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https://www.readbyqxmd.com/read/29145649/single-molecule-compaction-of-megabase-long-chromatin-molecules-by-multivalent-cations
#1
Anatoly Zinchenko, Nikolay V Berezhnoy, Sai Wang, William M Rosencrans, Nikolay Korolev, Johan R C van der Maarel, Lars Nordenskiöld
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145633/the-initiation-propagation-and-dynamics-of-crispr-spycas9-r-loop-complex
#2
Yan Zeng, Yang Cui, Yong Zhang, Yanruo Zhang, Meng Liang, Hui Chen, Jie Lan, Guangtao Song, Jizhong Lou
CRISPR-Cas9 system has been widely used for efficient genome editing. Although the structures of Cas9 protein in complex with single-guided RNA (sgRNA) and target DNA have been resolved, the molecular details about the formation of Cas9 endonuclease R-loop structure remain elusive. Here we examine the DNA cleavage activities of Streptococcus pyogenes Cas9 (SpyCas9) and its mutants using various target sequences and study the conformational dynamics of R-loop structure during target binding using single-molecule fluorescence energy transfer (smFRET) technique...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145242/the-association-of-genetic-variants-in-chemokine-genes-with-the-risk-of-psoriasis-vulgaris-in-chinese-population-a-case-control-study
#3
Jin Zhang, Qiuhe Song, Kun Zhu, Jun Lu, Xiaogang Xiong, Fei Hao
This study aimed to investigate the influence of polymorphisms in chemokine genes, including MCP1, CCR2, and CCR5 with psoriasis vulgaris (PV) risk in a Chinese population.The genotyping of studied polymorphisms through polymerase chain reaction (PCR) and sequencing was conducted in 142 PV patients and 147 healthy controls. The genotype distribution of the polymorphisms in the control group was checked to determine whether it conformed to Hardy-Weinberg equilibrium (HWE). The genotype and allele frequencies were compared between PV patients and the healthy controls using Chi-square test...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29145075/isolation-and-characterisation-of-an-unexpected-byproduct-in-the-regioselective-butane-diacetal-protection-of-%C3%AE-methyl-galactopyranoside
#4
Clément Q Fontenelle, Ramakrishna Kuppala, Mark Light, Bruno Linclau
The regioselective protection of both methyl galactopyranoside anomers at the 2 and 3-positions as the butane diacetal (BDA) is well known. Here we describe the formation of an unexpected byproduct, which mainly occurs when α-methyl galactopyranoside is reacted with 2,3-butanedione under BF3•OEt2 catalysis. The structure of the byproduct, which did not arise from anomerisation to the β-anomer or from BDA formation at the galactopyranoside 3,4-positions, was elucidated by NMR and X-ray crystallographic analysis, and proved to be the expected BDA protected galactopyranoside, but in which the stereochemistry of both its BDA acetal centres are inverted...
November 6, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/29145034/molecular-insight-into-mutation-induced-conformational-change-in-metastasic-bowel-cancer-braf-kinase-domain-and-its-implications-for-selective-inhibitor-design
#5
Kai Zhao, Xin Zhou, Ming Ding
Oncogenic BRAF V600E mutation confers constitutive activation for the kinase and is closely related to the pathogenesis of metastasic bowel cancer (MBC). Here, the V600E-induced conformational change in MBC BRAF kinase domain is characterized systematically at structural, energetic and dynamic levels. The mutation is observed to cause a conformational conversion of the kinase's activation loop from DFG-out to DFG-in, thus activating the kinase. Electrostatic force is primarily responsible for the conformational conversion and stabilization of DFG-in associated with the mutation...
November 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29145025/coupling-of-on-column-trypsin-digestion-peptide-mapping-and-principal-component-analysis-for-stability-and-biosimilarity-assessment-of-recombinant-human-growth-hormone
#6
Sara M Shatat, Basma M Eltanany, Abeer A Mohamed, Medhat A Al-Ghobashy, Faten A Fathalla, Samah S Abbas
Peptide mapping (PM) is a vital technique in biopharmaceutical industry. The fingerprint obtained helps to qualitatively confirm host stability as well as verify primary structure, purity and integrity of the target protein. Yet, in-solution digestion followed by tandem mass spectrometry is not suitable as a routine quality control test. It is time consuming and requires sophisticated, expensive instruments and highly skilled operators. In an attempt to enhance the fuctionality of PM and extract multi-dimentional data about various critical quality attributes and comparability of biosimilars, coupling of PM generated using immobilized trypsin followed by HPLC-UV to principal component analysis (PCA) is proposed...
November 11, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29144759/degree-of-unsaturation-and-backbone-orientation-of-amphiphilic-macromolecules-influence-local-lipid-properties-in-large-unilamellar-vesicles
#7
Kathryn E Uhrich, Alysha Moretti, Bin Zhang, Bernice Lee, Meenakshi Dutt
Liposomes have become increasingly common in the delivery of bioactive agents due to their ability to encapsulate hydrophobic and hydrophilic drugs with excellent biocompatibility. While commercial liposome formulations improve bioavailability of otherwise quickly eliminated or insoluble drugs, tailoring formulation properties for specific uses has become a focus of liposome research. Here, we report the design, synthesis, and characterization of two series of amphiphilic macromolecules (AMs), consisting of acylated polyol backbones conjugated to poly(ethylene glycol) (PEG) that can serve as the sole additives to stabilize and control hydrophilic molecule release rates from distearoyl-phosphatidylcholine- (DSPC-) based liposomes...
November 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29144742/successful-identification-of-cardiac-troponin-calcium-sensitizers-using-a-combination-of-virtual-screening-and-roc-analysis-of-known-troponin-c-binders
#8
Melanie L Aprahamian, Svetlana B Tikunova, Morgan V Price, Andres F Cuesta, Jonathan P Davis, Steffen Lindert
Calcium-dependent cardiac muscle contraction is regulated by the protein complex troponin. Calcium binds to the N-terminal domain of troponin C (cNTnC) which initiates the process of contraction. Heart failure is a consequence of a disruption of this process. With the prevalence of this condition, a strong need exists to find novel compounds to increase the calcium sensitivity of cNTnC. Desirable are small chemical molecules that bind to the interface between cTnC and the cTnI switch peptide and exhibit calcium sensitizing properties by possibly stabilizing cTnC in an open conformation...
November 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29144454/dynamics-of-p-type-atpase-transport-revealed-by-single-molecule-fret
#9
Mateusz Dyla, Daniel S Terry, Magnus Kjaergaard, Thomas L-M Sørensen, Jacob Lauwring Andersen, Jens Peter Andersen, Charlotte Rohde Knudsen, Roger B Altman, Poul Nissen, Scott C Blanchard
Phosphorylation-type (P-type) ATPases are ubiquitous primary transporters that pump cations across cell membranes through the formation and breakdown of a phosphoenzyme intermediate. Structural investigations suggest that the transport mechanism is defined by conformational changes in the cytoplasmic domains of the protein that are allosterically coupled to transmembrane helices so as to expose ion binding sites to alternate sides of the membrane. Here, we have used single-molecule fluorescence resonance energy transfer to directly observe conformational changes associated with the functional transitions in the Listeria monocytogenes Ca(2+)-ATPase (LMCA1), an orthologue of eukaryotic Ca(2+)-ATPases...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29144141/experimental-demonstration-of-a-sizeable-nonclassical-ch%C3%A2-%C3%A2-%C3%A2-g-hydrogen-bond-in-cyclohexane-derivatives-stabilization-of-an-axial-cyano-group
#10
Kyle M Lambert, Zachary D Stempel, Kenneth B Wiberg, William F Bailey
Base-catalyzed equilibration of anancomeric cyanocyclohexanes demonstrates that replacement of cis-3,5-dimethyl holding groups with electron-withdrawing CF3 groups dramatically increases the proportion of the axial cyano isomer present at equilibrium. The CF3 groups exert an effect on the conformational energy of the cyano group worth about 0.6 kcal/mol. A nonclassical hydrogen bond between the axial CN group and the syn-axial hydrogens is a major contributor to the axial stability of the group.
November 16, 2017: Organic Letters
https://www.readbyqxmd.com/read/29144127/area-controllable-stamping-of-semicrystalline-copolymer-ionogels-for-solid-state-electrolyte-gated-transistors-and-light-emitting-devices
#11
Hyun Je Kim, Hae Min Yang, Jaemok Koo, Moon Sung Kang, Kihyon Hong, Keun Hyung Lee
Two types of thin-film electrochemical devices (electrolyte-gated transistors and electrochemical light-emitting cells) are demonstrated by using area-controllable ionogel patches generated by transfer stamping. For the successful transfer of ionogel patches on various target substrates thermoreversible gelation by phase-separated polymer crystals within the ionogel is essential because it allows the gel to form a conformal contact with the acceptor substrate, and thereby lowering the overall Gibbs energy of the system upon transfer of the ionogel...
November 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29144022/collagen-a-review-on-its-sources-and-potential-cosmetic-applications
#12
REVIEW
María Isabela Avila Rodríguez, Laura G Rodríguez Barroso, Mirna Lorena Sánchez
Collagen is a fibrillar protein that conforms the conjunctive and connective tissues in the human body, essentially skin, joints, and bones. This molecule is one of the most abundant in many of the living organisms due to its connective role in biological structures. Due to its abundance, strength and its directly proportional relation with skin aging, collagen has gained great interest in the cosmetic industry. It has been established that the collagen fibers are damaged with the pass of time, losing thickness and strength which has been strongly related with skin aging phenomena [Colágeno para todo...
November 16, 2017: Journal of Cosmetic Dermatology
https://www.readbyqxmd.com/read/29143881/rmce-based-insect-cell-platform-to-produce-membrane-proteins-captured-on-hiv-1-gag-virus-like-particles
#13
João Vidigal, Bárbara Fernandes, Mafalda M Dias, Marco Patrone, António Roldão, Manuel J T Carrondo, Paula M Alves, Ana P Teixeira
Conformationally complex membrane proteins (MPs) are therapeutic targets in many diseases, but drug discovery has been slowed down by the lack of efficient production tools. Co-expression of MPs with matrix proteins from enveloped viruses is a promising approach to obtain correctly folded proteins at the surface of virus-like particles (VLPs), preserving their native lipidic environment. Here, we implemented a site-specific recombinase-mediated cassette exchange (RMCE) strategy to establish a reusable HIV-1 Gag-expressing insect cell line for fast production of target MPs on the surface of Gag-VLPs...
November 16, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29143866/haplotype-analysis-of-the-germacrene-a-synthase-gene-and-association-with-cynaropicrin-content-and-biological-activities-in-cynara-cardunculus
#14
Ana Margarida Ferro, Patrícia Ramos, Ângela Guerra, Paula Parreira, Teresa Brás, Olinda Guerreiro, Eliana Jerónimo, Carmen Capel, Juan Capel, Fernando J Yuste-Lisbona, Maria F Duarte, Rafael Lozano, M Margarida Oliveira, Sónia Gonçalves
Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropicrin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from different origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities...
November 16, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29143774/disrupting-vegf-vegfr1-interaction-de-novo-designed-linear-helical-peptides-to-mimic-the-vegf13-25-fragment
#15
Beatriz Balsera, M Ángeles Bonache, Marie Reille-Seroussi, Nathalie Gagey-Eilstein, Michel Vidal, Rosario González-Muñiz, María Jesús Pérez de Vega
The interaction between vascular endothelial growth factor (VEGF) and its receptors (VEGFR) has important implications in angiogenesis and cancer, which moved us to search for peptide derivatives able to block this protein-protein interaction. In a previous work we had described a collection of linear 13-mer peptides specially designed to adopt helical conformations (Ac-SSEEX⁵ARNX⁸AAX(12)N-NH₂), as well as the evaluation of seven library components for the inhibition of the interaction of VEGF with its Receptor 1 (VEGFR1)...
October 28, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29143731/the-treatment-of-depression-in-primary-care
#16
Sebastian Trautmann, Katja Beesdo-Baum
BACKGROUND: General practitioners play a key role in the care of patients with depressive disorders. We studied the frequency and type of treatment of depressive disorders in primary care. METHODS: In a cross-sectional epidemiological study on a particular day in six different regions in Germany, 253 physicians and 3563 unselected patients were asked to fill in a questionnaire assessing the diagnosis and treatment of depression. A total of 3431 usable patient data sets and 3211 sets of usable data from both the patient and the physician were subjected to further analysis...
October 27, 2017: Deutsches Ärzteblatt International
https://www.readbyqxmd.com/read/29143447/investigation-of-the-interactions-between-aptamer-and-misfolded-proteins-from-monomer-and-oligomer-to-fibril-by-single-molecule-force-spectroscopy
#17
Yan Zheng, Qing Wang, Xiaohai Yang, Zhiping Li, Lei Gao, Hua Zhang, Wenyan Nie, Xiuhua Geng, Kemin Wang
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability...
November 16, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29143424/restoration-of-ribozyme-tertiary-contact-and-function-using-a-molecular-glue-for-rna
#18
Chikara Dohno, Maki Kimura, Kazuhiko Nakatani
Some RNA classes require folding into the proper higher-order structures to exert their functions. Hammerhead ribozyme (HHR) requires a folding conformation stabilized by tertiary interaction for full activity. Here, we developed a rationally engineered HHR that was inactive, but could be activated by a synthetic RNA-binding ligand, naphthyridine carbamate tetramer with Z-stilbene linker (Z-NCTS). Binding of Z-NCTS could induce the formation of an active folding structure and thereby restore ribozyme activity, where Z-NCTS acts as a molecular glue to bring two isolated RNA loops into contact with each other...
November 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29143152/electrochemical-and-theoretical-studies-of-the-interactions-of-a-pyridyl-based-corrosion-inhibitor-with-iron-clusters-fe15-fe30-fe45-and-fe60
#19
Julian Cruz-Borbolla, Esteban Garcia-Ochoa, Jayanthi Narayanan, Pablo Maldonado-Rivas, Thangarasu Pandiyan, José M Vásquez-Pérez
The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP...
November 15, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29143081/generation-in-yeast-and-antigenic-characterization-of-hepatitis-e-virus-capsid-protein-virus-like-particles
#20
Martynas Simanavicius, Paulius Lukas Tamosiunas, Rasa Petraityte-Burneikiene, Reimar Johne, Rainer G Ulrich, Aurelija Zvirbliene, Indre Kucinskaite-Kodze
Hepatitis E is a globally distributed human disease caused by hepatitis E virus (HEV). In Europe, it spreads through undercooked pork meat or other products and with blood components through transfusions. There are no approved or golden standard serologic systems for HEV diagnostics. Commercially available HEV tests often provide inconsistent results which may differ among the assays. In this study, we describe generation in yeast and characterization of HEV genotype 3 (HEV-3) and rat HEV capsid proteins self-assembled into virus-like particles (VLPs) and the development of HEV-specific monoclonal antibodies (MAbs)...
November 15, 2017: Applied Microbiology and Biotechnology
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