqing Liu, Li Wang
The transformation effects of metal ions and temperature on the DNA bases guanine (G) metal-organic coordination motifs in water have been investigated by scanning tunneling microcopy (STM). The G molecules form an ordered hydrogen-bonded structure at the water- highly oriented pyrolytic graphite (HOPG) interface. The STM observations reveal that the canonical G/9H form can be transformed into the G/(3H, 7H) tautomer by increasing the temperature of the G solution to 38.6oC. Moreover, metal ions bind with G molecules to form G4Fe13+, G3Fe32+ and the heterochiral intermixed G4Na1+ metal-organic networks after the introduction of the alkali-metal ions in cellular environment...
June 15, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
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