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N Hamasaki-Katagiri, B C Lin, J Simon, R C Hunt, T Schiller, E Russek-Cohen, A A Komar, H Bar, C Kimchi-Sarfaty
INTRODUCTION: Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation...
December 9, 2016: Haemophilia: the Official Journal of the World Federation of Hemophilia
Ernna H Oliveira, Claudia Macedo, Cristhianna V Collares, Ana Carolina Freitas, Paula Barbim Donate, Elza T Sakamoto-Hojo, Eduardo A Donadi, Geraldo A Passos
Autoimmune regulator (Aire) is a transcriptional regulator of peripheral tissue antigens (PTAs) and microRNAs (miRNAs) in medullary thymic epithelial cells (mTECs). In this study, we tested the hypothesis that Aire also played a role as an upstream posttranscriptional controller in these cells and that variation in its expression might be associated with changes in the interactions between miRNAs and the mRNAs encoding PTAs. We demonstrated that downregulation of Aire in vivo in the thymuses of BALB/c mice imbalanced the large-scale expression of these two RNA species and consequently their interactions...
2016: Frontiers in Immunology
Ruihan Zhang, Jochen Erler, Jörg Langowski
The N-terminal tail of histone H4 is an indispensable mediator for inter-nucleosome interaction, which is required for chromatin fiber condensation. H4K16 acetylation (H4K16Ac) activates gene transcription by influencing both chromatin structure and interplay with nonhistone proteins. To understand the influence of H4K16Ac on inter-nucleosome interaction, we performed a simulation study for the H4 tail in the context of two nucleosomes in neighboring unit cells in the crystal structure. The binding conformation of H4 tail with/without K16Ac was sampled by replica exchange with solute tempering, and the free energy landscape was explored by metadynamics...
December 6, 2016: Biophysical Journal
Gang Zhao, Tailin Wang, Yongliang Shao, Yongzhong Wu, Baibiao Huang, Xiaopeng Hao
Based on the phase transformation of phosphorus and Gibbs free energy theory, a new mild method to fabricate black phosphorus nanosheets from their red phosphorus microsphere counterparts is proposed. Interestingly, the as-prepared black phosphorus nanosheets, as a kind of novel metal-free photocatalyst, exhibit excellent photocatalytic H2 production performance owing to their intrinsic layered polycrystalline structure. Besides, the nanosheet is also a kind of potential anode material in lithium-ion batteries and shows good electrochemical performance...
December 8, 2016: Small
Leila Karami, Ali Akbar Saboury, Elham Rezaee, Sayyed Abbas Tabatabai
The soluble epoxide hydrolase (sEH) enzyme plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. Inhibition of sEH provides a new approach to the treatment of inflammation, hypertension and atherosclerosis. In this study, the binding modes and inhibition mechanisms of the new oxadiazole-based amide inhibitors of the human soluble epoxide hydrolase were investigated by molecular docking and molecular dynamics (MD) simulation followed by the MM-GBSA method to calculate the binding free energy of each inhibitor to sEH...
December 7, 2016: European Biophysics Journal: EBJ
Camilo Andrés Mora Osorio, Andrés Fernando González Barrios
BACKGROUND: Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces...
December 7, 2016: BMC Bioinformatics
Kathryn Geiger-Schuller, Doug Barrick
Transcription activator-like effector proteins (TALEs) contain large numbers of repeats that bind double-stranded DNA, wrapping around DNA to form a continuous superhelix. Since unbound TALEs retain superhelical structure, it seems likely that DNA binding requires a significant structural distortion or partial unfolding. In this study, we use nearest-neighbor "Ising" analysis of consensus TALE (cTALE) repeat unfolding to quantify intrinsic folding free energies, coupling energies between repeats, and the free energy distribution of partly unfolded states, and to determine how those energies depend on the sequence that determines DNA-specificity (called the "RVD")...
December 6, 2016: Biophysical Journal
Martin J Fossat, Thuy P Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A McCallum, Angel E Garcia, Doug Barrick, Christian Roumestand, Catherine A Royer
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic...
December 6, 2016: Biophysical Journal
Bernhard Reischl, Paolo Raiteri, Julian D Gale, Andrew L Rohl
While the atomic force microscope (AFM) is able to image mineral surfaces in solution with atomic resolution, so far, it has been a matter of debate whether imaging point defects is also possible under these conditions. The difficulties stem from the limited knowledge of what types of defects may be stable in the presence of an AFM tip, as well as from the complicated imaging mechanism involving interactions between hydration layers over the surface and around the tip apex. Here, we present atomistic molecular dynamics and free energy calculations of the AFM imaging of vacancies and ionic substitutions in the calcite (101[over ¯]4) surface in water, using a new silica AFM tip model...
November 25, 2016: Physical Review Letters
Amélie Boyaval, Raphaël Mereau, Bruno Grignard, Christophe Detrembleur, Christine Jerome, Thierry Tassaing
The metal-free coupling of propargylic alcohols with carbon dioxide catalysed by guanidine derivatives was investigated in detail through the combination of online kinetic studies by in-situ ATR-IR spectroscopy and DFT calculations. Bicyclic guanidines, namely TBD and MTBD, are effective catalysts for the conversion of 2-methyl-3-butyn-2-ol to α-methylene cyclic carbonate and oxoalkyl acyclic carbonate under mild reaction conditions. The lower selectivity of TBD in comparison with MTBD towards the formation of α-methylene cyclic carbonate was elucidated from DFT calculations and is related to the bifunctional activity (base/H-bond donor) of TBD decreasing the Gibbs free energy of the reaction path for the formation of the acyclic carbonate...
December 7, 2016: ChemSusChem
Kai-Hsin Liou, Dun-Yen Kang, Li-Chiang Lin
Water shortage has become a critical issue. To facilitate the large-scale deployment of reverse-osmosis water desalination to produce fresh water, discovering novel membranes is essential. Here, we computationally demonstrate the great potential of single-walled aluminosilicate nanotubes (AlSiNTs), materials that can be synthesized through scalable methods, in desalination. State-of-the-art molecular dynamics simulations were employed to investigate the desalination performance and structure-performance relationship of AlSiNTs...
November 4, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Michael L Pegis, Bradley A McKeown, Neeraj Kumar, Kai Lang, Derek J Wasylenko, X Peter Zhang, Simone Raugei, James M Mayer
Improved electrocatalysts for the oxygen reduction reaction (ORR) are critical for the advancement of fuel cell technologies. Herein, we report a series of 11 soluble iron porphyrin ORR electrocatalysts that possess turnover frequencies (TOFs) from 3 s(-1) to an unprecedented value of 2.2 × 10(6) s(-1). These TOFs correlate with the ORR overpotential, which can be modulated by changing the E1/2 of the catalyst using different ancillary ligands, by changing the solvent and solution acidity, and by changing the catalyst's protonation state...
November 23, 2016: ACS Central Science
Tiantian Zhang, Tao Wei, Yuanyuan Han, Heng Ma, Mohammadreza Samieegohar, Ping-Wei Chen, Ian Lian, Yu-Hwa Lo
Protein-ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein-ligand interactions in relevant physiological conditions...
November 23, 2016: ACS Central Science
Kentaro Ishii, Masanori Noda, Susumu Uchiyama
The interactions of small molecules with proteins (protein-ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein-ligand interactions. These interactions typically accompany association-dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development...
2016: Biophysics and Physicobiology
Amandeep Kaur, Parampaul K Banipal, Tarlok S Banipal
The energetics and the impact on the conformation of heme containing protein myoglobin (Mb) due to the binding of three transition metal ions (Zn(2+), Ni(2+), and Mn(2+)) have been investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), UV-vis, and circular dichroism (CD) spectroscopy under physiological conditions. The binding affinity of the order of 10(4)M(-1) has been observed for all metal ions from calorimetry as well as from absorption spectroscopy. The binding of these metal ions with Mb is a spontaneous process that exposes the hydrophobic groups away from the protein core as exhibited by the negative Gibbs free energy change (ΔG) and positive heat capacity change (ΔCp) values...
November 27, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
Li-Kun Yang, Xia-Guang Zhang, Fang-Zu Yang, De-Yin Wu, Zhong-Qun Tian, Xiang-Yang Liu
Density functional theory calculations have been used to elucidate the mechanism of the addition reaction of acetaldehyde to the positively charged hydrogenated silicene (H-silicene). We find that the positively charged H-silicene plane could be partially restructured to form a vacant Si site, enabling a further nucleophilic addition reaction. After acetaldehyde molecule attached to the H-silicene plane, two competing pathways are involved in hydrogen abstraction process: a random reaction mechanism and a chain reaction mechanism...
December 6, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Christian J Burnham, Zdenek Futera, Niall J English
Building on our previous work (J. Phys. Chem. C, 2016, 120, 16561), using an empirical model we run both classical and path-integral molecular dynamics simulations for a type II clathrate hydrate containing different amounts of guest H2 molecules from 1 to 5 molecules per large cage, with results presented at temperatures of 50, 100 K and 200 K. We present results for the density isosurfaces of the guest molecules at all different occupations and temperatures, showing how the density approaches the perfect tetrahedral structure which has been found for the n = 4 case in which each molecule sits on the vertex of a tetrahedron about the centre of each large cage...
December 6, 2016: Physical Chemistry Chemical Physics: PCCP
Etelka Tombácz, Katalin Farkas, Imre Földesi, Márta Szekeres, Erzsébet Illés, Ildikó Y Tóth, Daniel Nesztor, Tamás Szabó
Nanoparticles do not exist in thermodynamical equilibrium because of high surface free energy, thus they have only kinetic stability. Spontaneous changes can be delayed by designed surface coating. In biomedical applications, superparamagnetic iron oxide nanoparticles (SPIONs) require an optimized coating in order to fulfil the expectation of medicine regulatory agencies and ultimately that of biocompatibility. In this work, we show the high surface reactivity of naked SPIONs due to ≡Fe-OH sites, which can react with H(+)/OH(-) to form pH- and ionic strength-dependent charges...
December 6, 2016: Interface Focus
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