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https://www.readbyqxmd.com/read/28101950/molecular-binding-of-toxic-phenothiazinium-derivatives-azures-to-bovine-serum-albumin-a-comparative-spectroscopic-calorimetric-and-in-silico-study
#1
Somnath Das, Md Maidul Islam, Gopal Chandra Jana, Anirudha Patra, Pradeep K Jha, Maidul Hossain
In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA...
January 19, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28101708/characterization-of-interaction-between-amino-acids-and-fulvic-like-organic-matter-by-fluorescence-spectroscopy-combining-thermodynamic-calculation
#2
Tao Lin, Bingwei Hou, Jian Wang, Yaqun Xu, Wei Chen
Dissolved organic matter (DOM), as a very fine colloidal suspension, could inevitably affect the transformation process of dissolved organic nitrogen (DON) in drinking water treatment. Tryptophan and tyrosine were used as representatives of DON to investigate the interactions between amino acids and fulvic-like components of fluorescent DOM using titration experiments. The fluorescence intensity decreased significantly with the increasing fulvic acid (FA) concentration, suggesting that FA could greatly quench the intrinsic fluorescence of amino acids such as tryptophan and tyrosine...
January 18, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28099026/unimer-assisted-exfoliation-for-high-concentrated-aqueous-dispersion-solutions-of-single-and-few-layered-van-der-waals-materials
#3
Changbong Yeon, Inyeal Lee, Gil-Ho Kim, Sun Jin Yun
We suggest unimer-assisted exfoliation method for the exfoliation of Van der Waals two-dimensional (2D) materials such as graphene, MoS2, and h-BN, and show that the micellar size is a critical parameter for enhancing the exfoliation efficiency. To explain the effectiveness of the unimers on the exfoliation, the influence of micellar size of a biocompatible block copolymer, Pluronic F-68, is evaluated in view of the yield and thickness of exfoliated 2D flakes. By the addition of water-soluble alcohols, the surfactants exist in the form of unimer, which facilitates the intercalation into the layered materials and their exfoliation...
January 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28098447/the-stories-tryptophans-tell-exploring-protein-dynamics-of-heptosyltransferase-i-from-escherichia-coli
#4
Joy M Cote, Carlos Andres Ramirez-Mondragon, Zarek S Siegel, Daniel Joseph Czyzyk, Jiali Gao, Yuk Yin Sham, Ishita Mukerji, Erika A Taylor
Heptosyltransferase I (HepI) catalyzes the addition of a single L-glycero-β-D-manno-heptose sugar (heptose) onto the membrane incorporated Kdo2-Lipid A as part of the biosynthesis of the core region of lipopolysaccharide (LPS). Gram-negative bacteria with gene knockouts of HepI have reduced virulence with enhanced susceptibility to hydrophobic antibiotics, making design of inhibitors against HepI of interest. Previous studies have shown that HepI protein dynamics are partially rate limiting, and therefore disruption of protein dynamics might provide a new strategy for inhibiting HepI...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098209/crystal-growth-of-dirac-semimetal-zrsis-with-high-magnetoresistance-and-mobility
#5
Raman Sankar, G Peramaiyan, I Panneer Muthuselvam, Christopher J Butler, Klauss Dimitri, Madhab Neupane, G Narsinga Rao, M-T Lin, F C Chou
High quality single crystal ZrSiS as a theoretically predicted Dirac semimetal has been grown successfully using a vapor phase transport method. The single crystals of tetragonal structure are easy to cleave into perfect square-shaped pieces due to the van der Waals bonding between the sulfur atoms of the quintuple layers. Physical property measurement results including resistivity, Hall coefficient (RH), and specific heat are reported. The transport and thermodynamic properties suggest a Fermi liquid behavior with two Fermi pockets at low temperatures...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097692/structural-role-of-a-conserved-active-site-cis-proline-in-the-thermotoga-maritima-acetyl-esterase-from-the-carbohydrate-esterase-family-7
#6
Mrityunjay K Singh, Narayanan Manoj
A conserved cis proline residue located in the active site of Thermotoga maritima acetyl esterase (TmAcE) from the carbohydrate esterase family 7 (CE7) has been substituted by alanine. The residue was known to play a crucial role in determining the catalytic properties of the enzyme. To elucidate the structural role of the residue, the crystal structure of the Pro228Ala variant (TmAcEP228A ) was determined at 2.1 Å resolution. The replacement does not affect the overall secondary, tertiary and quaternary structures and moderately decreases the thermal stability...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097462/thermally-stable-schiff-base-and-its-metal-complexes-molecular-docking-and-protein-binding-studies
#7
Umran Duru Kamaci, Musa Kamaci, Aysegul Peksel
In this paper, interaction of Schiff base and its metal complexes carrying naphthalene ring in the structure with bovine serum albumin (BSA) were investigated using UV-vis absorption, fluorescence spectroscopies and molecular docking methods. The effect on the binding mechanism and properties of these compounds containing metal-free, iron and copper ions were also investigated. The fluorescence spectroscopy results showed that fluorescence intensity of BSA in the presence of different concentration of ligands was decreased through a static quenching mechanism...
January 18, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28096578/the-effect-of-pregabalin-and-s-ketamine-in-total-knee-arthroplasty-patients-a-randomized-trial
#8
Lajla Kadic, Frank G van Haren, Oliver Wilder-Smith, Jorgen Bruhn, Jacques J Driessen, Maarten C de Waal Malefijt
BACKGROUND AND AIMS: Pain reduction is important for rehabilitation after total knee arthroplasty. Intra- and peri-articular infiltration with local anesthetics may be an alternative to commonly used locoregional techniques. Adding pregabalin orally and s-ketamine intravenously may further reduce postoperative pain. MATERIAL AND METHODS: This prospective, randomized, double-blind, placebo-controlled study compared two methods of perioperative analgesia. Control patients received a standardized multimodal postoperative analgesic regime of paracetamol, diclofenac, and piritramide-patient-controlled analgesia, including ropivacaine knee infiltration during surgery...
October 2016: Journal of Anaesthesiology, Clinical Pharmacology
https://www.readbyqxmd.com/read/28096330/spectroscopic-evidence-for-bulk-band-inversion-and-three-dimensional-massive-dirac-fermions-in-zrte5
#9
Zhi-Guo Chen, R Y Chen, R D Zhong, John Schneeloch, C Zhang, Y Huang, Fanming Qu, Rui Yu, Q Li, G D Gu, N L Wang
Three-dimensional topological insulators (3D TIs) represent states of quantum matters in which surface states are protected by time-reversal symmetry and an inversion occurs between bulk conduction and valence bands. However, the bulk-band inversion, which is intimately tied to the topologically nontrivial nature of 3D Tis, has rarely been investigated by experiments. Besides, 3D massive Dirac fermions with nearly linear band dispersions were seldom observed in TIs. Recently, a van der Waals crystal, ZrTe5, was theoretically predicted to be a TI...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094971/predicting-nanoscale-dynamics-of-a-glass-forming-liquid-from-its-macroscopic-bulk-behavior-and-vice-versa
#10
Karolina Adrjanowicz, Kamil Kaminski, Magdalena Tarnacka, Grzegorz Szklarz, Marian Paluch
The properties of a molecular liquid confined at the nanometer length scale can be very much distinct from the bulk. For that reason, the macro- and the nanoscopic behaviors of glass-forming liquids are regarded as two non-connected realms, governed by their own rules. Here, we show that the glassy dynamics in molecular liquids confined to nanometer pores might obey the density scaling relation, /T, just like in bulk fluids. Even more surprisingly, the same value of the scaling exponent  superposes the -relaxation time measured at different state points in nanoscale confinement and on increased pressure...
January 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28094374/combined-in-and-ex-situ-studies-of-pyrazine-adsorption-into-the-aliphatic-mof-al-cau-13-structures-dynamics-and-correlations
#11
Helge Reinsch, Jannik Benecke, Martin Etter, Niclas Heidenreich, Norbert Stock
The intercalation of different pyrazines (pyrazine, methylpyrazine, 2,5-dimethylpyrazine, 2,3-dimethylpyrazine, trimethylpyrazine and tetramethylpyrazine) into the trans-1,4-cyclohexanedicarboxylate (CDC(2-)) based Al-MOF [Al(OH)(CDC)], denoted as CAU-13, was investigated. The adsorption of the guest molecules into the flexible MOF was carried out from an aqueous solution or via vapour phase adsorption, starting with the hydrated narrow-pore form of the framework [Al(OH)(O2C-C6H10-CO2)]·H2O (CAU-13-np). The obtained host-guest systems were characterised by thermogravimetry and vibrational spectroscopy and their crystal structures were elucidated using powder X-ray diffraction (PXRD) data...
January 17, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28094372/theoretical-studies-on-fgfr-isoform-selectivity-of-fgfr1-fgfr4-inhibitors-by-molecular-dynamics-simulations-and-free-energy-calculations
#12
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
https://www.readbyqxmd.com/read/28094253/dynamical-importance-of-van-der-waals-saddle-and-excited-potential-surface-in-c-1-d-d2-complex-forming-reaction
#13
Zhitao Shen, Haitao Ma, Chunfang Zhang, Mingkai Fu, Yanan Wu, Wensheng Bian, Jianwei Cao
Encouraged by recent advances in revealing significant effects of van der Waals wells on reaction dynamics, many people assume that van der Waals wells are inevitable in chemical reactions. Here we find that the weak long-range forces cause van der Waals saddles in the prototypical C((1)D)+D2 complex-forming reaction that have very different dynamical effects from van der Waals wells at low collision energies. Accurate quantum dynamics calculations on our highly accurate ab initio potential energy surfaces with van der Waals saddles yield cross-sections in close agreement with crossed-beam experiments, whereas the same calculations on an earlier surface with van der Waals wells produce much smaller cross-sections at low energies...
January 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28092835/effects-of-the-central-potassium-ions-on-the-g-quadruplex-and-stabilizer-binding
#14
Zhiguo Wang, Jun-Ping Liu
Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K(+) in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K(+) with the parallel G-quadruplex is a coordinated water directed step-wise process. The K(+) above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K(+) binding...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28091890/a-theoretical-study-of-the-inhibition-effect-of-pamam-molecule-on-silica-scale
#15
Chunyu Chen, Ni Bai, Yan Zhang, Lina Jiao, Mingzhu Xia, Gang Chen
In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-terminated groups are stronger than those of generation 1.5 with terminated carboxyl group. The composition of adsorption interactions are the dominating electrostatic interactions and van de Waals interactions as well as H-bond interactions...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28090811/antibacterial-combination-therapy-using-co-3-cu-2-zn-2-and-pd-2-complexes-their-calf-thymus-dna-binding-studies
#16
Fatemeh Khosravi, Hassan Mansouri-Torshizi
Four Co(III)-, Cu(II)-, Zn(II)- and Pd(II)- based potent antibacterial complexes of formula K3[Co(ox)3].3H2O (I), [Cu(bpy)2Cl]Cl.5H2O (II), [Zn(bpy)3]Cl2 (III) and [Pd(bpy)2](NO3)2 (IV) (where ox is oxalate and bpy is 2,2'-bipyridine) were synthesized. They were characterized by elemental analyses, molar conductance measurements, UV-Vis, FT-IR, (1)H NMR and (13)C NMR spectra. These metal complexes were ordered in three combination series of I+II, I+II+III and I+II+III+IV. Antibacterial activity was tested for each of these four metal complexes and their combinations against gram positive and gram negative bacteria...
January 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28081101/design-of-many-body-spin-states-of-rydberg-atoms-excited-to-highly-tunable-magnetic-sublevels
#17
Svetlana A Malinovskaya
Quantum control methodology is presented to design many-body spin states in a spin chain of Rydberg atoms using laser pulses and a magnetic field. A two-photon ladder-type configuration is implemented, which is advantageous due to the combined action of the one-photon and two-photon detunings as control parameters. Many-body spin states are designed consisting of an ensemble of spins encoded in sublevels of Rydberg states and coupled via the van der Waals interactions.
January 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28080057/identification-of-binding-modes-for-amino-naphthalene-2-cyanoacrylate-anca-probes-to-amyloid-fibrils-from-molecular-dynamics-simulations
#18
Huan He, Juan Xu, Dan-Yang Cheng, Li Fu, Yu-Shu Ge, Feng-Lei Jiang, Yi Liu
Amino naphthalene 2-Cyanoacrylate (ANCA) probe is a kind of fluorescent amyloid binding probe that can report a different fluorescence emission when bound to different types of amyloid deposits in tissue, while their interactions with amyloid fibrils remain unclear due to the insoluble nature of amyloid fibrils. Here, all atom molecular dynamics simulations were used to investigate the interaction between ANCA probes with three different amyloid fibrils. Two common binding modes of ANCA probes on Aβ40 amyloid fibrils were identified by cluster analysis of multiple simulations...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28080040/insights-into-thiol-aromatic-interactions-a-stereoelectronic-basis-for-s-h-%C3%AF-interactions
#19
Christina R Forbes, Sudipta Kumar Sinha, Himal Kanti Ganguly, Shi Bai, Glenn P A Yap, Sandeep Patel, Neal J Zondlo
Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-L-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol...Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C...
January 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28079199/structural-influence-of-proteins-upon-adsorption-to-mos2-nanomaterials-comparison-of-mos2-force-field-parameters
#20
Zonglin Gu, Phil De Luna, Zaixing Yang, Ruhong Zhou
Molybdenum disulfide (MoS2) has recently emerged as a promising nanomaterial in a wide range of applications due to its unique and impressive properties. For example, MoS2 has gained attention in the biomedical field because of its ability to act as an antibacterial and anticancer agent. However, the potential influence of this exciting nanomaterial on biomolecules is yet to be extensively studied. Molecular dynamics (MD) simulations are invaluable tools in the examination of protein interactions with nanomaterials such as MoS2...
January 12, 2017: Physical Chemistry Chemical Physics: PCCP
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