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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
Shuoxing Jiang, Fan Hong, Huiyu Hu, Hao Yan, Yan Liu
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time, and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios...
August 16, 2017: ACS Nano
Rahul Ranjan, Kamla Rawat, H B Bohidar
Herein, we report on folic acid (FA, a low molecular weight gelator) thermoreversible supramolecular organo (in 1 : 1 (v/v) water-DMSO binary solvent), and ionogels made in 1-ethyl-3-methyl imidazolium chloride, [C2mim][Cl], and 1-octyl-3-methyl imidazolium chloride, [C8mim][Cl], solutions with 0.1 ≤ [IL] ≤ 5% (w/v). The self-assembled fibrils of folic acid were largely formed due to secondary forces, such as π-π stacking, H-bonding, and hydrophobic interactions above a gelator concentration of 0...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
Solene Bechelli, Brittany Gonzalez, Vincent Piquet, Ilham Essafri, Caroline Desgranges, Jerome Delhommelle
Using molecular simulation, we shed light on the crystal nucleation process in systems of Cu, Ni and their nanoalloy. For each system, we simulate the formation of the crystal nucleus along the entire nucleation pathway and determine the free energy barrier overcome by the system to form a critical nucleus. Comparing the results obtained for the pure metals to those for the nanoalloy, we analyze the impact of alloying on the free energy of nucleation, as well as on the size and structure of the crystal nucleus...
August 16, 2017: Journal of Physical Chemistry. B
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6. The combination of principal component analysis and different secondary structure order metrics as reaction coordinates has been used to characterize and identify all the underlying attractive basins corresponding to the folded and the unfolded states for each trpzip at 300 K. Our results reveal that even a single mutation in the hydrophobic core perturbs the stability of the folded peptide and the conformational preferences for the partially folded and unfolded states significantly, leading to concomitant alterations in the free energy landscape of trpzips...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
Praveen Kumar Bommineni, Sudeep N Punnathanam
Co-crystal formation from fluid-mixtures is quite common in a large number of systems. The simplest systems that show co-crystal (also called substitutionally ordered solids) formation are binary hard sphere mixtures. In this work, we study the nucleation of AB2 type solid compounds using Monte Carlo molecular simulations in binary hard sphere mixtures with the size ratio of 0.55. The conditions chosen for the study lie in the region where nucleation of an AB2 type solid competes with that of a pure A solid with a face-centered-cubic structure...
August 14, 2017: Journal of Chemical Physics
Jacek Dudowicz, Jack F Douglas, Karl F Freed
The theoretical description of the phase behavior of polymers dissolved in binary mixtures of water and other miscible solvents is greatly complicated by the self- and mutual-association of the solvent molecules. As a first step in treating these complex and widely encountered solutions, we have developed an extension of Flory-Huggins theory to describe mixtures of two self- and mutually-associating fluids comprised of small molecules. Analytic expressions are derived here for basic thermodynamic properties of these fluid mixtures, including the spinodal phase boundaries, the second osmotic virial coefficients, and the enthalpy and entropy of mixing these associating solvents...
August 14, 2017: Journal of Chemical Physics
Ezequiel L Murina, Roberto Fernández-Prini, Claudio Pastorino
We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface...
August 14, 2017: Journal of Chemical Physics
Guojie Zhang, Marcus Müller
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i...
August 14, 2017: Journal of Chemical Physics
Roland Hermann Alfons Winter, Mimi Gao, Christoph Held, Satyajit Patra, Loana Arns, Gabriele Sadowski
The free energy and conformational landscape of biomolecular systems as well as biochemical reactions depend not only on temperature and pressure, but also only the particular solution conditions. Such conditions include the effects of cosolvents (for example osmolytes) and macromolecular crowding, which are crucial components to understand the energetics and kinetics of biological processes in living system. Such conditions are also important for the understanding of many debilitating diseases, such as those where misfolding and amyloid formation of proteins are involved...
August 15, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Jianyi Wang, Qing Chen, Mian Wang, Cheng Zhong
To obtain new insights into the resistance caused by T315I and the differential selectivities of dasatinib and axitinib against BCR-ABL1(WT) and BCR-ABL1(T315), molecular dynamics simulations and free energy calculations were performed. A rule is summarized that the opening/closure of the P-loop and hinge of BCR-ABL1 could reflect the low/high bioactivities of dasatinib and axitinib. This may be because strong interactions of the ligands with key residues induce the P-loop and hinge of BCR-ABL1 to close, being favorable for the retention of the ligand in the binding site...
August 15, 2017: Physical Chemistry Chemical Physics: PCCP
Daniel Ciupka, Holger Gohlke
The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question...
August 14, 2017: Scientific Reports
Swarup Roy, Shailendra K Saxena, Suryakant Mishra, Priyanka Yogi, P R Sagdeo, Rajesh Kumar
In the featured work interaction between biosynthesized gold nanoparticles (GNP) and lysozyme (Lys) has been studied using multi-spectroscopic approach. A moderate association constant (Kapp) of 2.66×10(4)L/mol has been observed indicative of interactive nature. The binding constant (Kb) was 1.99, 6.30 and 31.6×10(4)L/mol at 291, 298 and 305K respectively and the number of binding sites (n) was found to be approximately one. Estimated values of thermodynamic parameters (Enthalpy change, ΔH=141.99kJ/mol, entropy change, ΔS=570J/mol/K, Gibbs free energy change, ΔG=-27...
August 8, 2017: Journal of Photochemistry and Photobiology. B, Biology
Jennifer M Macleod, Josh Lipton-Duffin, Chaoying Fu, Tyler Taerum, Dmitrii F Perepichka, Federico Rosei
Two-dimensional (2D) molecular self-assembly allows for the formation of well-defined supramolecular layers with tailored geometrical, compositional and chemical properties. To date, random intermixing and entropic effects in these systems have largely been associated with crystalline disorder and glassy phases. Here we describe a 2D crystalline self-assembled molecular system that exhibits random incorporation of substitutional molecules. The lattice is formed from a mixture of trimesic acid (TMA) and terthienobenzenetricarboxylic acid (TTBTA), C3-symmetric hydrogen-bonding units of very different sizes (0...
August 14, 2017: ACS Nano
Ming-Sheng Teng, Lung-An Hsu, Shu-Hui Juan, Wen-Chi Lin, Ming-Cheng Lee, Cheng-Wen Su, Semon Wu, Yu-Lin Ko
Growth differentiation factor 15 (GDF15) is a strong predictor of cardiovascular events and mortality in individuals with or without cardiovascular diseases. Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) target sites, also known as miRSNPs, are known to enhance or weaken miRNA-mRNA interactions and have been linked to diseases such as cardiovascular disease and cancer. In this study, we aimed to elucidate the functional significance of the miRSNP rs1054564 in regulating GDF15 levels. Two rs1054564-containing binding sites for hsa-miR-873-5p and hsa-miR-1233-3p were identified in the 3' untranslated region (UTR) of the GDF15 transcript using bioinformatics tools...
2017: PloS One
Matthew Douglas Watson, Jeremy Monroe, Daniel P Raleigh
Changes in protein stability are commonly reported as changes in the melting temperature, ΔTM, or as changes in unfolding free energy at a particular temperature, ΔΔG°. Using data for 1124 mutants from 16 proteins we examine the relationship between ΔΔG° and ΔTM. A linear relationship is observed for each protein. The slopes of the plots of ΔTM vs ΔΔG° for different proteins scale as N(-1) where N is the number of residues in the protein. Thus, a given change in ΔG° causes a much larger change in TM for a small protein relative to the effect observed for a large protein...
August 14, 2017: Journal of Physical Chemistry. B
Jing Zhou, Micholas Dean Smith, Sarah J Cooper, Xiaolin Cheng, Jeremy C Smith, Jerry M Parks
Cellular uptake and export are important steps in the biotransformation of mercury (Hg) by microorganisms. However, the mechanisms of transport across biological membranes remain unclear. Membrane-bound transporters are known to be relevant, but passive permeation may also be involved. Inorganic Hg(II) and methylmercury ([CH3Hg]+) are commonly complexed with thiolate ligands. Here, we have performed extensive molecular dynamics simulations of the passive permeation of Hg(II) and [CH3Hg]+ complexes with thiolate ligands through a model bacterial cytoplasmic membrane...
August 14, 2017: Environmental Science & Technology
Chao-Ting Guan, Jin Jiang, Cong-Wei Luo, Jun Ma, Su-Yan Pang, Yang Zhou, Yi Yang
This work demonstrated that bromophenols (BrPs) could be readily oxidized by peroxydisulfate (PDS) activated by a commercial carbon nanotube (CNT), while furfuryl alcohol (a chemical probe for singlet oxygen (1O2)) was quite refractory. Results obtained by radical quenching experiments, electron paramagnetic resonance spectroscopy, and Fourier transform infrared spectroscopy further confirmed the involvement of nonradical PDS-CNT complexes rather than 1O2. Bicarbonate and chloride ion exhibited negligible impacts on BrPs degradation by the PDS/CNT system, while a significant inhibitory effect was observed for natural organic matter...
August 14, 2017: Environmental Science & Technology
Emmi Pohjolainen, Sami Malola, Gerrit Groenhof, Hannu Häkkinen
Bio-compatible gold nanoclusters can be utilized as contrast agents in virus imaging. The labeling of viruses can be achieved non-covalently but site-specifically by linking the cluster to the hydrophobic pocket of a virus via a lipid-like pocket factor. We have estimated the binding affinities of three different pocket factors of echovirus 1 (EV1) in molecular dynamics simulations combined with non-equilibrium free energy calculations. We have also studied the effects on binding affinities with a pocket factor linked to the Au102pMBA44 nanocluster in different protonation states...
August 14, 2017: Bioconjugate Chemistry
Madhusudan Ghosh, K K Swain, Rakesh Verma
In this work, we report the sorption of Nb on iron oxides and the effect of humic acid. Iron oxides viz. goethite, hematite and magnetite were chemically synthesised and characterised by X-ray diffraction, particle size, surface area and zeta potential measurement. The sorption of Nb on all the three iron oxides was low (∼40%) at pH 1, increased to ∼ 90% at pH 8 and decreased marginally above pH 8. The effect of humic acid on the sorption was very small. Thermodynamic parameters viz. activation energy, enthalpy, entropy, free energy and sticking probability were calculated to understand the mechanism of the sorption process...
August 10, 2017: Journal of Environmental Radioactivity
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