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https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#1
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936493/new-additions-to-the-cluspro-server-motivated-by-capri
#2
Sandor Vajda, Christine Yueh, Dmitri Beglov, Tanggis Bohnuud, Scott E Mottarella, Bing Xia, David R Hall, Dima Kozakov
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for Small Angle X-ray Scattering (SAXS) data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936491/intrinsic-%C3%AE-helix-propensities-compact-hydrodynamic-radii-in-intrinsically-disordered-proteins
#3
Lance R English, Erin C Tilton, Benjamin J Ricard, Steven T Whitten
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936472/relaxant-effect-of-sodium-tanshinone-iia-sulphonate-on-mouse-tracheal-smooth-muscle
#4
Yi-Lin Zhang, Jia-Wen Xu, Xiong-Hao Wu, Peng-Xiao Chen, Fang Wei, Dong-Dong Gao, Xiao-Wen Chen, Yu-Li Luo, Yun-Xin Zhu, Jiehong Huang, Ya-Xia Tan, Lei Zhao, Wen-Liang Zhou
Sodium tanshinone IIA sulphonate, a water-soluble derivative of tanshinone IIA, has been proven to possess versatile biological properties, but its pharmacological effect on tracheal smooth muscle remains elusive. This paper presents a study on the relaxant effect and underlying mechanisms of sodium tanshinone IIA sulphonate on mouse tracheal smooth muscle. The relaxant effect of sodium tanshinone IIA sulphonate was evaluated in mouse tracheal rings using a mechanical recording system. Intracellular Ca(2+) concentration was measured in primary cultured tracheal smooth muscle cells using confocal imaging system...
December 9, 2016: Planta Medica
https://www.readbyqxmd.com/read/27936466/dpp4-cd26-overexpression-in-urothelial-carcinoma-confers-an-independent-prognostic-impact-and-correlates-with-intrinsic-biological-aggressiveness
#5
Peir-In Liang, Bi-Wen Yeh, Wei-Ming Li, Ti-Chun Chan, I-Wei Chang, Chun-Nung Huang, Ching-Chia Li, Hung-Lung Ke, Hsin-Chih Yeh, Wen-Jeng Wu, Chien-Feng Li
Urothelial carcinoma (UC) is common cancer worldwide. The molecular aberrations regarding tumor progression remain unclear. Pericellular proteolysis is crucial in tumorigenesis, but its significance is unexplored in UC. By data mining the datasets in Gene Expression Omnibus, specifically focus on the proteolysis pathway, and followed by a preliminary validation in a pilot batch of tumor samples, we identified that the upregulation of dipeptidyl peptidase 4 (DPP4) was most significantly associated with clinical aggressiveness of UCs...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27936453/biological-mechanisms-of-depression-following-treatment-with-interferon-for-chronic-hepatitis-c-a-critical-systematic-review
#6
REVIEW
Myrela O Machado, Giovanni Oriolo, Beatrice Bortolato, Cristiano A Köhler, Michael Maes, Marco Solmi, Iria Grande, Rocío Martín-Santos, Eduard Vieta, André F Carvalho
BACKGROUND: A significant subset of patients infected by the hepatitis C virus (HCV) develops a major depressive episode (MDE) during Interferon-alpha (IFN-α) based immunotherapy. We performed a systematic review of studies which examined biological mechanisms contributing to the onset of a MDE during IFN-α-based immunotherapy for HCV. METHODS: Major electronic databases were searched from inception up until 15th February 2016 for peer-reviewed prospective studies that had enrolled HCV infected patients who received IFN-α treatment...
November 27, 2016: Journal of Affective Disorders
https://www.readbyqxmd.com/read/27936445/synthesis-and-antifungal-activity-of-novel-indole-replaced-streptochlorin-analogues
#7
Ming-Zhi Zhang, Chen-Yang Jia, Yu-Cheng Gu, Nick Mulholland, Sarah Turner, David Beattie, Wei-Hua Zhang, Guang-Fu Yang, John Clough
Based on examples of the successful applications in drug discovery of bioisosterism, a series of streptochlorin analogues in which indole has been replaced by other heterocycles has been designed and synthesized, as a continuation of our studies aimed at the discovery of novel streptochlorin analogues with improved antifungal activity. Biological testing showed that most of the indole-replaced streptochlorin analogues were inactive, though compound 6f had a broad spectrum of antifungal activity with significant activity against Alternaria solani...
December 2, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27936443/antifungal-potential-of-marine-natural-products
#8
REVIEW
Ebaa M El-Hossary, Cheng Cheng, Mostafa M Hamed, Ashraf Nageeb El-Sayed Hamed, Knut Ohlsen, Ute Hentschel, Usama Ramadan Abdelmohsen
Fungal diseases represent an increasing threat to human health worldwide which in some cases might be associated with substantial morbidity and mortality. However, only few antifungal drugs are currently available for the treatment of life-threatening fungal infections. Furthermore, plant diseases caused by fungal pathogens represent a worldwide economic problem for the agriculture industry. The marine environment continues to provide structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents...
November 14, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27936436/spectroscopic-single-crystal-x-ray-hirshfeld-in-vitro-and-in-silico-biological-evaluation-of-a-new-series-of-potent-thiazole-nucleus-integrated-with-pyrazoline-scaffolds
#9
Vinutha V Salian, Badiadka Narayana, Balladka K Sarojini, Madan S Kumar, Govinahalli S Nagananda, Kullaiah Byrappa, Avinash K Kudva
In the present study, the spectroscopic characterization of a new series of substituted thiazole linked pyrazoline scaffolds 4a-l was performed. The formation of 4a-l from the intermediate 3-(4-chlorophenyl)-5-[4-(propan-2-yl)phenyl]-4,5-dihydro-1H-pyrazole-1-carbothioamide 2 and substituted 2-bromo-1-phenylethanone 3a-l was evidenced through the changes in FTIR, (1)H NMR, (13)C NMR, LCMS data. The X-ray diffraction studies revealed that compound 2 and 4g crystallized in monoclinic crystal system with P21/n space group...
November 28, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/27936430/collagen-tissue-treated-with-chitosan-solution-in-h2o-co2-mixtures-influence-of-clathrates-hydrates-on-the-structure-and-mechanical-properties
#10
Ivan S Chaschin, Natalia P Bakuleva, Timofei E Grigoriev, Sergey V Krasheninnikov, Lev N Nikitin
A mixture of water/carbon dioxide is a "green" perspective solvent from the viewpoint of biomedical applications. Clathrate hydrates are formed this solvent under certain conditions and a very interesting question is the impact of clathrates hydrates on the structure and properties of bovine pericardium, which is used in biomedicine, in particular as a main part of biological heart valve prostheses. The aim of the present work is to investigate the influence of clathrates on the structure and mechanical properties of the collagen tissue treated with chitosan in H2O/CO2 mixtures under pressure 3...
November 30, 2016: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/27936415/hydraulic-fracturing-in-cells-and-tissues-fracking-meets-cell-biology
#11
REVIEW
Marino Arroyo, Xavier Trepat
The animal body is largely made of water. A small fraction of body water is freely flowing in blood and lymph, but most of it is trapped in hydrogels such as the extracellular matrix (ECM), the cytoskeleton, and chromatin. Besides providing a medium for biological molecules to diffuse, water trapped in hydrogels plays a fundamental mechanical role. This role is well captured by the theory of poroelasticity, which explains how any deformation applied to a hydrogel causes pressure gradients and water flows, much like compressing a sponge squeezes water out of it...
December 6, 2016: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/27936412/contribution-of-cellular-autolysis-to-tissular-functions-during-plant-development
#12
REVIEW
Sacha Escamez, Hannele Tuominen
Plant development requires specific cells to be eliminated in a predictable and genetically regulated manner referred to as programmed cell death (PCD). However, the target cells do not merely die but they also undergo autolysis to degrade their cellular corpses. Recent progress in understanding developmental cell elimination suggests that distinct proteins execute PCD sensu stricto and autolysis. In addition, cell death alone and cell dismantlement can fulfill different functions. Hence, it appears biologically meaningful to distinguish between the modules of PCD and autolysis during plant development...
December 6, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27936408/biased-mu-opioid-receptor-ligands-a-promising-new-generation-of-pain-therapeutics
#13
REVIEW
Edward R Siuda, Richard Carr, David H Rominger, Jonathan D Violin
Opioid chemistry and biology occupy a pivotal place in the history of pharmacology and medicine. Morphine offers unmatched efficacy in alleviating acute pain, but is also associated with a host of adverse side effects. The advent of biased agonism at G protein-coupled receptors has expanded our understanding of intracellular signaling and highlighted the concept that certain ligands are able to differentially modulate downstream pathways. The ability to target one pathway over another has allowed for the development of biased ligands with robust clinical efficacy and fewer adverse events...
December 6, 2016: Current Opinion in Pharmacology
https://www.readbyqxmd.com/read/27936401/adsorptive-removal-and-separation-of-chemicals-with-metal-organic-frameworks-contribution-of-%C3%AF-complexation
#14
REVIEW
Nazmul Abedin Khan, Sung Hwa Jhung
Efficient removal and separation of chemicals from the environment has become a vital issue from a biological and environmental point of view. Currently, adsorptive removal/separation is one of the most promising approaches for cleaning purposes. Selective adsorption/removal of various sulfur- and nitrogen-containing compounds, olefins, and π-electron-rich gases via π-complex formation between an adsorbent and adsorbate molecules is very competitive. Porous metal-organic framework (MOF) materials are very promising in the adsorption/separation of various liquids and gases owing to their distinct characteristics...
November 27, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27936355/sample-size-determination-for-a-three-arm-equivalence-trial-of-poisson-and-negative-binomial-responses
#15
Yu-Wei Chang, Yi Tsong, Zhigen Zhao
Assessing equivalence or similarity has drawn much attention recently as many drug products have lost or will lose their patents in the next few years, especially certain best-selling biologics. To claim equivalence between the test treatment and the reference treatment when assay sensitivity is well-established from historical data, one has to demonstrate both superiority of the test treatment over placebo and equivalence between the test treatment and the reference treatment. Thus, there is urgency for practitioners to derive a practical way to calculate sample size for a three-arm equivalence trial...
December 9, 2016: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/27936351/metal-exposures-at-three-u-s-electronic-scrap-recycling-facilities
#16
Diana Ceballos, Catherine Beaucham, Elena Page
Many metals found in electronic scrap are known to cause serious health effects, including but not limited to cancer and respiratory, neurologic, renal, and reproductive damage. The National Institute for Occupational Safety and Health/Centers for Disease Control and Prevention performed three health hazard evaluations at electronic scrap recycling facilities in the U.S. to characterize employee exposure to metals and recommend control strategies to reduce these exposures. We performed air, surface, and biological monitoring for metals...
December 9, 2016: Journal of Occupational and Environmental Hygiene
https://www.readbyqxmd.com/read/27936347/the-infectious-intracellular-lifestyle-of-salmonella-enterica-relies-on-the-adaptation-to-nutritional-conditions-within-the-salmonella-containing-vacuole
#17
Lautaro Diacovich, Lucía Lorenzi, Mauro Tomassetti, Stéphane Méresse, Hugo Gramajo
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that causes various host-specific diseases. During their life cycle, Salmonellae survive frequent exposures to a variety of environmental stresses, e.g. carbon-source starvation. The virulence of this pathogen relies on its ability to establish a replicative niche, named Salmonella-containing vacuole, inside host cells. However, the microenvironment of the SCV and the bacterial metabolic pathways required during infection are largely undefined...
December 9, 2016: Virulence
https://www.readbyqxmd.com/read/27936342/bbmri-eric-directory-515-biobanks-with-over-60-million-biological-samples
#18
Petr Holub, Morris Swertz, Robert Reihs, David van Enckevort, Heimo Müller, Jan-Eric Litton
No abstract text is available yet for this article.
December 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27936329/chemomechanical-coupling-in-hexameric-protein-protein-interfaces-harness-energy-within-v-type-atpases
#19
Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, Klaus Schulten
ATP synthase is the most prominent bioenergetic macromolecular motor in all life-forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase...
December 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27936318/copper-ii-thymine-coordination-polymer-nanoribbons-as-potential-oligonucleotide-nanocarriers
#20
Verónica G Vegas, Romina Lorca, Ana Latorre, Khaled Hassanein, Carlos J Gómez-García, Oscar Castillo, Álvaro Somoza, Félix Zamora, Pilar Amo-Ochoa
The direct reaction between copper nitrate, thymine-1-acetic acid, and 4,4'-bipyridine in water leads to the formation of a blue colloid comprising uniform crystalline nanoribbons (length >1 μm; width ca. 150-185 nm; diameter ca. 15-60 nm) of a coordination polymer. The polymer displays a thymine-based structure freely available for supramolecular interactions. These nanostructures show significant selective interaction with single-stranded oligonucleotides based on adenine. Remarkably, they present low cell toxicity in three cell lines-despite the copper(II) content-and can be used as nanocarriers of oligonucleotides...
December 9, 2016: Angewandte Chemie
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