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https://www.readbyqxmd.com/read/28813625/detection-of-first-line-drug-resistance-mutations-and-drug-protein-interaction-dynamics-from-tuberculosis-patients-in-south-india
#1
Somanna Ajjamada Nachappa, Sumana M Neelambike, Chokkanna Amruthavalli, Nallur B Ramachandra
Diagnosis of drug-resistant tuberculosis predominantly relies on culture-based drug susceptibility testing, which take weeks to produce a result and a more time-efficient alternative method is multiplex allele-specific PCR (MAS-PCR). Also, understanding the role of mutations in causing resistance helps better drug designing. AIMS: To evaluate the ability of MAS-PCR in the detection of drug resistance and to understand the mechanism of interaction of drugs with mutant proteins in Mycobacterium tuberculosis...
August 16, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28813456/a-simple-molecular-mechanism-explains-multiple-patterns-of-cell-size-regulation
#2
Morgan Delarue, Daniel Weissman, Oskar Hallatschek
Increasingly accurate and massive data have recently shed light on the fundamental question of how cells maintain a stable size trajectory as they progress through the cell cycle. Microbes seem to use strategies ranging from a pure sizer, where the end of a given phase is triggered when the cell reaches a critical size, to pure adder, where the cell adds a constant size during a phase. Yet the biological origins of the observed spectrum of behavior remain elusive. We analyze a molecular size-control mechanism, based on experimental data from the yeast S...
2017: PloS One
https://www.readbyqxmd.com/read/28813143/effect-of-structure-and-disorder-on-the-charge-transport-in-defined-self-assembled-monolayers-of-organic-semiconductors
#3
Thomas Schmaltz, Bastian Gothe, Andreas Krause, Susanne Leitherer, Hans-Georg Steinrück, Michael Thoss, Timothy Clark, Marcus Halik
Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising new type of organic electronic device but also allow uniquely detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations, allows us to characterize self-assembled monolayer (SAM-) based devices in unprecedented detail...
August 16, 2017: ACS Nano
https://www.readbyqxmd.com/read/28813018/biophysical-and-computational-studies-of-the-vcci-vmip-ii-complex
#4
Anna F Nguyen, Nai-Wei Kuo, Laura J Showalter, Ricardo Ramos, Cynthia M Dupureur, Michael E Colvin, Patricia J LiWang
Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8)...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28813011/insights-into-the-effect-of-the-g245s-single-point-mutation-on-the-structure-of-p53-and-the-binding-of-the-protein-to-dna
#5
Marco Gaetano Lepre, Sara Ibrahim Omar, Gianvito Grasso, Umberto Morbiducci, Marco Agostino Deriu, Jack A Tuszynski
The transcription factor p53 is a potent tumor suppressor dubbed as the "guardian of the genome" because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28813004/lactose-binding-induces-opposing-dynamics-changes-in-human-galectins-revealed-by-nmr-based-hydrogen-deuterium-exchange
#6
Chih-Ta Henry Chien, Meng-Ru Ho, Chung-Hung Lin, Shang-Te Danny Hsu
Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8(NTD) and hGal8(CTD), respectively)...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28812902/charge-effects-on-the-efflorescence-in-single-levitated-droplets
#7
Gunter Hermann, Yan Zhang, Bernhard Wassermann, Henry Fischer, Marcel Quennet, Eckart Ruehl
The influence of electrical excess charges on the crystallization from supersaturated aqueous sodium chloride solutions is reported. This is accomplished by efflorescence studies on single levitated microdroplets using optical and electrodynamic levitation. Specifically, a strong increase in efflorescence humidity is observed as a function of the droplet's negative excess charge, ranging up to -2.1 pC, with a distinct threshold behavior, increasing the relative efflorescence humidity, at which spontaneous nucleation occurs, from 44% for the neutral microparticle to 60%...
August 16, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28812901/behavior-of-methylammonium-dipoles-in-mapbx3-x-br-and-i
#8
Sharada Govinda, Bhushan P Kore, Menno Bokdam, Pratibha Mahale, Abhinav Kumar, Somnath Pal, Biswajit Bhattacharyya, Jonathan Lahnsteiner, Georg Kresse, Cesare Franchini, Anshu Pandey, D D Sarma
Dielectric constants of MAPbX3 (X = Br, I) in 1 kHz-1 MHz range show strong temperature dependencies near the room temperature in contrast to the nearly temperature independent dielectric constant of CsPbBr3. This strong temperature dependence for MAPbX3 in the tetragonal phase is attributed to the MA(+) dipoles rotating freely within the probing time scale. This interpretation is supported by ab initio molecular dynamics simulations on MAPbI3 that establish these dipoles as randomly oriented with a rotational relaxation time scale of ~7 ps at 300 K...
August 16, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28812895/correlating-free-volume-hole-distribution-to-the-glass-transition-temperature-of-epoxy-polymers
#9
Amin Aramoon, Timothy D Breitzman, Christopher F Woodward, Jaafar A El-Awady
A new algorithm is developed to quantify the free-volume hole distribution and its evolution in coarse-grained molecular dynamics simulations of polymeric networks. This is achieved by analyzing the geometry of the network rather than a voxelized image of the structure to accurately and efficiently find and quantify free-volume hole distributions within large scale simulations of polymer networks. The free-volume holes are quantified by fitting the largest ellipsoids and spheres in the free-volumes between polymer chains...
August 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28812889/influence-of-small-fluorophilic-and-lipophilic-organic-molecules-on-dppc-bilayers
#10
Martin Brehm, Ghulam Saddiq, Tobias Watermann, Daniel Sebastiani
In this study, we investigate the effect of a series of additive molecules with different types of philicities on the structure and dynamics of DPPC bilayers. To this aim, we performed extensive force field molecular dynamics simulations of the systems, using our recently developed perfluoroalkane force field. We found that addition of perfluoro-n-decane and fluorotelomer alcohol at 323 K leads to a phase transition of the membrane from liquid crystalline to gel phase, whereas the addition of n-decane and partially fluorinated n-decane leaves the liquid crystalline phase intact...
August 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28812545/dynamics-of-microtubules-highlights-of-recent-computational-and-experimental-investigations
#11
Valeri Barsegov, Jennifer Ross, Ruxandra Dima
Microtubules are found in most eukaryotic cells, with homologs in eubacteria and archea, and they have functional roles in mitosis, cell motility, intracellular transport, and the maintenance of cell shape. Numerous efforts have been expended over the last two decades to characterize the interactions between microtubules and the wide variety of microtubule associated proteins that control their dynamic behavior in cells resulting in microtubules being assembled and disassembled where and when they are required by the cell...
August 16, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28812539/investigating-ebola-virus-pathogenicity-using-molecular-dynamics
#12
Morena Pappalardo, Francesca Collu, James Macpherson, Martin Michaelis, Franca Fraternali, Mark N Wass
BACKGROUND: Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812082/a-broader-view-on-ion-heating-in-traveling-wave-devices-using-fragmentation-of-csi-clusters-and-extent-of-h%C3%AB-migration-as-molecular-thermometers
#13
Frederik Lermyte, Frank Sobott
Electron transfer dissociation (ETD) is becoming increasingly important in mass spectrometry-based analysis of peptides and proteins. Supplemental collisional activation of undissociated electron transfer products can significantly increase fragmentation yield and sequence coverage, but hydrogen rearrangements - specifically, transfer of a hydrogen radical from a c to a z fragment - lead to distorted isotope distributions and increased potential for signal overlap. Concomitant collisional activation during the ion/ion reaction significantly reduces these rearrangements, but, in ion traps, also leads to lower reaction rates and reduced overlap of anion and cation clouds...
August 16, 2017: Analyst
https://www.readbyqxmd.com/read/28811631/development-of-a-primary-human-co-culture-model-of-inflamed-airway-mucosa
#14
Lael M Yonker, Hongmei Mou, Kengyeh K Chu, Michael A Pazos, Huimin Leung, Dongyao Cui, Jinhyeob Ryu, Rhianna M Hibbler, Alexander D Eaton, Tim N Ford, J R Falck, T Bernard Kinane, Guillermo J Tearney, Jayaraj Rajagopal, Bryan P Hurley
Neutrophil breach of the mucosal surface is a common pathological consequence of infection. We present an advanced co-culture model to explore neutrophil transepithelial migration utilizing airway mucosal barriers differentiated from primary human airway basal cells and examined by advanced imaging. Human airway basal cells were differentiated and cultured at air-liquid interface (ALI) on the underside of 3 µm pore-sized transwells, compatible with the study of transmigrating neutrophils. Inverted ALIs exhibit beating cilia and mucus production, consistent with conventional ALIs, as visualized by micro-optical coherence tomography (µOCT)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811600/exploring-leishmania-secretory-proteins-to-design-b-and-t-cell-multi-epitope-subunit-vaccine-using-immunoinformatics-approach
#15
Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Visceral leishmaniasis (VL) is a fatal form of leishmaniasis which affects 70 countries, worldwide. Increasing drug resistance, HIV co-infection, and poor health system require operative vaccination strategy to control the VL transmission dynamics. Therefore, a holistic approach is needed to generate T and B memory cells to mediate long-term immunity against VL infection. Consequently, immunoinformatics approach was applied to design Leishmania secretory protein based multi-epitope subunit vaccine construct consisting of B and T cell epitopes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811540/ultralow-lattice-thermal-conductivity-of-the-random-multilayer-structure-with-lattice-imperfections
#16
Pranay Chakraborty, Lei Cao, Yan Wang
Randomizing the layer thickness of superlattices (SL) can lead to localization of coherent phonons and thereby reduces the lattice thermal conductivity κ l . In this work, we propose strategies that can suppress incoherent phonon transport in the above random multilayer (RML) structure to further reduce κ l . Molecular dynamics simulations are conducted to investigate phonon heat conduction in SLs and RMLs with lattice imperfections. We found that interfacial species mixing enhances thermal transport across single interfaces and few-period SLs through the phonon "bridge" mechanism, while it substantially reduces the κ l of many-period SLs by breaking the phonon coherence...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811526/observation-of-the-unexpected-morphology-of-graphene-wrinkle-on-copper-substrate
#17
Wen Wang, Shudu Yang, Ashu Wang
Graphene, a two-dimensional material, has a wide range of unique properties and could be used in the development of varieties of mechanic, electronic and photonic devices, therefore methods to synthesis large-area high-quality graphene films are urgently required. Chemical vapor deposition (CVD) has been of particular interest recently due to its simplicity and low cost. However, because of the mismatch of thermal expansion coefficients, high densities of wrinkles are commonly observed. Despite their prevalence and potential impact on large-scale graphene properties, relatively little is known about their structural morphology and formation mechanism...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811299/twenty-years-of-menin-emerging-opportunities-for-restoration-of-transcription-in-men1
#18
Koen M A Dreijerink, Marc Timmers, Myles Brown
Since the discovery of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997, elucidation of the molecular function of its protein product, menin, has been a challenge. Biochemical, proteomics, genetics and genomics approaches have identified various potential roles, which converge on gene expression regulation. The most consistent findings show that menin connects transcription factors and chromatin modifying enzymes, in particular the histone H3K4 methyltransferase complexes MLL1 and MLL2. Chromatin immunoprecipitation combined with next generation sequencing has enabled studying genome-wide dynamics of chromatin binding by menin...
August 15, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28811279/zebrafish-earns-its-stripes-for-in-vivo-asc-speck-dynamics
#19
Jelena S Bezbradica, Kate Schroder
Assembly of the ASC speck is critical for signaling by the inflammasome. In this issue, Kuri et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201703103) use live microscopy to track fluorescently tagged endogenous ASC in the zebrafish, describing the molecular domains driving ASC speck assembly and identifying a key role for macrophages in ASC speck removal in vivo.
August 15, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28811118/prediction-and-characterization-of-the-stability-enhancing-effect-of-the-cherry-tag%C3%A2-in-highly-concentrated-protein-solutions-by-complex-rheological-measurements-and-md-simulations
#20
Pascal Baumann, Marie-Therese Schermeyer, Hannah Burghardt, Cathrin Dürr, Jonas Gärtner, Jürgen Hubbuch
Solution stability attributes are one of the key parameters within the production and launching phase of new biopharmaceuticals. Instabilities of active biological compounds can reduce the yield of biopharmaceutical productions, and may induce undesired reactions in patients, such as immunogenic rejections. Protein solution stability thus needs to be engineered and monitored throughout production and storage. In contrast to the gold standard of long-term storage experiments applied in industry, novel experimental and in silico molecular dynamics tools for predicting protein solution stability can be applied within several minutes or hours...
August 12, 2017: International Journal of Pharmaceutics
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