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https://www.readbyqxmd.com/read/30025319/binding-and-hydrolysis-properties-of-engineered-cellobiohydrolases-and-endoglucanases
#1
Xianqin Lu, Xiaoting Feng, Xuezhi Li, Jian Zhao
Because cellulase was the main enzyme used in bioconversion of lignocellulose, it was a valid way to reduce the hydrolysis cost by increasing the adsorption and hydrolysis efficiency of cellulase. In this study, modified cellobiohydrolases (CBHs) and endoglucanases (EGs) were constructed. Two engineered cellulases CBH-TrCBMV27E,P30D,Link1 and EG-TrCBMV27E,P30D,Link1 well-performed during hydrolysis. Compared to wild-type enzymes, EG-TrCBMV27E,P30D,Link1 had relatively less adsorption ability to lignin and greater affinity to cellulose, especially Avicel...
June 19, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/30025289/binding-interaction-of-phenazinium-based-cationic-photosensitizers-with-human-hemoglobin-exploring-the-effects-of-ph-and-chemical-structure
#2
Swagata Sen, Bijan K Paul, Nikhil Guchhait
The present study demonstrates a spectroscopic study on the interaction of two phenazinium-based cationic photosensitizers, namely, phenosafranin (PSF) and safranin-O (SO) with human hemoglobin (Hb) with particular emphasis on exploring the effects of pH and chemical structures of the dye molecules on the binding phenomenon. The protein (Hb) undergoes complex conformational transitions depending on the medium pH. The dye molecules exhibit a prominent fluorescence quenching following interaction with Hb under various experimental conditions (pH 3...
July 10, 2018: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/30025241/replacing-calcium-with-ammonium-counterion-in-lignosulfonates-from-paper-mills-affects-their-molecular-properties-and-bioactivity
#3
Davide Savy, Vincenza Cozzolino, Marios Drosos, Pierluigi Mazzei, Alessandro Piccolo
Lignosulfonates are important by-products of the paper industry and may be transformed into different commodities. We studied the molecular properties of ammonium (LS-AM) and calcium Lignosulfonates (LS-C) and evaluated their bioactivity towards the early development of maize plantlets. The FT-IR, 13 C NMR and 1 H-13 C-HSQC-NMR spectra showed that the two lignosulfonates varied in hydroxyl, sulfonate and phenolic content, while DOSY-NMR spectroscopy suggested a similar diffusivity. High Performance Size Exclusion Chromatography (HPSEC) was used to simulate the effects of root-exuded acids and describe the conformational dynamics of both LS substrates in acidic aqueous solutions...
July 16, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/30025209/structural-analysis-of-the-bacterial-effector-avra-identifies-a-critical-helix-involved-in-mkk4-substrate-recognition
#4
Jonathan Labriola, Yifan Zhou, Bhushan Nagar
Bacterial effector proteins are essential for the infection and proliferation of pathogenic bacteria through manipulation of host immune response pathways. AvrA is a Salmonella effector belonging to the YopJ family of acetyltransferases, which suppresses c-JUN N-terminal kinase (JNK) signaling in mammals through acetylation of mitogen activated receptor kinase kinase 4/7 (MKK4/7). Interestingly, two paralogues of AvrA exist that differ by only a single internal leucine residue, which when absent (AvrA∆L140), abrogates the ability to suppress JNK signaling...
July 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/30025204/revisiting-the-vibrational-and-optical-properties-of-p3ht-a-combined-experimental-and-theoretical-study
#5
Léa Farouil, Fabienne Alary, Elena Bedel-Pereira, Jean-Louis Heully
We demonstrate that DFT-based calculations can provide straightforward means to analyze the effect of aggregation on the optical properties of regioregular P3HT oligomers of different lengths (up to 20-mers) and of bi-oligomers of 8-mers in two different conformations. Our conclusions substantially differ from those obtained previously by applying the exciton model. Indeed, analysis of Huang-Rhys factors has evidenced that two vibrational modes, a collective mode and an effective mode, are combined in the vibronic structuration of the absorption spectrum of oligothiophene...
July 19, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/30025203/self-assembly-of-water-soluble-platinum-ii-based-metallacalixarenes-and-tuning-their-conformational-interconversion-via-synergistic-effect-between-solvents-and-anions
#6
Shu-Yan Yu, Wei Deng, Zhengsu Yu, Hongwei Ma
The aqueous self-assembly of the flexible ligand L bis(1H-benz[d]imidazole-1-yl)methane and cis-coordinated Pt(II) precursors [(en)Pt2+, (tmeda)Pt2+, en = ethylenediamine, tmeda =N,N,N',N'-tetramethylethylenediamine)] led to the formation of the metallacalixarenes with full alternative conformations (e.g., two novel water-soluble metallacalixarenes [M2L2]4+ and [M3L3]6+ with D2 and D3 symmetry, respectively). Their molecular structures were determined by single crystal X-ray analyses in solid state. The two metallacalixarenes present different cavity size and the [M3L3]6+ cavity encapsulates one NO3- inside...
July 19, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/30024984/amyloidogenic-cross-seeding-of-tau-protein-transient-emergence-of-structural-variants-of-fibrils
#7
Bartosz Nizynski, Hanna Nieznanska, Robert Dec, Solomiia Boyko, Wojciech Dzwolak, Krzysztof Nieznanski
Amyloid aggregates of Tau protein have been implicated in etiology of many neurodegenerative disorders including Alzheimer's disease (AD). When amyloid growth is induced by seeding with preformed fibrils assembled from the same protein, structural characteristics of the seed are usually imprinted in daughter generations of fibrils. This so-called conformational memory effect may be compromised when the seeding involves proteins with non-identical sequences leading to the emergence of distinct structural variants of fibrils (amyloid 'strains')...
2018: PloS One
https://www.readbyqxmd.com/read/30024857/jak2-v617f-promotes-venous-thrombosis-through-%C3%AE-1-%C3%AE-2-integrin-activation
#8
Bärbel Edelmann, Nibedita Gupta, Tina M Schnöder, Anja M Oelschlegel, Khurrum Shahzad, Jürgen Goldschmidt, Lars Philipsen, Sönke Weinert, Aniket Ghosh, Felix C Saalfeld, Subbaiah Chary Nimmagadda, Peter Müller, Rüdiger C Braun-Dullaeus, Juliane Mohr, Denise Wolleschak, Stefanie Kliche, Holger Amthauer, Florian H Heidel, Burkhart Schraven, Berend Isermann, Andreas Müller, Thomas Fischer
JAK2-V617F-positive chronic myeloproliferative neoplasia (CMN) is marked by dysfunction of integrins and adhesion molecules expressed on platelets, erythrocytes and leukocytes. However, the mechanism by which the two major leukocyte integrin chains, β1 and β2, mediate CMN pathophysiology remained unclear. β1 (α4β1; VLA-4) and β2 (αLβ2; LFA-1) integrins are essential regulators for attachment of leukocytes to endothelial cells. We here show enhanced adhesion of granulocytes from JAK2+/VF knock-in mice to vascular cell adhesion molecule 1 (VCAM1) and intercellular adhesion molecule 1 (ICAM1) coated surfaces...
July 19, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/30024766/identification-and-self-reaction-kinetics-of-criegee-intermediates-syn-ch-3-choo-and-ch-2-oo-via-high-resolution-infrared-spectra-with-a-quantum-cascade-laser
#9
Pei-Ling Luo, Yasuki Endo, Yuan-Pern Lee
The Criegee intermediates, carbonyl oxides produced in ozonolysis of unsaturated hydrocarbons, play important roles in atmospheric chemistry. The two conformers of CH3 CHOO exhibit distinct reactivity toward several atmospheric species, but a distinct conformer-specific probe is challenging because ultraviolet and infrared absorption bands of syn- and anti-CH3 CHOO overlap at low-resolution. Employing a quantum-cascade laser and a Herriott cell, we recorded the O-O stretching bands of CH2 OO and syn-CH3 CHOO in region 880-932 cm-1 at resolution 0...
July 19, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30024745/density-functional-theory-computational-reexamination-of-the-anomeric-effect-in-2-methoxy-and-2-cyano-1-3-dioxanes-and-1-3-dithianes-stereoelectronic-interactions-involving-the-cyano-c%C3%A2-n-group-revealed-by-natural-bond-orbital-nbo-analysis
#10
Eusebio Juaristi, Rafael Notario
The present study reports DFT geometry optimization of the anancomeric (ring conformationally anchored) axial r2-methoxy-trans-4,trans-6-dimethyl- and r2-cyano-trans-4,trans-6-dimethyl-1,3-dioxanes (1-ax and 3-ax), the equatorial isomers (2-eq and 4-eq), the axial r2-cyano-trans-4,trans-6-dimethyl-1,3-dithianes (5-ax and 7-ax) and the equatorial isomers (6-eq and 8-eq). The computational results do reproduce the anomeric effect in 1-8, and most importantly Weinhold's NBO analysis supports the contribution of n(X) → σ*(C-Y) stereoelectronic interactions that stabilize the axial isomers...
July 19, 2018: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/30024742/electrospray-ionization-of-polypropylene-glycol-rayleigh-charged-droplets-competing-pathways-and-charge-state-dependent-conformations
#11
Quentin Duez, Haidy Metwally, Lars Konermann
Recent molecular dynamics (MD) simulations from various laboratories have advanced the general understanding of electrospray ionization (ESI)-related processes. Unfortunately, computational cost has limited most of those previous endeavors to ESI droplets with radii of ~3 nm or less, which represent the low end of the size distribution in the ESI plume. The current work extends this range by conducting simulations on aqueous ESI droplets with radii of 5.5 nm (~23000 water molecules). Considering that computational cost increases with r6, this is a significant step forward...
July 19, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/30024730/proton-transfer-and-tautomerism-in-2-aminopurine-thymine-and-pyrrolocytosine-guanine-base-pairs
#12
Graham D Bull, Katherine C Thompson
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases...
July 19, 2018: Biochemistry
https://www.readbyqxmd.com/read/30024165/conformational-free-energy-changes-via-an-alchemical-path-without-reaction-coordinates
#13
Peng He, Bin W Zhang, Shima Arasteh, Lingle Wang, Robert Abel, Ronald M Levy
We introduce a novel method called Restrain - Free Energy Perturbation - Release (R-FEP-R) to estimate conformational free energy changes via an alchemical path, which for some conformational landscapes like those associated with cellular signaling proteins in the kinase family is more direct and readily converged than the corresponding free energy changes along the physical path. The R-FEP-R method was developed from the dual topology free energy perturbation method that is widely applied to estimate the binding free energy difference between two ligands...
July 19, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30024109/arylpyrrolyldiketone-boron-complexes-exhibiting-various-anion-binding-modes-based-on-dynamic-conformation-changes
#14
Atsuko Kuno, Masaya Fujiwara, Yohei Haketa, Hiromitsu Maeda
Arylpyrrolyldiketone boron complexes as anion-responsive π-electronic molecules were synthesized by Claisen condensations of acetylpyrrole and corresponding arylesters. The synthesized π-electronic molecules exhibited anion-binding behavior with various binding modes including pyrrole-inverted and non-inverted [1+1]-type anion complexes as well as [2+1]-type complexes due to the presence of only a single pyrrole ring. Furthermore, solid-state ion-pairing assemblies, comprising receptor-anion complexes and countercations, were constructed based on fairly planar [2+1]-type complexes...
July 19, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/30023868/silk-fibroin-acts-as-a-self-emulsifier-to-prepare-hierarchically-porous-silk-fibroin-scaffolds-through-emulsion-ice-dual-templates
#15
Jianchuan Wen, Jinrong Yao, Xin Chen, Zhengzhong Shao
Silk fibroin (SF) has shown enormous potentials in various fields; however, application of SF in emulsion technology is quite limited. Here, we use SF as a self-emulsifier to form an oil-in-water (O/W) emulsion by emulsifying 1-butanol in SF aqueous solution. This showed that SF possessed strong surface activity to stabilize the O/W emulsion without the need for any other surface-active agent until its solidification because of 1-butanol-induced conformational transition of SF to β-sheet. After freezing the preformed emulsions at -20 °C, robust three-dimensional porous SF scaffolds were prepared without the need for any further post-treatment...
March 31, 2018: ACS Omega
https://www.readbyqxmd.com/read/30023848/biomimetic-synthesis-of-polydopamine-coated-znfe-2-o-4-composites-as-anode-materials-for-lithium-ion-batteries
#16
Hongyun Yue, Ting Du, Qiuxian Wang, Zhenpu Shi, Hongyu Dong, Zhaoxia Cao, Yun Qiao, Yanhong Yin, Ruimin Xing, Shuting Yang
Metal oxides as anode materials for lithium storage suffer from poor cycling stability due to their conversion mechanisms. Here, we report an efficient biomimetic method to fabricate a conformal coating of conductive polymer on ZnFe2 O4 nanoparticles, which shows outstanding electrochemical performance as anode material for lithium storage. Polydopamine (PDA) film, a bionic ionic permeable film, was successfully coated on the surfaces of ZnFe2 O4 particles by the self-polymerization of dopamine in the presence of an alkaline buffer solution...
March 31, 2018: ACS Omega
https://www.readbyqxmd.com/read/30023827/phytochemicals-as-dynamic-surface-ligands-to-control-nanoparticle-protein-interactions
#17
Amanda N Abraham, Tarun K Sharma, Vipul Bansal, Ravi Shukla
The rapid formation of the protein corona on to the nanoparticle (NP) surface is the key that confers biological identity to NPs and subsequently dictates their fate both in vitro and in vivo. Despite significant efforts, the inability to control the spontaneous interaction of serum proteins with the administered NPs remains a major constraint in clinical translation of nanomedicines. The ligands present on the NP surface offer promise in controlling their biological interactions; however, their influence on the NP-protein interaction is not well-understood...
February 28, 2018: ACS Omega
https://www.readbyqxmd.com/read/30023823/distance-matched-tagging-sequence-optimizes-live-cell-protein-labeling-by-a-biarsenical-fluorescent-reagent-ascy3_e
#18
Karen A Hecht, Yijia Xiong, Daniel A Barrack, Nicole R Ford, Guritno Roesijadi, Thomas C Squier
Cell permeable biarsenical fluorescent dyes built around a cyanine scaffold (AsCy3) create the ability to monitor the structural dynamics of tagged proteins in living cells. To extend the capability of this photostable and bright biarsenical probe to site-specifically label cellular proteins, we have compared the ability of AsCy3 to label two different tagging sequences (i.e., CCKAEAACC and CCKAEAAKAEAAKCC), which were separately engineered onto enhanced green fluorescent proteins (EGFPs) and expressed in Escherichia coli ...
February 28, 2018: ACS Omega
https://www.readbyqxmd.com/read/30023821/role-of-counterions-in-constant-ph-molecular-dynamics-simulations-of-pamam-dendrimers
#19
Pedro B P S Reis, Diogo Vila-Viçosa, Sara R R Campos, António M Baptista, Miguel Machuqueiro
Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer ( J. Chem. Theory Comput ...
February 28, 2018: ACS Omega
https://www.readbyqxmd.com/read/30023775/simultaneous-binding-of-folic-acid-and-methotrexate-to-human-serum-albumin-insights-into-the-structural-changes-of-protein-and-the-location-and-competitive-displacement-of-drugs
#20
Sudipta Panja, Deb Kumar Khatua, Mintu Halder
Protein structure can be flexible to adopt multiple conformations to house small molecules. In this paper, we have attempted to experimentally figure out how the structure of a transport protein steer the drug-drug competition (DDC) by maintaining the equilibrium distribution of the bound and unbound fractions of drugs. This understanding is an important facet in biophysical and medicinal chemistry to ascertain the effectiveness of drugs. It is important to note that majority of studies involving small-molecule-transport protein interaction aimed at characterizing the binding process, and because these proteins can interact with thousands of molecules, there are hundreds of reports on such interactions...
January 31, 2018: ACS Omega
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