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https://www.readbyqxmd.com/read/28231553/a-reusable-aptasensor-of-thrombin-based-on-dna-machine-employing-resonance-light-scattering-technique
#1
Yining Hou, Jifeng Liu, Min Hong, Xia Li, Yanhua Ma, Qiaoli Yue, Chen-Zhong Li
The design of molecular nanodevices attracted great interest in these years. Herein, a reusable, sensitive and specific aptasensor was constructed based on an extension-contraction movement of DNA interconversion for the application of human thrombin detection. The present biosensor was based on resonance light scattering (RLS) using magnetic nanoparticles (MNPs) as the RLS probe. MNPs coated with streptavidin can combine with biotin labeled thrombin aptamers. The combined nanoparticles composite is monodispersed in aqueous medium...
February 20, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28231524/discovery-of-novel-cdk8-inhibitors-using-multiple-crystal-structures-in-docking-based-virtual-screening
#2
Taijin Wang, Zhuang Yang, Yongguang Zhang, Wei Yan, Fang Wang, Linhong He, Yuanyuan Zhou, Lijuan Chen
The cyclin dependent kinase CDK8, along with Med12 and Med13, form the kinase module of the Mediator complex. CDK8 expression associates with the activation of β-catenin in colon and gastric cancers. Herein, we applied docking-based virtual screening (VS) using the multiple crystal structures to identify several potent CDK8 inhibitors. The appropriate use of multiple crystal structures obtained a better enrichment of CDK8 conformations to cope with the protein flexibility. Later on, the 2D similarity search was used to find the derivatives of the high inhibitory CDK8 inhibitors we discovered by VS...
February 9, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#3
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28230998/influence-of-the-anomeric-conformation-in-the-intermolecular-interactions-of-glucose
#4
Imanol Usabiaga, Jorge González, Iker León, Pedro Felipe Arnaiz, Emilio J Cocinero, Jose A Fernandez
Carbohydrates are together with amino acids, DNA bases and lipids the building blocks of living beings. They play a central role in basic functions as immunity and signaling, which are governed by non-covalent interactions between sugar units and/or with other biomolecules. To get insights on such interactions between monosaccharide units, we used a combination of mass-resolved laser spectroscopy in supersonic expansions and molecular structure calculations. The results obtained clearly demonstrate that the small stability difference between the α/β anomers of glucopyranose derivatives is reversed and amplified during molecular aggregation, making the complexes of the β-anomers significantly more stable...
February 23, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28230982/synthesis-of-%C3%AE-1-2-linked-6-deoxy-l-altropyranose-oligosaccharides-via-gold-i-catalyzed-glycosylation-of-a-ortho-hexynylbenzoate-donor
#5
Zhengnan Shen, Hani Mobarak, Wei Li, Göran Widmalm, Biao Yu
The β-(1-2)-linked 6-deoxy-L-altropyranose di- to penta-saccharides 2-5, relevant to the O-antigen of the infectious Yersinia enterocolitica O:3, were synthesized for the first time. The challenging 1,2-cis-altropyranosyl linkage was assembled effectively via glycosylation with 2-O-benzyl-3,4-di-O-benzoyl-6-deoxy-L-altropyranosyl ortho-hexynylbenzoate (7) under the catalysis of PPh3AuNTf2. NMR and molecular modeling studies showed that the pentasaccharide (5) adopted a left-handed helical conformation.
February 23, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28230965/fluorine-functionalized-graphene-quantum-dots-as-inhibitor-against-hiapp-amyloid-aggregation
#6
Maryam Yousaf, Huan Huang, Ping Li, Chen Wang, Yanlian Yang
Fibrillar deposits of the human islet amyloid polypeptide (hIAPP) is considered as a root of Type II diabetes mellitus. Fluorinated graphene quantum dots (FGQDs) are new carbon nanomaterials with unique physicochemical properties containing highly electronegative F atoms. Herein we report a single step synthesis method of FGQDs with an inhibitory effect on aggregation and cytotoxicity of hIAPP in vitro. Highly fluorescent and water dispersible FGQDs, less than 3 nm in size were synthesized by the microwave-assisted hydrothermal method...
February 23, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28230735/new-evidence-for-the-theory-of-chromosome-organization-by-repetitive-elements-core
#7
Shao-Jun Tang
Repetitive DNA elements were proposed to coordinate chromatin folding and interaction in chromosomes by their intrinsic homology-based clustering ability. A recent analysis of the data sets from chromosome-conformation-capture experiments confirms the spatial clustering of DNA repeats of the same family in the nuclear space, and thus provides strong new support for the CORE theory.
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28230657/stabilized-hiv-1-envelope-glycoprotein-trimers-for-vaccine-use
#8
Max Medina-Ramírez, Rogier W Sanders, Quentin J Sattentau
PURPOSE OF REVIEW: To provide an update on the latest developments in the field of HIV-1 antibody-based soluble envelope glycoprotein (Env) trimer design for vaccine use. RECENT FINDINGS: The development of soluble native-like HIV-1 Env trimer immunogens has moved the field of antibody-based vaccine design forward dramatically over the past few years with refinement of various stabilizing approaches. However, despite this progress, significant challenges remain...
February 21, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28230529/single-molecule-fret-unveils-induced-fit-mechanism-for-substrate-selectivity-in-flap-endonuclease-1
#9
Fahad Rashid, Paul D Harris, Manal S Zaher, Mohamed A Sobhy, Luay I Joudeh, Chunli Yan, Hubert Piwonski, Susan E Tsutakawa, Ivaylo Ivanov, John A Tainer, Satoshi Habuchi, Samir M Hamdan
Human flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage...
February 23, 2017: ELife
https://www.readbyqxmd.com/read/28230370/coarse-grained-prediction-of-peptide-binding-to-g-protein-coupled-receptors
#10
Bartholomé Delort, Pedro Renault, Landry Charlier, Florent Raussin, Jean Martinez, Nicolas Floquet
In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initially positioned in the surrounding water box. Using a protocol based on Replica Exchange Molecular Dynamics (REMD), both opening of the receptors and entry of the peptides into their dedicated pockets were observed on the μs time-scale...
February 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28230364/modeling-protein-conformational-transition-pathways-using-collective-motions-and-the-lasso-method
#11
Thomas W Hayes, Iain H Moal
Many proteins can adopt multiple distinct conformational states which often play different functional roles. Previous studies have shown that the underlying global dynamics through which these states are accessed are, at least in part, encoded by the protein's topology. In this work we present a method for generating transition pathways between states by perturbing the protein towards a target conformational state along thermally accessible collective motions calculated from the starting conformation. Specifically, the least absolute shrinkage and selection operator (LASSO) is used to identify the most parsimonious route along soft modes calculated using the anisotropic network model...
February 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28230284/formation-of-%C3%AE-lactones-with-anti-baeyer-villiger-regiochemistry-investigations-into-the-mechanism-of-the-cerium-catalyzed-aerobic-coupling-of-%C3%AE-oxoesters-with-enol-acetates
#12
Jens Christoffers, Irina Geibel, Anna Dierks, Thomas Müller
The cerium-catalyzed, aerobic coupling of β-oxoesters with enol acetates and dioxygen yields δ-lactones with a 1,4-diketone moiety. In contrast to the Baeyer-Villiger oxidation (BVO), where the higher substituted residue migrates, in this case of an oxidative C-C coupling reaction the less substituted alkyl residue undergoes a 1,2-shift. An endoperoxidic oxycarbenium ion comparable to the Criegee intermediate in the BVO is proposed as a reaction intermediate and submitted to conformational analysis by computational methods...
February 23, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28230174/a-hydrophobic-patch-surrounding-trp154-in-human-neuroserpin-controls-the-helix-f-dynamics-with-implications-in-inhibition-and-aggregation
#13
Mohammad Farhan Ali, Abhinav Kaushik, Charu Kapil, Dinesh Gupta, Mohamad Aman Jairajpuri
Neuroserpin (NS) mediated inhibition of tissue-type plasminogen activator (tPA) is important for brain development, synapse formation and memory. Aberrations in helix F and β-sheet A movement during inhibition can directly lead to epilepsy or dementia. Conserved W154 residue in a hydrophobic patch between helix F and β-sheet A is ideally placed to control their movement during inhibition. Molecular Dynamics (MD) simulation on wild type (WT) NS and its two variants (W154A and W154P) demonstrated partial deformation in helix F and conformational differences in strands 1A and 2A only in W154P...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230071/probing-the-molecular-mechanism-of-human-soluble-guanylate-cyclase-activation-by-no-in-vitro-and-in-vivo
#14
Jie Pan, Hong Yuan, Xiaoxue Zhang, Huijuan Zhang, Qiming Xu, Yajun Zhou, Li Tan, Shingo Nagawa, Zhong-Xian Huang, Xiangshi Tan
Soluble guanylate cyclase (sGC) is a heme-containing metalloprotein in NO-sGC-cGMP signaling. NO binds to the heme of sGC to catalyze the synthesis of the second messenger cGMP, which plays a critical role in several physiological processes. However, the molecular mechanism for sGC to mediate the NO signaling remains unclear. Here fluorophore FlAsH-EDT2 and fluorescent proteins were employed to study the NO-induced sGC activation. FlAsH-EDT2 labeling study revealed that NO binding to the H-NOX domain of sGC increased the distance between H-NOX and PAS domain and the separation between H-NOX and coiled-coil domain...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229516/a-direct-link-from-the-gas-to-the-condensed-phase-a-rotational-spectroscopic-study-of-2-2-2-trifluoroethanol-trimers
#15
Javix Thomas, Nathan A Seifert, Wolfgang Jäger, Yunjie Xu
Rotational spectra of the three most stable conformers (I, II, III) of the ternary 2,2,2-trifluoroethanol (TFE) cluster were measured using Fourier transform microwave spectrometers, and unambiguously assigned with the aid of ab initio calculations. The most stable conformer, I, contains one trans-TFE subunit which is unstable in its isolated gas phase form. The study offers new insights into how the trans conformation is stabilized in TFE clusters of increasing size, and eventually becomes a dominant conformation in the liquid phase...
February 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28229468/time-will-tell-a-longitudinal-investigation-of-brain-behavior-relationships-during-reading-development
#16
Mallory C Stites, Sarah Laszlo
ERPs are a powerful tool for the study of reading, as they are both temporally precise and functionally specific. These are essential characteristics for studying a process that unfolds rapidly and consists of multiple, interactive subprocesses. In work with adults, clear, specific models exist linking components of the ERP with individual subprocesses of reading including orthographic decoding, phonological processing, and semantic access (e.g., Grainger & Holcomb, 2009). The relationships between ERP components and reading subprocesses are less clear in development; here, we address two questions regarding these relationships...
February 23, 2017: Psychophysiology
https://www.readbyqxmd.com/read/28229338/investigation-of-the-encapsulation-of-metal-cations-cu-2-zn-2-ca-2-and-ba-2-by-the-dipeptide-phe-phe-using-natural-bond-orbital-theory-and-molecular-dynamics-simulation
#17
Snehasis Bhunia, Ajeet Singh, Animesh K Ojha
Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28229334/specific-amyloid-binding-of-polybasic-peptides-in-vivo-is-retained-by-%C3%AE-sheet-conformers-but-lost-in-the-disrupted-coil-and-all-d-amino-acid-variants
#18
Jonathan S Wall, Angela Williams, Tina Richey, Alan Stuckey, Craig Wooliver, J Christopher Scott, Robert Donnell, Emily B Martin, Stephen J Kennel
PURPOSE: The heparin-reactive, helical peptide p5 is an effective amyloid imaging agent in mice with systemic amyloidosis. Analogs of p5 with modified secondary structure characteristics exhibited altered binding to heparin, synthetic amyloid fibrils, and amyloid extracts in vitro. Herein, we further study the effects of peptide helicity and chirality on specific amyloid binding using a mouse model of systemic inflammation-associated (AA) amyloidosis. PROCEDURES: Peptides with disrupted helical structure [p5(coil) and p5(Pro3)], with an extended sheet conformation [p5(sheet)] or an all-D enantiomer [p5(D)], were chemically synthesized, radioiodinated, and their biodistribution studied in WT mice as well as transgenic animals with severe systemic AA amyloidosis...
February 22, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28229200/-current-impact-of-cardiac-implantable-electronic-devices
#19
J Kuschyk, B Rudic, M Borggrefe, I Akin
Sudden cardiac death and chronic heart failure are among the main contributors to persisting high mortality rates in Germany. In addition to removal of causal factors and guideline-conform pharmacological therapy, therapy with cardiac implantable electronic devices (CIED) is of undisputed importance. Subcutaneous defibrillators have the advantage that they do not have intracardiac electrodes but still have the same efficacy and safety. For patients with a wide QRS complex and reduced ejection fraction, cardiac resynchronization has led to a reduction of morbidity and mortality...
February 22, 2017: Herz
https://www.readbyqxmd.com/read/28229161/high-levels-of-latent-antithrombin-in-plasma-from-patients-with-antithrombin-deficiency
#20
María de la Morena-Barrio, Edna Sandoval, Pilar Llamas, Ewa Wypasek, Mara Toderici, José Navarro-Fernández, Agustín Rodríguez-Alen, Nuria Revilla, Raquel López-Gálvez, Antonia Miñano, José Padilla, Belén de la Morena-Barrio, Jorge Cuesta, Javier Corral, Vincente Vincente
Antithrombin is an anticoagulant serpin that efficiently inhibits multiple procoagulant proteases. The cost for the structural flexibility required for this function is the vulnerability to mutations that impact its folding pathway. Most conformational mutations identified in serpins cause polymerisation. Only three mutations in SERPINC1 affecting two residues have been found to favour transformation to the latent conformation of antithrombin, another hyperstable non-anticoagulant form with strong antiangiogenic activity that constitutes 3 % of plasma antithrombin in healthy subjects...
February 23, 2017: Thrombosis and Haemostasis
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