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Na Li, Yunhuan Yan, Angke Zhang, Jiming Gao, Chong Zhang, Xue Wang, Gaopeng Hou, Gaiping Zhang, Jinbu Jia, En-Min Zhou, Shuqi Xiao
Many viruses encode microRNAs (miRNAs) that are small non-coding single-stranded RNAs which play critical roles in virus-host interactions. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically impactful viruses in the swine industry. The present study sought to determine whether PRRSV encodes miRNAs that could regulate PRRSV replication. Four viral small RNAs (vsRNAs) were mapped to the stem-loop structures in the ORF1a, ORF1b and GP2a regions of the PRRSV genome by bioinformatics prediction and experimental verification...
October 17, 2016: Oncotarget
Rongsheng Zhu, Zhanguo Zhang, Yang Li, Zhenbang Hu, Dawei Xin, Zhaoming Qi, Qingshan Chen
Previous studies have confirmed that there are many differences between animal and plant microRNAs (miRNAs), and that numerical features based on sequence and structure can be used to predict the function of individual miRNAs. However, there is little research regarding numerical differences between animal and plant miRNAs, and whether a single numerical feature or combination of features could be used to distinguish animal and plant miRNAs or not. Therefore, in current study we aimed to discover numerical features that could be used to accomplish this...
2016: PloS One
Tobias Dornheim, Simon Groth, Travis Sjostrom, Fionn D Malone, W M C Foulkes, Michael Bonitz
We perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N=1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F_{xc} of the macroscopic electron gas with an unprecedented accuracy of |ΔV|/|V|,|ΔF_{xc}|/|F|_{xc}∼10^{-3}...
October 7, 2016: Physical Review Letters
Jesús Ignacio Mendieta-Moreno, Daniel G Trabada, Jesus Mendieta, James P Lewis, Paulino Gómez-Puertas, Jose Ortega
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics / molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between non-reactive and reactive conformations leading to the photolesion...
October 21, 2016: Journal of Physical Chemistry Letters
Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Michel Alain Cuendet, Harel Weinstein, Michael V LeVine
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery...
October 21, 2016: Journal of Chemical Theory and Computation
Xiang Gao, Shaolong Wu, Jimu Yan, Xiongfei Zhai, Xiaofeng Li
Semiconductor nanostructure photoelectrochemical (PEC) cells for sunlight conversion have the potential to supply continuous, low-cost, high-efficiency and carbon-free energy; however, in order to provide economically competitive energy, long-time stability and high-efficiency are requisite. In this work, the saturation photocurrent density (Jsat) and stability of the silicon nanowires (SiNWs) in a PEC cell are significantly improved via surface modification with Ag@SiO2 nanoparticles and conformal TiO2 ultrathin film...
October 21, 2016: ACS Applied Materials & Interfaces
Sohag Biswas, Bhabani S Mallik
We present the characteristic proton transfer process from water to the pyrazole anion, infrared signatures of hydroxyl groups and the free energy profile of the process in aqueous solution combining first principles simulations, wavelet analysis and metadynamics. Our results show that the presence of minimum three water molecules in the gas phase cluster with a particular arrangement is sufficient to facilitate the proton transfer process from water to the anion. The overall reaction is very rapid in aqueous solution, and the free energy barrier for this process is found to be 4...
October 21, 2016: Physical Chemistry Chemical Physics: PCCP
A G Dimitrov
The membrane transporters (pumps and co-transporters) are the main players in maintaining the cell homeostasis. Models of various types, each with their own drawbacks, describe transporter behavior. The aim of this study is to find the link between the biophysically based and empirical models to face and solve their specific problems. Instead of decreasing the number of states and using few complex rate constants as is usually done, we use the number of states as great as possible. Then, each transition in the cycle can represent an elementary process and we can apply the mass action law, according to which if rate constants depend on concentrations the dependence is linear...
October 17, 2016: Journal of Theoretical Biology
Zhong Ni, Xiting Wang, Tianchen Zhang, Rong Zhong Jin
Anaplastic lymphoma kinase (ALK) has become as an important target for the treatment of various human cancers, especially non-small-cell lung cancer. A mutation, F1174C, suited in the C-terminal helix αC of ALK and distal from the small-molecule inhibitor ceritinib bound to the ATP-binding site, causes the emergence of drug resistance to ceritinib. However, the detailed mechanism for the allosteric effect of F1174C resistance mutation to ceritinib remains unclear. Here, molecular dynamics (MD) simulations and binding free energy calculations [Molecular Mechanics/Generalized Born Surface Area (MM/GBSA)] were carried out to explore the advent of drug resistance mutation in ALK...
October 11, 2016: Computational Biology and Chemistry
Xu Jiao, Yuvaraja Gutha, Weijiang Zhang
The utilization of CS/PVA/CuO as a novel adsorbent for the removal of Pb(II) from aqueous solution has been examined in a batch adsorption process with several experimental conditions including initial solution pH, dose, contact time, initial metal ion concentration, and temperature. The new and novel material was characterized by structural (XRD), spectral (FTIR), morphological with elemental (SEM with EDS), and size of the nanoparticles (TEM) analyses. The pseudo-first-order, pseudo-second-order and intraparticle diffusion kinetics equations were used to analyze the kinetic data of the adsorption process and the data was fitted well with the pseudo-second-order kinetic model with R(2) values (close to the unity)...
October 13, 2016: Colloids and Surfaces. B, Biointerfaces
Fengjing Wu, Xiaojuan Liu, Chaktong Au
The polyamide reverse osmosis (RO) membranes were prepared through interfacial polymerization of m-phenylenediamine (MPD) and trimesoyl chloride (TMC). The use of dimethyl sulfoxide (DMSO) and glycerol as additives for the formation of thin-film composite (TFC) was investigated. We studied the effect of DMSO and glycerol addition on membrane property and RO performance. Microscopic morphology was examined by atomic force microscopy and scanning electron microscopy. The surface hydrophilicity was characterized on the basis of water contact angle and surface solid-liquid interfacial free energy (-ΔGSL)...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Guang Yang, Daniel T Hallinan
Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions...
October 20, 2016: Scientific Reports
Navnit Kumar Mishra, Anil Kumar Sharma, Tapan Kumar Mukherjee
Melanoma is a cancer associated with melanocytes of epidermis. There has been a consistent increase in the number of melanoma patients because of the depletion of the ozone layer which makes it of paramount importance to explore the immunogenic potential of various peptides in melanoma therapy. In the current study, a mutated decapeptide (ELAGIGILTV) epitope ID 12941 was taken from the melanoma antigen recognized by T-cells. This epitope displayed relatively better affinity for histocompatibility leukocyte antigen influencing the proliferation of cytotoxic T-cells...
November 2016: Journal of Molecular Modeling
Fredrik Elinder, Michael Madeja, Hugo Zeberg, Peter Århem
The transmembrane voltage needed to open different voltage-gated K (Kv) channels differs by up to 50 mV from each other. In this study we test the hypothesis that the channels' voltage dependences to a large extent are set by charged amino-acid residues of the extracellular linkers of the Kv channels, which electrostatically affect the charged amino-acid residues of the voltage sensor S4. Extracellular cations shift the conductance-versus-voltage curve, G(V), by interfering with these extracellular charges...
October 18, 2016: Biophysical Journal
Xiaoyu Zhuang, Bing Zhao, Shu Liu, Fengrui Song, Fengchao Cui, Zhiqiang Liu, Yunqi Li
Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in the etiology amyotrophic lateral sclerosis (ALS). The use of small molecules may stabilize the spatial structure of SOD1 dimer, thus preventing its dissociation and aggregation. In this study, "native" mass spectrometry (MS) was used to study the non-covalent interactions between SOD1 and flavonoid compounds. MS experiments were performed on a quadruple time-of-flight (Q-ToF) mass spectrometer with an electrospray ionization (ESI) source and T-wave ion mobility...
October 19, 2016: Analytical Chemistry
Jolanta Cieśla, Magdalena Kopycińska, Małgorzata Łukowska, Andrzej Bieganowski, Monika Janczarek
Rhizobium leguminosarum bv. trifolii is a soil bacterium able to establish symbiosis with agriculturally important legumes, i.e., clover plants (Trifolium spp.). Cell surface properties of rhizobia play an essential role in their interaction with both biotic and abiotic surfaces. Physicochemical properties of bacterial cells are underpinned by the chemical composition of their envelope surrounding the cells, and depend on various environmental conditions. In this study, we performed a comprehensive characterization of cell surface properties of a wild-type R...
2016: PloS One
Donato Belmonte, Carlo Gatti, Giulio Armando Ottonello, Pascal Richet, Marino Vetuschi Zuccolini
Thermodynamic and thermophysical properties of Na2SiO3 in the Cmc21 structural state are computed ab-initio using the hybrid B3LYP density functional method. The static properties at the athermal limit are first evaluated through a symmetry-preserving relaxation procedure. The thermodynamic properties that depend on vibrational frequencies viz, heat capacities, thermal expansion, thermal derivative of the bulk modulus, thermal correction to internal energy, enthalpy, Gibbs free energy, are then computed in the framework of quasi-harmonic approximation...
October 19, 2016: Journal of Physical Chemistry. A
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
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