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https://www.readbyqxmd.com/read/28109294/probing-the-intermolecular-interactions-of-ppar%C3%AE-lbd-with-polyunsaturated-fatty-acids-and-their-anti-inflammatory-metabolites-to-infer-most-potential-binding-moieties
#1
Shalini Muralikumar, Umashankar Vetrivel, Angayarkanni Narayanasamy, Undurti N Das
BACKGROUND: PPARγ is an isoform of peroxisome proliferator-activated receptor (PPAR) belonging to a super family of nuclear receptors. PPARγ receptor is found to play a crucial role in the modulation of lipid and glucose homeostasis. Its commotion has been reported to play a significant role in a broad spectrum of diseases such as type 2 diabetes mellitus, inflammatory diseases, Alzheimer's disease, and in some cancers. Hence, PPARγ is an important therapeutic target. Polyunsaturated fatty acids (PUFAs) and their metabolites (henceforth referred to as bioactive lipids) are known to function as agonists of PPARγ...
January 21, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/28109252/rna-tvcurve-a-web-server-for-rna-secondary-structure-comparison-based-on-a-multi-scale-similarity-of-its-triple-vector-curve-representation
#2
Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma
BACKGROUND: RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis...
January 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28108961/effects-of-negatively-and-positively-charged-ti-metal-surfaces-on-ceramic-coating-adhesion-and-cell-response
#3
Rodney Marcelo do Nascimento, Vanessa Rafaela de Carvalho, José Silvio Govone, Antônio Carlos Hernandes, Nilson Cristino da Cruz
This manuscript reports an evaluation of the effects of simple chemical-heat treatments on the deposition of different ceramic coatings, i.e., TiO2, CaTiO3 and CaP, on commercially pure titanium (cp-Ti) and Ti6Al4V and the influence of the coatings on cells interaction with the surfaces. The ceramic materials were prepared by the sol-gel method and the coating adhesion was analyzed by pull-off bending tests. The wettability of positively or negatively charged surfaces was characterized by contact angle measurements, which also enabled the calculation of the surface free energy through the polar-apolar liquids approach...
February 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28107751/molecular-modeling-study-of-cp-690550-derivatives-as-jak3-kinase-inhibitors-through-combined-3d-qsar-molecular-docking-and-dynamics-simulation-techniques
#4
Jing Li Wang, Li Ping Cheng, Tian Chi Wang, Wei Deng, Fan Hong Wu
To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28106995/nucleophilicity-parameters-of-arylsulfonyl-substituted-halomethyl-anions
#5
Zhen Li, Quan Chen, Peter Mayer, Herbert Mayr
The rates of the reactions of the arylsulfonyl substituted carbanions carrying α-chloro and α-bromo substituents 1a-e with quinone methides 2a-g and benzylidenemalonates 2h-i in DMSO were determined photometrically at 20 °C. The reactions were carried out under pseudo-first-order conditions, and the second-order rate constants were obtained as the slopes of the plots of the pseudo-first-order rate constants versus the concentrations of the reactants used in excess. The second-order rate constants correlate linearly with the parameters E of the reference electrophiles according to the linear free-energy relationship log k2(20 °C) = sN(N + E), which allowed to derive the nucleophile-specific parameters N and sN of the carbanions 1a-e...
January 20, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28106196/solubility-origin-at-the-nanoscale-enthalpic-and-entropic-contributions-in-polar-and-nonpolar-environments
#6
Eudes Fileti, Vitaly V Chaban
Nanostructures are known to be poorly soluble, irrespective of their elemental composition, shape, electronic structure, dipole moment, hydrophobicity/hydrophilicity and the employed solvent. The methods of colloid chemistry allow for preparing suspensions - metastable systems, the stabilities of which differ greatly from one another - but not real solutions. A systematic investigation of the solubility origin at the nanoscale is hereby reported in terms of its fundamental constituents: enthalpy and entropy...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28103745/analysis-of-water-sorption-isotherms-of-amorphous-food-materials-by-solution-thermodynamics-with-relevance-to-glass-transition-evaluation-of-plasticizing-effect-of-water-by-the-thermodynamic-parameters
#7
Eriko Shimazaki, Akiko Tashiro, Hitomi Kumagai, Hitoshi Kumagai
Relation between the thermodynamic parameters obtained from water sorption isotherms and the degree of reduction in the glass transition temperature (Tg), accompanied by water sorption, was quantitatively studied. Two well-known glassy food materials namely, wheat gluten and maltodextrin were used as samples. The difference between the chemical potential of water in a solution and that of pure water ([Formula: see text]), the difference between the chemical potential of solid in a solution and that of a pure solid ([Formula: see text]), and the change in the integral Gibbs free energy ([Formula: see text]) were obtained by analyzing the water sorption isotherms using solution thermodynamics...
January 20, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28103438/acylguanidine-beta-secretase-1-inhibitors-a-combined-experimental-and-free-energy-perturbation-study
#8
Henrik Keränen, Laura Pérez-Benito, Myriam Ciordia, Francisca Delgado, Thomas B Steinbrecher, Daniel Oehlrich, Herman W T Van Vlijmen, Andrés A Trabanco, Gary Tresadern
A series of acylguanidine beta secretase 1 (BACE1) inhibitors with modified scaffold and P3 pocket substituent was synthesized and studied with Free Energy Perturbation (FEP) calculations. The resulting molecules showed potencies in enzymatic BACE1 inhibition assays up to 1 nM. The correlation between the predicted activity from the FEP calculations and the experimental activity was good for the P3 pocket substituents. The average mean unsigned error (MUE) between prediction and experiment was 0.68 ± 0.17 kcal/mol for the default 5 ns lambda window simulation time improving to 0...
January 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28102416/phase-separation-in-driven-granular-gases-exploring-the-elusive-character-of-nonequilibrium-steady-states
#9
S Herminghaus, M G Mazza
The emergence of patterns and phase separation in many-body systems far from thermal equilibrium is discussed using the example of driven granular gases. It is shown that phase separation follows a similar mechanism as in the systems of active Brownian particles. Depending on the quantities chosen for observation, it may or may not be easy to find functionals analogous to the free energy in equilibrium statistical physics. We argue that although such functionals can always be derived from the dynamics, it is of only limited value for predicting relevant aspects of the nonequilibrium steady state of the system...
January 19, 2017: Soft Matter
https://www.readbyqxmd.com/read/28102376/insights-into-the-mechanism-of-electrochemical-ozone-production-via-water-splitting-on-the-ni-and-sb-doped-sno2-catalyst
#10
Gregory Gibson, Ziyun Wang, Christopher Hardacre, Wen-Feng Lin
The H2O splitting mechanism is a very attractive alternative used in electrochemistry for the formation of O3. The most efficient catalysts employed for this reaction at room temperature are SnO2-based, in particular the Ni/Sb-SnO2 catalyst. In order to investigate the H2O splitting mechanism density functional theory (DFT) was performed on a Ni/Sb-SnO2 surface with oxygen vacancies. By calculating different SnO2 facets, the (110) facet was deemed most stable, and further doped with Sb and Ni. On this surface, the H2O splitting mechanism was modelled paying particular attention to the final two steps, the formation of O2 and O3...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28102071/temperature-induced-misfolding-in-prion-protein-evidences-of-multiple-partially-disordered-states-stabilized-by-non-native-hydrogen-bonds
#11
Neharika G Chamachi, Suman Chakrabarty
The structural basis of misfolding pathways of a cellular Prion (PrP(C)) into the toxic scrapie form (PrP(SC)) and identification of possible intermediates (e.g. PrP(*)) still eludes us. In this work, we have used a cumulative ~65µs of Replica Exchange Molecular Dynamics simulation data to construct the conformational free energy landscapes and capture the structural and thermodynamic characteristics associated with various stages of the thermal denaturation process in human Prion protein. The temperature dependent free energy surfaces consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds, thus rendering the protein prone towards misfolding...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28101966/the-free-energy-of-locking-a-ring-changing-a-deoxyribonucleoside-to-a-locked-nucleic-acid
#12
You Xu, Alessandra Villa, Lennart Nilsson
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28101951/rigidity-and-flexibility-in-the-tetrasaccharide-linker-of-proteoglycans-from-atomic-resolution-molecular-simulation
#13
Cathy Ng, Padmavathy Nandha Premnath, Olgun Guvench
Proteoglycans (PGs) are covalent conjugates between protein and carbohydrate (glycosaminoglycans). Certain classes of glycosaminoglycans such as chondroitin sulfate/dermatan sulfate and heparan sulfate utilize a specific tetrasaccharide linker for attachment to the protein component: GlcAβ1-3Galβ1-3Galβ1-4Xylβ1-O-Ser. Toward understanding the conformational preferences of this linker, the present work used all-atom explicit-solvent molecular dynamics (MD) simulations combined with Adaptive Biasing Force (ABF) sampling to determine high-resolution, high-precision conformational free energy maps ΔG(φ, ψ) for each glycosidic linkage between constituent disaccharides, including the variant where GlcA is substituted with IdoA...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28100151/renin-inhibition-by-soyasaponin-i-a-potent-native-anti-hypertensive-compound
#14
Zeinab Tavassoli, Majid Taghdir, Bijan Ranjbar
One way to control hypertension is inactivation of the Renin- Angiotensin- Aldosterone System (RAAS). Inhibition of renin as a rate-limiting step of this system is an effective way to stop up RAAS. It has been proved that soyasaponin I, an herbal compound obtained from soybeans, has anti-hypertensive effect via renin inhibition, so it has the potential of being an anti-hypertensive drug. Herein, some theoretical approaches such as Docking Simulation, Molecular Dynamics (MD) Simulation and MMPBSA analysis have been used to study how soyasaponin I inhibits renin at the structural level...
January 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28100048/unanticipated-stickiness-of-%C3%AE-pinene
#15
Hilary M Chase, Junming Ho, Mary Alice Upshur, Regan J Thomson, Victor S Batista, Franz M Geiger
Hilary M. Chase1#, Junming Ho2#, Mary Alice Upshur1, Regan J. Thomson1, Victor S. Batista3, Franz M. Geiger1* 1Department of Chemistry, Northwestern University, Evanston, IL. 60208, United States; 2 Agency for Science, Technology and Research, Institute of High Performance Computing, 1 Fusionopolis Way #16-16 Connexis North, Singapore 138632; 3Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT. 06520, United States # These authors contributed equally to this work. *corresponding author: geigerf@chem...
January 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28097726/role-of-the-edge-properties-in-hydrogen-evolution-reaction-on-mos2
#16
Petr Lazar, Michal Otyepka
Molybdenum disulfide, in particular its edges, has attracted considerable attention as possible substitute of platinum catalysts for hydrogen evolution reaction. Complex nature of the reaction complicates its detailed experimental investigations, which are mostly indirect and sample dependent. Therefore, we employed density functional theory calculations to study how the properties of MoS2 Mo-edge influence the thermodynamics of hydrogen adsorption onto the edge. We discuss the effect of the computational model (one-dimensional nanostripe), border symmetry imposed by its length, sulfur saturation of the edge, and dimensionality of the material...
January 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28095675/elucidating-important-sites-and-the-mechanism-for-amyloid-fibril-formation-by-coarse-grained-molecular-dynamics
#17
Ana Rojas, Nika Maisuradze, Khatuna Kachlishvili, Harold A Scheraga, Gia G Maisuradze
Fibrils formed by the β-amyloid (Aβ) peptide play a central role in the development of Alzheimer's disease. In this study, the principles governing their growth and stability are investigated by analyzing canonical and replica-exchange molecular dynamics trajectories of Aβ(9-40) fibrils. In particular, an unstructured monomer was allowed to interact freely with an Aβ fibril template. Trajectories were generated with the coarse-grained united-residue force field, and one- and two-dimensional free-energy landscapes (FELs) along the backbone virtual-bond angle θ and backbone virtual-bond-dihedral angle γ of each residue and principal components, respectively, were analyzed...
January 18, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28095341/effect-of-the-r119g-mutation-on-human-p5cr-structure-and-its-interactions-with-nad-insights-derived-from-molecular-dynamics-simulation-and-free-energy-analysis
#18
Peng Sang, Yue-Hui Xie, Lin-Hua Li, Yu-Jia Ye, Wei Hu, Jing Wang, Wen Wan, Rui Li, Long-Jun Li, Lin-Ling Ma, Zhi Li, Shu-Qun Liu, Zhao-Hui Meng
Pyrroline-5-carboxylate reductase (P5CR), an enzyme with conserved housekeeping roles, is involved in the etiology of cutis laxa. While previous work has shown that the R119G point mutation in the P5CR protein is involved, the structural mechanism behind the pathology remains to be elucidated. In order to probe the role of the R119G mutation in cutis laxa, we performed molecular dynamics (MD) simulations, essential dynamics (ED) analysis, and Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on wild type (WT) and mutant P5CR-NAD complex...
January 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28094951/diabat-interpolation-for-polymorph-free-energy-differences
#19
Kartik Kamat, Baron Peters
Existing methods to compute free energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free energy perturbations. This work demonstrates how Bennett's diabat interpolation method (J.Comp. Phys. 1976, 22, 245) can be combined with energy gaps from lattice switch Monte Carlo techniques (Phys. Rev. E 2001, 61, 906) to swiftly estimate polymorph free energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph...
January 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28094372/theoretical-studies-on-fgfr-isoform-selectivity-of-fgfr1-fgfr4-inhibitors-by-molecular-dynamics-simulations-and-free-energy-calculations
#20
Weitao Fu, Lingfeng Chen, Zhe Wang, Yanting Kang, Chao Wu, Qinqin Xia, Zhiguo Liu, Jianmin Zhou, Guang Liang, Yuepiao Cai
The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
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