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https://www.readbyqxmd.com/read/27933736/structural-insight-into-the-anti-prion-compound-inhibition-mechanism-of-native-prion-folding-over-misfolding
#1
Jiwon Choi, Rajiv Gandhi Govindaraj, Jae Wook Hyeon, Kyungro Lee, SongLing Ma, Su Yeon Kim, Jeongmin Lee, Kyoung Tai No
Transition of a physiological folded prion (PrP(C) ) into a pathogenic misfolded prion (PrP(S)(c) ) causes lethal neurodegenerative disorders and prion diseases. Anti-prion compounds have been developed to prevent this conversion; however, their mechanism of action remains unclear. Recently, we reported two anti-prion compounds, BMD29 and 35, identified by in silico and in vitro screening. In this study, we used extensive explicit-solvent molecular dynamics simulations to investigate ligand binding inhibition by anti-prion compounds in prion folding over misfolding behavior at acidic pH...
December 9, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27933733/mannich-bases-of-1-2-4-triazole-3-thione-containing-adamantane-moiety-synthesis-preliminary-anticancer-evaluation-and-molecular-modeling-studies
#2
Milorad Z Milošev, Katarina Jakovljević, Milan D Joksović, Tatjana Stanojković, Ivana Z Matić, Milka Perović, Vesna Tešić, Selma Kanazir, Milan Mladenović, Marko V Rodić, Vukadin M Leovac, Snežana Trifunović, Violeta Marković
A series of 18 novel N-Mannich bases derived from 5-adamantyl-1,2,4-triazole-3-thione was synthesized and characterized using NMR spectroscopy and X-ray diffraction technique. All derivatives were evaluated for their anticancer potential against four human cancer cell lines. Several tested compounds exerted good cytotoxic activities on K562 and HL-60 cell lines, along with pronounced selectivity, showing lower cytotoxicity against normal fibroblasts MRC-5 compared to cancer cells. The effects of compounds 5b, 5e and 5j on the cell cycle were investigated by flow cytometric analysis...
December 9, 2016: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/27933673/a-biophysical-and-computational-study-unraveling-the-molecular-interaction-mechanism-of-a-new-janus-kinase-inhibitor-tofacitinib-with-bovine-serum-albumin
#3
Ali Saber Abdelhameed, Saima Nusrat, Mohammad Rehan Ajmal, Syed Mohammad Zakariya, Masihuz Zaman, Rizwan Hasan Khan
The interaction of a recently certified kinase inhibitor Tofacitinib (TFB) with bovine serum albumin (BSA) has been studied, by spectroscopic and molecular docking studies. Spectrofluorimetric measurements at 3 different temperatures (288, 298, and 310 K) showed that TFB quench the intrinsic fluorescence of BSA upon forming a nonfluorescent complex. The intrinsic fluorescence data showed that TFB binds to BSA with binding constant (Kb ) of approximately 10(4) M(-1) , affirming a significant affinity of TFB with BSA...
December 9, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27933430/structural-dynamics-of-nucleosome-mediated-by-acetylations-at-h3k56-and-h3k115-122
#4
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Ilya Ioshikhes, Amutha Ramaswamy
Post translational modifications have a profound role in the regulation of several biological processes such as transcription, replication, and DNA repair. Acetylation and phosphorylation form a major class of post translational modifications involved in nucleosomal regulation by modifying its structure. The effect of post translational modifications on nucleosome structure could be better explored when the molecular trajectories explaining the time dependent structural evolution over a period of time is examined at the atomic level...
December 8, 2016: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/27932576/mammalian-synthetic-biology-for-studying-the-cell
#5
REVIEW
Melina Mathur, Joy S Xiang, Christina D Smolke
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes...
December 8, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27932456/physico-chemical-fingerprinting-of-rna-genes
#6
Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwal, B Jayaram
We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27932026/gene-environment-interactions-in-cortical-interneuron-development-and-dysfunction-a-review-of-preclinical-studies
#7
REVIEW
Lydia J Ansen-Wilson, Robert J Lipinski
Cortical interneurons (cINs) are a diverse group of locally projecting neurons essential to the organization and regulation of neural networks. Though they comprise only ∼20% of neurons in the neocortex, their dynamic modulation of cortical activity is requisite for normal cognition and underlies multiple aspects of learning and memory. While displaying significant morphological, molecular, and electrophysiological variability, cINs collectively function to maintain the excitatory-inhibitory balance in the cortex by dampening hyperexcitability and synchronizing activity of projection neurons, primarily through use of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA)...
December 5, 2016: Neurotoxicology
https://www.readbyqxmd.com/read/27931680/reactivation-or-reinfection-in-adult-tuberculosis-is-that-the-question
#8
Pere-Joan Cardona
Looking at the chapter on "natural history" in any tuberculosis (TB) reference book, there is a kind of certainty regarding TB in adults. That is the concept of "post-primary" TB described as the reactivation of dormant bacilli hidden in an old lesion developed during infancy due to a type of local immunosuppression. Intriguingly, this concept involves at least two major uncertainties: how can dormant bacilli remain for such a long period, almost a lifetime, in an old lesion, taking into account granuloma dynamism; and what sort of local immunosuppression is the one that facilitates reactivation? The controversy between reactivation and exogenous reinfection as the cause of active TB started very soon in TB research...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27931226/culex-pipiens-forms-and-urbanization-effects-on-blood-feeding-sources-and-transmission-of-avian-plasmodium
#9
Josué Martínez-de la Puente, Martina Ferraguti, Santiago Ruiz, David Roiz, Ramón C Soriguer, Jordi Figuerola
BACKGROUND: The wide spread mosquito Culex pipiens pipiens have two forms molestus and pipiens which frequently hybridize. The two forms have behavioural and physiological differences affecting habitat requirements and host selection, which may affect the transmission dynamic of Cx. p. pipiens-borne diseases. METHODS: During 2013, blood engorged Cx. p. pipiens mosquitoes were captured in urban, rural and natural areas from Southern Spain. In 120 mosquitoes, we identified the blood meal origin at vertebrate species/genus level and the mosquito form...
December 8, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27930922/molecular-dynamics-simulations-of-cesium-adsorption-on-illite-nanoparticles
#10
Laura N Lammers, Ian C Bourg, Masahiko Okumura, Kedarnath Kolluri, Garrison Sposito, Masahiko Machida
The charged surfaces of micaceous minerals, especially illite, regulate the mobility of the major radioisotopes of Cs ((134)Cs, (135)Cs, (137)Cs) in the geosphere. Despite the long history of Cs adsorption studies, the nature of the illite surface sites remains incompletely understood. To address this problem, we present atomistic simulations of Cs competition with Na for three candidate illite adsorption sites - edge, basal plane, and interlayer. Our simulation results are broadly consistent with affinities and selectivities that have been inferred from surface complexation models...
November 29, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27930841/self-healing-behavior-in-a-thermo-mechanically-responsive-cocrystal-during-a-reversible-phase-transition
#11
Guangfeng Liu, Jie Liu, Xin Ye, Lina Nie, Peiyang Gu, Xutang Tao, Qichun Zhang
The molecular-level motions of a coronene-based supramolecular rotator are amplified into macroscopic changes of crystals by co-assembly of coronene and TCNB (1,2,4,5-tetracyanobenzene) into a charge-transfer complex. The as-prepared cocrystals show remarkable self-healing behavior and thermo-mechanical responses during thermally-induced reversible single-crystal-to-single-crystal (SCSC) phase transitions. Comprehensive analysis of the microscopic observations as well as differential scanning calorimetry (DSC) measurements and crystal habits reveal that a thermally-reduced-rate-dependent dynamic character exists in the phase transition...
December 8, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27930823/cultivable-microbiome-of-fresh-white-button-mushrooms
#12
Werner Rossouw, Lise Korsten
Microbial dynamics on commercially grown white button mushrooms is of importance in terms of food safety assurance and quality control. The purpose of this study was to establish the microbial profile of fresh white button mushrooms. The total microbial load was determined through standard viable counts. Presence and isolation of gram-negative bacteria including coagulase positive Staphylococci were performed using a selective enrichment approach. Dominant and presumptive organisms were confirmed using molecular methods...
December 8, 2016: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/27930318/janus-effect-of-antifreeze-proteins-on-ice-nucleation
#13
Kai Liu, Chunlei Wang, Ji Ma, Guosheng Shi, Xi Yao, Haiping Fang, Yanlin Song, Jianjun Wang
The mechanism of ice nucleation at the molecular level remains largely unknown. Nature endows antifreeze proteins (AFPs) with the unique capability of controlling ice formation. However, the effect of AFPs on ice nucleation has been under debate. Here we report the observation of both depression and promotion effects of AFPs on ice nucleation via selectively binding the ice-binding face (IBF) and the non-ice-binding face (NIBF) of AFPs to solid substrates. Freezing temperature and delay time assays show that ice nucleation is depressed with the NIBF exposed to liquid water, whereas ice nucleation is facilitated with the IBF exposed to liquid water...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929542/autophagy-and-epithelial-mesenchymal-transition-an-intricate-interplay-in-cancer
#14
REVIEW
Mila Gugnoni, Valentina Sancisi, Gloria Manzotti, Greta Gandolfi, Alessia Ciarrocchi
Autophagy and epithelial to mesenchymal transition (EMT) are major biological processes in cancer. Autophagy is a catabolic pathway that aids cancer cells to overcome intracellular or environmental stress, including nutrient deprivation, hypoxia and drugs effect. EMT is a complex transdifferentiation through which cancer cells acquire mesenchymal features, including motility and metastatic potential. Recent observations indicate that these two processes are linked in a complex relationship. On the one side, cells that underwent EMT require autophagy activation to survive during the metastatic spreading...
December 8, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27929168/a-computational-study-of-self-assembled-hexapeptide-inhibitors-against-amyloid-%C3%AE-a%C3%AE-aggregation
#15
Yuan Qiao, Mingzhen Zhang, Ya'nan Liang, Jie Zheng, Guizhao Liang
The fibrillation and deposition of amyloid-β (Aβ) peptides in human brains are pathologically linked to Alzheimer's disease (AD). Development of different inhibitors (peptides, organic molecules, and nanoparticles) to prevent Aβ aggregation becomes a promising therapeutic strategy for AD treatment. We recently propose a "like-interacts-like" design principle to computationally design/screen and experimentally validate a new set of hexapeptide inhibitors with completely different sequences from the Aβ sequence...
December 8, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27929151/principal-molecular-axis-and-transition-dipole-moment-orientations-in-liquid-crystal-systems-an-assessment-based-on-studies-of-guest-anthraquinone-dyes-in-a-nematic-host
#16
Mark T Sims, Laurence C Abbott, Stephen J Cowling, John W Goodby, John N Moore
An assessment of five different definitions of the principal molecular axis along which molecules align in a nematic liquid crystal system has been made by analysing fully atomistic molecular dynamics (MD) simulations of a set of anthraquinone dyes in the cyanobiphenyl-based nematic host mixture E7. Principal molecular axes of the dyes defined by minimum moment of inertia, minimum circumference, minimum area, maximum aspect ratio, and surface tensor models were tested, and the surface tensor model was found to give the best description...
December 8, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27929106/channel-morphology-effect-on-water-transport-through-graphene-bilayers
#17
Bo Liu, Renbing Wu, Adrian Wing-Keung Law, Xi-Qiao Feng, Lichun Bai, Kun Zhou
The application of few-layered graphene-derived functional thin films for molecular filtration and separation has recently attracted intensive interests. In practice, the morphology of the nanochannel formed by the graphene (GE) layers is not ideally flat and can be affected by various factors. This work investigates the effect of channel morphology on the water transport behaviors through the GE bilayers via molecular dynamics simulations. The simulation results show that the water flow velocity and transport resistance highly depend on the curvature of the graphene layers, particularly when they are curved in non-synergic patterns...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27929079/from-function-to-phenotype-impaired-dna-binding-and-clustering-correlates-with-clinical-severity-in-males-with-missense-mutations-in-mecp2
#18
Taimoor I Sheikh, Juan Ausió, Hannah Faghfoury, Josh Silver, Jane B Lane, James H Eubanks, Patrick MacLeod, Alan K Percy, John B Vincent
Mutations in the MECP2 gene cause Rett syndrome (RTT). MeCP2 binds to chromocentric DNA through its methyl CpG-binding domain (MBD) to regulate gene expression. In heterozygous females the variable phenotypic severity is modulated by non-random X-inactivation, thus making genotype-phenotype comparisons unreliable. However, genotype-phenotype correlations in males with hemizygousMECP2 mutations can provide more accurate insights in to the true biological effect of specific mutations. Here, we compared chromatin organization and binding dynamics for twelve MeCP2 missense mutations (including two novel and the five most common MBD missense RTT mutations) and identifiedacorrelation with phenotype in hemizygous males...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27929074/probing-the-role-of-cation-%C3%AF-interaction-in-the-thermotolerance-and-catalytic-performance-of-endo-polygalacturonases
#19
Tao Tu, Yeqing Li, Xiaoyun Su, Kun Meng, Rui Ma, Yuan Wang, Bin Yao, Zhemin Lin, Huiying Luo
Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparent Tms increased by 0...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928960/research-advances-in-molecular-modeling-in-cyclodextrins
#20
Qianqian Zhao, Weixiang Zhang, Runmiao Wang, Yitao Wang, Defang Ouyang
BACKGROUND: Cyclodextrins (CDs), as one type of the novel pharmaceutical excipients, have been widely used in drug delivery and pharmaceutical industry. Over the past decades, a large amount of molecular modeling studies in CDs were reported for profound understanding of structural, dynamic and energetic features of CDs systems. Thus, this review is focused on qualitative and quantitative analysis of research outputs on molecular modeling in CDs. METHODS: The original data were collected from Web of Science and analyzed by scientific knowledge mapping tools, including Citespace, Science of Science, VOSviewer, GPSvisualizer and Gephi software...
December 8, 2016: Current Pharmaceutical Design
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