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https://www.readbyqxmd.com/read/28544261/mechanical-properties-structure-bioadhesion-and-biocompatibility-of-pectin-hydrogels
#1
Pavel A Markov, Nikita S Krachkovsky, Eugene A Durnev, Ekaterina A Martinson, Sergey G Litvinets, Sergey V Popov
The surface structure, biocompatibility, textural and adhesive properties of calcium hydrogels derived from 1, 2 and 4% solutions of apple pectin were examined in this study. An increase in the pectin concentration in hydrogels was shown to improve their stability toward elastic and plastic deformation. The elasticity of pectin hydrogels, measured as Young's modulus, ranged from 6 to 100 kPa. The mechanical properties of the pectin hydrogels were shown to correspond to those of soft tissues. The characterization of surface roughness in terms of the roughness profile (Ra) and the root-mean-square deviation of the roughness profile (Rq) indicated an increased roughness profile for hydrogels depending on their pectin concentration...
May 22, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28542806/structural-and-functional-study-of-a-simple-rapid-and-label-free-dnazyme-based-dna-biosensor-for-optimization-activity
#2
Narges Shahbazi, Saman Hosseinkhani, Khosro Khajeh, Bijan Ranjbar
Peroxidase-mimicking DNAzyme has a potential to self-assemble into a G-quadruplex and shows peroxidase activity. In comparison to proteins, peroxidase-mimicking DNAzyme is less expensive and more stable. Herein, it is used in fabricating non-labeling biosensors. This paper investigates the structural and functional properties of a DNA biosensor based on split DNAzyme with a detection limit in nM range (9.48 nM). Two halves of DNAzyme were linked by a complementary sequence of DNA target. Hybridization of the DNA target pulled two DNAzyme halves apart and peroxidase activity decreased...
May 20, 2017: Biopolymers
https://www.readbyqxmd.com/read/28540354/data-on-the-exon-intron-organization-of-genes-coding-for-b-cell-receptor-like-proteins
#3
Sergey Y Morozov, Anna V Pankratenko, Anastasia K Atabekova, Andrey G Solovyev
B-cell receptor-associated protein (BAP) family plays important roles in the ER homeostasis and stress responses of eukaryotic cells [1]. We reported the analysis of plant BAP-like (PBL) genes and the encoded proteins of higher land plants [2]. The origin and functional divergence of these genes among all eukaryotes, however, are poorly studied, which impedes our understanding of the functional relationships and diversity among BAP-like proteins. One possible reason for the potential functional diversity may be the differences in the exon-intron structure of PBL genes...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28539441/chikungunya-virus-overcomes-polyamine-depletion-by-mutation-of-nsp1-and-the-opal-stop-codon-to-confer-enhanced-replication-and-fitness
#4
Bryan C Mounce, Teresa Cesaro, Lea Vlajnić, Anna Vidiņa, Thomas Vallet, James Weger-Lucarelli, Gabriella Pasoni, Kenneth A Stapleford, Jean-Pierre Levraud, Marco Vignuzzi
Polyamines, small positively-charge molecules present in all cells, play important roles in the replication of DNA and RNA viruses. Chikungunya virus (CHIKV) relies on polyamines for translation of the viral genome upon viral entry, and pharmacological depletion of polyamines limits viral replication. However, the potential development of antiviral resistance necessitates a better understanding of how polyamines function and can be targeted via compounds that alter polyamine levels. We have isolated CHIKV that is resistant to polyamine depletion that contains two mutations in the non-structural protein 1 (nsP1) coding region in combination with mutation to the opal stop codon preceding nsP4...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28537245/-impact-of-mutations-in-nucleoprotein-on-replication-of-influenza-virus-a-hong-kong-1-68-162-35-reassortants-at-different-temperatures
#5
A A Pulkina, M V Sergeeva, S V Petrov, A V Fadeev, A B Komissarov, E A Romanovskaya-Romanko, M V Potapchuk, L M Tsybalova
The nucleoprotein (NP) of influenza virus is a multifunctional RNA binding protein. The role of NP in the adaptation of influenza viruses to a host has been experimentally proved. Ambiguous data are available on the role of nucleoprotein in the attenuation of influenza A viruses, which is characterized by ability to replicate at low temperature (26°C) and inability to replicate at high temperature (39°C). Influenza virus donor strain A/Hong Kong/1/68/162/35 (H3N2), adapted to growth at low temperature, differs from the wild type virus by 14 amino acid mutations in the internal and non-structural proteins...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28537193/isolated-potato-virus-a-coat-protein-possesses-unusual-properties-and-forms-different-short-virus-like-particles
#6
Alexander L Ksenofontov, Eugeny N Dobrov, Natalia V Fedorova, Marina V Serebryakova, Andrei N Prusov, Ludmila A Baratova, Viiu Paalme, Lilian Järvekülg, Eleonora V Shtykova
In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency of to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF Mass Spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy and synchrotron small angle X-ray scattering (SAXS)...
May 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28534849/evaluation-and-comparison-of-the-pathogenicity-and-host-immune-responses-induced-by-a-g2b-taiwan-porcine-epidemic-diarrhea-virus-strain-pintung-52-and-its-highly-cell-culture-passaged-strain-in-conventional-5-week-old-pigs
#7
Yen-Chen Chang, Chi-Fei Kao, Chia-Yu Chang, Chian-Ren Jeng, Pei-Shiue Tsai, Victor Fei Pang, Hue-Ying Chiou, Ju-Yi Peng, Ivan-Chen Cheng, Hui-Wen Chang
A genogroup 2b (G2b) porcine epidemic diarrhea virus (PEDV) Taiwan Pintung 52 (PEDVPT) strain was isolated in 2014. The pathogenicity and host antibody responses elicited by low-passage (passage 5; PEDVPT-P5) and high-passage (passage 96; PEDVPT-P96) PEDVPT strains were compared in post-weaning PEDV-seronegative pigs by oral inoculation. PEDVPT-P5-inoculation induced typical diarrhea during 1-9 days post inoculation with fecal viral shedding persisting for 26 days. Compared to PEDVPT-P5, PEDVPT-P96 inoculation induced none-to-mild diarrhea and lower, delayed fecal viral shedding...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28530639/calcium-binding-protein-s100a4-confers-mesenchymal-progenitor-cell-fibrogenicity-in-idiopathic-pulmonary-fibrosis
#8
Hong Xia, Adam Gilbertsen, Jeremy Herrera, Emilian Racila, Karen Smith, Mark Peterson, Timothy Griffin, Alexey Benyumov, Libang Yang, Peter B Bitterman, Craig A Henke
Idiopathic pulmonary fibrosis (IPF) is a progressive disease with a prevalence of 1 million persons worldwide. The fibrosis spreads from affected alveoli into contiguous alveoli and leads to death by asphyxiation. We previously discovered that the IPF lung harbors fibrogenic mesenchymal progenitor cells (MPCs) that serve as a cell of origin for disease-mediating myofibroblasts. In a prior genomewide transcriptional analysis, we found that IPF MPCs displayed increased expression of S100 calcium-binding A4 (S100A4), a protein linked to cancer cell proliferation and invasiveness...
May 22, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28528213/optimal-electrostatic-interactions-between-substrate-and-protein-are-essential-for-radical-chemistry-in-ornithine-4-5-aminomutase
#9
Caitlyn Makins, Douglas A Whitelaw, Michael McGregor, Alix Petit, Robert G Mothersole, Kathleen E Prosser, Kirsten R Wolthers
Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting D-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, D-ornithine...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28527814/desmoplakin-missense-and-non-missense-mutations-in-arrhythmogenic-right-ventricular-cardiomyopathy-genotype-phenotype-correlation
#10
Silvia Castelletti, Annina S Vischer, Petros Syrris, Lia Crotti, Carla Spazzolini, Alice Ghidoni, Gianfranco Parati, Sharon Jenkins, Maria-Christina Kotta, William J McKenna, Peter J Schwartz, Antonis Pantazis
BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is traditionally considered as primarily affecting the right ventricle. Mutations in genes encoding desmosomal proteins account for 40-60% of cases. Genotype-phenotype correlations are scant and mostly non gene-specific. Accordingly, we assessed the genotype-phenotype correlation for desmoplakin (DSP) missense and non-missense mutations causing ARVC. METHODS AND RESULTS: We analyzed 27 ARVC patients carrying a missense or a non-missense DSP mutation, with complete clinical assessment...
May 10, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28527439/preferential-binding-effects-on-protein-structure-and-dynamics-revealed-by-coarse-grained-monte-carlo-simulation
#11
R B Pandey, D J Jacobs, B L Farmer
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered...
May 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28527408/subcellular-localization-based-comparative-study-on-radioresistant-bacteria-a-novel-approach-to-mine-proteins-involve-in-radioresistance
#12
Divya Vishambra, Malay Srivastava, Kamal Dev, Varun Jaiswal
Radioresistant bacteria (RRB) are among the most radioresistant organisms and has a unique role in evolution. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-aging and anti-cancer treatment. The study of radiation resistance in RRB was mainly focused on cytosolic mechanisms such as DNA repair mechanism, cell cleansing activity and high antioxidant activity. Although it was known that protein localized on outer areas of cell play role in resistance towards extreme condition but the mechanisms/proteins localized on the outer area of cells are not studied for radioresistance...
May 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28526530/insights-into-the-early-stage-of-pinus-nigra-arn-somatic-embryogenesis-using-discovery-proteomics
#13
Katarína Klubicová, Lubica Uvácková, Maksym Danchenko, Peter Nemecek, Ludovít Skultéty, Ján Salaj, Terézia Salaj
The somatic embryogenesis in conifers represents a suitable model of plant regeneration system facilitating studies of fundamental aspects of an early development as well as in vitro micropropagation. The aim of our study was to deeper understand the somatic embryogenesis in the conifer tree Pinus nigra Arn. Comparative proteomic analysis based on 2D-PAGE in 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) initiated from cotyledons of somatic seedlings of the same genotypes, 3) embryogenic tissues that lost the maturation capacity (E-L) of two cell lines (E362, E366)...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526057/recognition-of-a-structural-domain-rwdbd-in-gcn1-proteins-that-interacts-with-the-rwd-domain-containing-proteins
#14
Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger, Narayanaswamy Srinivasan
The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for its importance for cells to sense and overcome amino acid starvation. Gcn1 directly binds to the RWD (RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases) domain of the protein kinase Gcn2, and this is essential for delivering the starvation signal to Gcn2...
May 19, 2017: Biology Direct
https://www.readbyqxmd.com/read/28524918/urotensin-ii-peptidomimetic-incorporating-a-non-reducible-1-5-triazole-disulfide-bond-reveals-a-pseudo-irreversible-covalent-binding-mechanism-to-the-urotensin-g-protein-coupled-receptor
#15
Salvatore Pacifico, Aidan Kerckhoffs, Andrew J Fallow, Rachel E Foreman, Remo Guerrini, John McDonald, David G Lambert, Andrew G Jamieson
The urotensin-II receptor (UTR) is a class A GPCR that predominantly binds to the pleiotropic cyclic peptide urotensin-II (U-II). U-II is constrained by a disulfide bridge that induces a β-turn structure and binds pseudo-irreversibly to UTR and is believed to result in a structural rearrangement of the receptor. However, it is not well understood how U-II binds pseudo-irreversibly and the nature of the reorganization of the receptor that results in G-protein activation. Here we describe a series of U-II peptidomimetics incorporating a non-reducible disulfide bond structural surrogate to investigate the feasibility that native U-II binds to the G protein-coupled receptor through disulfide bond shuffling as a mechanism of covalent interaction...
May 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28524877/optimized-fragmentation-schemes-and-data-analysis-strategies-for-proteome-wide-cross-link-identification
#16
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J R Heck
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28524652/optical-characteristics-and-tumor-imaging-capabilities-of-near-infrared-dyes-in-free-and-nano-encapsulated-formulations-comprised-of-viral-capsids
#17
Yadir Guerrero, Sheela Singh, Turong Mai, Ravoori Murali, Leela Tanikella, Atta Zahedi, Vikas Kundra, Bahman Anvari
Near infrared (NIR) fluorescent molecules and nano-sized structures can serve as potential optical probes for image-guided removal of small tumor nodules (≈ < 1 mm diameter). While indocyanine green (ICG) remains as the only FDA-approved NIR dye, other organic dyes are under extensive development for enhanced imaging capabilities. One such dye is BrCy106-NHS where bromine is substituted for aromatic structures in cyanine dyes. Herein, we investigate the absorption and fluorescence characteristics of ICG and BrCy106-NHS, and quantitatively assess their tumor imaging capabilities in free (non-encapsulated) and a nano-encapsulated form that utilizes the capsid protein (CP) from genome-depleted plant-infecting brome mosaic virus as the encapsulating shell...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28522938/mucin-1-antibody-conjugated-mesoporous-silica-nanoparticles-for-selective-breast-cancer-detection-in-a-mucin-1-transgenic-murine-mouse-model
#18
Didier Dréau, Laura Jeffords Moore, Merlis P Alvarez-Berrios, Mubin Tarannum, Pinku Mukherjee, Juan L Vivero-Escoto
Mucin-1 (MUC1), a transmembrane glycoprotein is aberrantly expressed on ~90% of breast cancer and is an excellent target for nanoparticulate targeted imaging. In this study, the development of a dye-doped NIR emitting mesoporous silica nanoparticles platform conjugated to tumor-specific MUC1 antibody (ab-tMUC1-NIR-MSN) for in vivo optical detection of breast adenocarcinoma tissue is reported. The structural properties, the in vitro and in vivo performance of this nanoparticle-based probe were evaluated. In vitro studies showed that the MSN-based optical imaging nanoprobe is non-cytotoxic and targets efficiently mammary cancer cells overexpressing human tMUC1 protein...
December 2016: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/28522605/structure-function-analysis-of-human-sucrase-isomaltase-identifies-key-residues-required-for-catalytic-activity
#19
Birthe Gericke, Natalie Schecker, Mahdi Amiri, Hassan Y Naim
Sucrase-isomaltase (SI) is an intestinal membrane-associated α-glucosidase that breaks down di- and oligosaccharides to absorbable monosaccharides. SI has two homologous functional subunits (sucrase and isomaltase) that both belong to the glycoside hydrolase family 31 (GH31) and differ in substrate specificity. All GH31 enzymes share a consensus sequence harboring an aspartic acid residue as a catalytic nucleophile. Moreover, crystallographic structural analysis of isomaltase predicts that another aspartic acid residue functions as a proton donor in hydrolysis...
May 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28520443/effective-interactions-and-colloidal-stability-of-bovine-%C3%AE-globulin-in-solution
#20
Stefano Da Vela, Felix Roosen-Runge, Maximilian W A Skoda, Robert M J Jacobs, Tilo Seydel, Henrich Frielinghaus, Michael Sztucki, Ralf Schweins, Fajun Zhang, Frank Schreiber
Interactions and phase behavior of γ-globulins are of fundamental interest in biophysical and pharmaceutical research, as these are among the most abundant proteins in blood plasma. In this work, we report the characterization of the oligomeric state of bovine γ-globulin, the effective protein-protein interactions and the colloidal stability in aqueous solution as a function of protein concentration and ionic strength. Classical biochemical techniques, such as size exclusion chromatography (SEC) and gel electrophoresis together with small angle X-ray and neutron scattering (SAXS/SANS) were employed for this study...
May 18, 2017: Journal of Physical Chemistry. B
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