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Biased molecules

Wentao Li, Jiuchuang Yuan, Meiling Yuan, Yong Zhang, Minghai Yao, Zhigang Sun
A new global potential energy surface (PES) of the O+ + H2 system was constructed with the permutation invariant polynomial neural network method, using about 63 000 ab initio points, which were calculated by employing the multi-reference configuration interaction method with aug-cc-pVTZ and aug-cc-pVQZ basis sets. For improving the accuracy of the PES, the basis set was extrapolated to the complete basis set limit by the two-point extrapolation method. The root mean square error of fitting was only 5.28 × 10-3 eV...
December 13, 2017: Physical Chemistry Chemical Physics: PCCP
Wenqing Shi, Yuhan Zeng, Cheng Zhu, Yucheng Xiao, Theodore R Cummins, Jianghui Hou, Lane A Baker
Integration of dual-barrel membrane patch-ion channel probes (MP-ICPs) to scanning ion conductance microscopy (SICM) holds promise of providing a revolutionized approach of spatially resolved chemical sensing. A series of experiments are performed to further the understanding of the system and to answer some fundamental questions, in preparation for future developments of this approach. First, MP-ICPs are constructed that contain different types of ion channels including transient receptor potential vanilloid 1 and large conductance Ca2+ -activated K+ channels to establish the generalizability of the methods...
December 11, 2017: Small
Veerle Van Meervelt, Misha Soskine, Shubham Singh, Gea Schuurman-Wolters, Hein J Wijma, Bert Poolman, Giovanni Maglia
Protein conformations play crucial roles in most, if not all, biological processes. Here we show that the current carried through a nanopore by ions allows monitoring conformational changes of native substrate-binding domains (SBD) of an ATP-Binding Cassette importer in real-time. Comparison with single-molecule Förster Resonance Energy Transfer (smFRET) and ensemble measurements revealed that proteins trapped inside the nanopore have bulk-like properties. Two ligand-free and two ligand-bound conformations of SBD proteins were inferred and their kinetic constants were determined...
December 5, 2017: Journal of the American Chemical Society
Sabrina Marcazzan, Silvio Taschieri, Roberto Lodovico Weinstein, Massimo Del Fabbro
In the presence of large bone defects, delayed bone union, or nonunion and fractures, bone reconstruction may be necessary. Different strategies have been employed to enhance bone healing among which the use of autologous platelet concentrates (APCs). Due to the high content of platelets and platelet-derived bioactive molecules (e.g., growth factors, antimicrobial peptides), they are promising candidates to enhance bone healing. However, both preclinical and clinical studies produced contrasting results, mainly due to a high heterogeneity in study design, objectives, techniques adopted, and outcomes assessed...
December 5, 2017: Platelets
S Bonovas, T Lytras, G Nikolopoulos, L Peyrin-Biroulet, S Danese
BACKGROUND: Biological therapies have improved the care of patients with ulcerative colitis (UC). Tofacitinib, an oral small-molecule Janus kinase inhibitor, is potentially a new treatment option. AIM: To comparatively assess efficacy and harm of tofacitinib and biologics (infliximab, adalimumab, golimumab and vedolizumab) in adult patients not previously exposed to TNF antagonists. METHODS: We performed a comprehensive search of PubMed, Embase, Scopus, clinical trial registries, regulatory authorities' websites and major conference proceedings, through August 2017, to identify randomised, placebo-controlled or head-to-head trials assessing tofacitinib or biologics as induction and/or maintenance therapy in moderate-to-severe UC...
December 4, 2017: Alimentary Pharmacology & Therapeutics
Sharon Lefler, Roi Vizel, Ella Yeor, Eran Granot, Omri Heifler, Moria Kwiat, Vadim Krivitsky, Miguel Weil, Yuval E Yaish, Fernando Patolsky
Silicon-based photodetectors cannot distinguish between different wavelengths. Therefore, these detectors relay on color-specific filters to achieve color separation. Color filters add complexity to color sensitive device fabrication, and hinder miniaturization of such devices. Here we report an ultra-small (as small as ~20 nm by 300 nm), red-green-blue-violet (RGBV) filter-free spectrally-gated FET (SGFET) detectors. These photodetectors are based on organic-SiNW hybrid FET devices, capable of detecting specific visible wavelength spectrum with FWHM under 100 nm...
December 4, 2017: Nano Letters
Hagen Tilgner, Fereshteh Jahanbani, Ishaan Gupta, Paul Collier, Eric Wei, Morten Rasmussen, Michael P Snyder
Understanding transcriptome complexity is crucial for understanding human biology and disease. Technologies such as Synthetic long-read RNA sequencing (SLR-RNA-seq) delivered five million isoforms and allowed assessing splicing coordination. Pacific Biosciences and Oxford Nanopore increase throughput also but require high input amounts or amplification. Our new droplet-based method, sparse isoform sequencing (spISO-seq), sequences 100k-200k partitions of 10-200 molecules at a time, enabling analysis of 10-100 million RNA molecules...
December 1, 2017: Genome Research
Christopher E Smith, Zuoti Xie, Ioan Bâldea, C Daniel Frisbie
Conducting probe atomic force microscopy (CP-AFM) was employed to examine electron tunneling in self-assembled monolayer (SAM) junctions. A 2.3 nm long perylene tetracarboxylic acid diimide (PDI) acceptor molecule equipped with isocyanide linker groups was synthesized, adsorbed onto Ag, Au and Pt substrates, and the current-voltage (I-V) properties were measured by CP-AFM. The dependence of the low-bias resistance (R) on contact work function indicates that transport is LUMO-assisted ('n-type behavior'). A single-level tunneling model combined with transition voltage spectroscopy (TVS) was employed to analyze the experimental I-V curves and to extract the effective LUMO position εl = ELUMO - EF and the effective electronic coupling (Γ) between the PDI redox core and the contacts...
December 1, 2017: Nanoscale
Kristen A Marino, Marta Filizola
An increasing number of G protein-coupled receptor (GPCR) crystal structures provide important-albeit static-pictures of how small molecules or peptides interact with their receptors. These high-resolution structures represent a tremendous opportunity to apply molecular dynamics (MD) simulations to capture atomic-level dynamical information that is not easy to obtain experimentally. Understanding ligand binding and unbinding processes, as well as the related responses of the receptor, is crucial to the design of better drugs targeting GPCRs...
2018: Methods in Molecular Biology
Jungeui Hong, David Gresham
Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing...
November 1, 2017: BioTechniques
Bruna Miglioranza Scavuzzi, Andréa Name Colado Simão, Tatiana Mayumi Veiga Iriyoda, Marcell Alysson Batisti Lozovoy, Nicole Perugini Stadtlober, Lorena Flor da Rosa Franchi Santos, Tamires Flauzino, Fabiano Aparecido de Medeiros, Marcelo Cândido de Sá, Luana Consentin, Edna Maria Vissoci Reiche, Michael Maes, Isaias Dichi
This study investigated nitro-oxidative stress in patients with systemic lupus erythematosus (SLE) in association with disease activity, immune-inflammatory biomarkers, and adhesion molecules. Two-hundred-four patients with SLE and 256 healthy volunteers were enrolled in this case-control study, which measured nitro-oxidative stress biomarkers, including lipid peroxides (LOOH), advanced oxidation protein products (AOPPs), nitric oxide metabolites (NOx), sulfhydryl (-SH) groups, products of deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) oxidative degradation, and total radical-trapping anti-oxidant parameter (TRAP)...
November 29, 2017: Immunologic Research
Paulo V S Dias, Fernanda S Arthuso, João E Oliveira, Miriam F Suzuki, José M Sousa, Maria Teresa C P Ribela, Paolo Bartolini, Carlos R J Soares
Reversed-phase high-performance liquid chromatography (RP-HPLC) has been used to analyze Interferon α-2 (IFN-α2) as a pure protein or as a pharmaceutical preparation: a method for analyzing periplasmic IFN-α2 directly in osmotic shock extract has, however, never been reported. This work describes an RP-HPLC methodology for the qualitative and quantitative analysis of human IFN-α2a and IFN-α2b directly in bacterial periplasmic extracts or in purified preparations. The analytical method has been set up and validated for accuracy, precision, linearity, sensitivity and specificity...
November 21, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Gang Li, Jeffrey E Montgomery, Mark A Eckert, Jae Won Chang, Samantha M Tienda, Ernst Lengyel, Raymond E Moellering
Integration of chemical probes into proteomic workflows enables the interrogation of protein activity, rather than abundance. Current methods limit the biological contexts that can be addressed due to sample homogenization, signal-averaging, and bias toward abundant proteins. Here we report a platform that integrates family-wide chemical probes with proximity-dependent oligonucleotide amplification and imaging to quantify enzyme activity in native contexts with high spatial resolution. Application of this method, activity-dependent proximity ligation (ADPL), to serine hydrolase and cysteine protease enzymes enables quantification of differential enzyme activity resulting from endogenous changes in localization and expression...
November 24, 2017: Nature Communications
John F Kellie, Jonathan R Kehler, Molly Z Karlinsey, Scott G Summerfield
AIM: Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. METHODOLOGY: Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented...
November 24, 2017: Bioanalysis
Rupendeep Kaur, Jupinder Kaur
Fullerenes are the most popular molecules to use in applications related to molecular electronics because of their superconductive nature. These molecules show a diverse range of properties, including optical, electronic, and structural characteristics. In this work, we focused on the electronic transport properties of molecular devices consisting of the fullerene B40 or B40 with different anchor atoms between two gold electrodes in a two-probe configuration. The elements used as anchor atoms in the B40 molecules were oxygen, selenium, and sulfur, i...
November 22, 2017: Journal of Molecular Modeling
Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently...
November 21, 2017: Journal of Chemical Physics
Y-H Tang, C-J Lin, K-R Chiang
We proposed a single-molecule magnetic junction (SMMJ), composed of a dissociated amine-ended benzene sandwiched between two Co tip-like nanowires. To better simulate the break junction technique for real SMMJs, the first-principles calculation associated with the hard-hard coupling between a amine-linker and Co tip-atom is carried out for SMMJs with mechanical strain and under an external bias. We predict an anomalous magnetoresistance (MR) effect, including strain-induced sign reversal and bias-induced enhancement of the MR value, which is in sharp contrast to the normal MR effect in conventional magnetic tunnel junctions...
June 14, 2017: Journal of Chemical Physics
Yulia Artemenko, Peter N Devreotes
Chemotaxis, or migration up a gradient of a chemoattractant, is the best understood mode of directed migration. Studies using social amoeba Dictyostelium discoideum revealed that a complex signal transduction network of parallel pathways amplifies the response to chemoattractants, and leads to biased actin polymerization and protrusion of a pseudopod in the direction of a gradient. In contrast, molecular mechanisms driving other types of directed migration, for example, due to exposure to shear flow or electric fields, are not known...
November 9, 2017: Journal of Visualized Experiments: JoVE
Clémence Dupré, Olivier Bruno, Anne Bonnaud, Adeline Giganti, Olivier Nosjean, Céline Legros, Jean A Boutin
Melatonin receptors belong to the family of G-protein coupled receptors. Agonist-induced receptor activation is terminated with the recruitment of β-arrestin, which leads to receptor internalization. Furthermore, agonist binding induces a shift in cellular shape that translates into a change in the electric impedance of the cell. In the present study, we employed engineered cells to study these internalization-related processes in the context of the two melatonin receptors, MT1 and MT2. To assess these three receptor internalization-related functions and validate the results, we employed four classical ligands of melatonin receptors: the natural agonist melatonin; the super-agonist 2-iodo-melatonin and the two antagonists luzindole and 4-phenyl-2-propionamidotetralin...
November 15, 2017: European Journal of Pharmacology
Arkadii Lin, Dragos Horvath, Valentina Afonina, Gilles Marcou, Reymond Jean-Louis, Alexandre Varnek
This is, to our knowledge, the to-date most comprehensive analysis based on Generative Topographic Mapping (GTM) of the fragment-like chemical space (40M molecules with no more than 17 heavy atoms, both from the theoretically enumerated GDB-17, and real-world PubChem/ChEMBL). The challenge was to prove that a robust map of fragment-like chemical space can actually be built, in spite of a limited (<105) maximal number of compounds ("frame set") usable for fitting the GTM manifold. An evolutionary map building strategy has been updated with a "coverage check" step, discarding manifolds failing to accommodate compounds outside the frame set...
November 20, 2017: ChemMedChem
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