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https://www.readbyqxmd.com/read/29452363/structuremapper-a-high-throughput-algorithm-for-analyzing-protein-sequence-locations-in-structural-data
#1
Anssi Nurminen, Vesa P Hytönen, Alfonso Valencia
Motivation: StructureMapper is a high-throughput algorithm for automated mapping of protein primary amino sequence locations to existing three-dimensional protein structures. The algorithm is intended for facilitating easy and efficient utilization of structural information in protein characterization and proteomics. StructureMapper provides an analysis of the identified structural locations that includes surface accessibility, flexibility, protein-protein interfacing, intrinsic disorder prediction, secondary structure assignment, biological assembly information, and sequence identity percentages, among other metrics...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452226/quantitative-proteomic-analysis-reveals-synaptic-dysfunction-in-the-amygdala-of-rats-susceptible-to-chronic-mild-stress
#2
Mi Zhou, Zhao Liu, Jia Yu, Shuiming Li, Min Tang, Li Zeng, Haiyang Wang, Hong Xie, Li Peng, Haojun Huang, Chanjuan Zhou, Peng Xie, Jian Zhou
The amygdala plays a key role in the pathophysiology of depression, but the molecular mechanisms underlying amygdalar hyperactivity in depression remain unclear. In this study, we used a chronic mild stress (CMS) protocol to separate susceptible and insusceptible rat subgroups. Proteomes in the amygdalae were analyzed differentially across subgroups based on labeling with isobaric tags for relative and absolute quantitation (iTRAQ) combined with mass spectrometry. Of 2,562 quantified proteins, 102 were differentially expressed...
February 13, 2018: Neuroscience
https://www.readbyqxmd.com/read/29452211/impact-of-change-of-matrix-crystallinity-and-polymorphism-on-ovalbumin-release-from-lipid-based-implants
#3
Luisa Duque, Martin Körber, Roland Bodmeier
The objectives of this study were to prepare lipid-based implants by hot melt extrusion (HME) for the prolonged release of ovalbumin (OVA), and to relate protein release to crystallinity and polymorphic changes of the lipid matrix. Two lipids, glycerol tristearate and hydrogenated palm oil, with different composition and degree of crystallinity were studied. Solid OVA was dispersed within the lipid matrixes and it preserved its stability during extrusion. This was partially attributed to a protective effect of the lipidic matrix...
February 13, 2018: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29452186/lectin-obtained-from-the-red-seaweed-bryothamnion-triquetrum-secondary-structure-and-anti-inflammatory-activity-in-mice
#4
Thais Pontes Carvalho Fontenelle, Glauber Cruz Lima, Jacilane Ximenes Mesquita, José Luiz de Souza Lopes, Tarcísio Vieira de Brito, Francisco das Chagas Vieira Júnior, Adriano Bezerra Sales, Karoline Saboia Aragão, Marcellus Henrique Loiola Ponte Souza, André Luiz Dos Reis Barbosa, Ana Lúcia Ponte Freitas
Seaweeds are sources of biomolecules with biological activities and pharmacological potential - for example, lectins, a group of proteins that can bind reversibly to carbohydrates or compounds containing them. The aim of this study was to elucidate the structural properties of a lectin extracted from the red seaweed Bryothamnion triquetrum (BtL) and to investigate its anti-inflammatory activity in mice. The lectin was purified by precipitation with ammonium sulfate and ion-exchange chromatography. Its secondary structure and tryptophan (Trp) microenvironment were analyzed by circular dichroism spectroscopy and steady-state fluorescence spectroscopy, respectively...
February 13, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29452183/purification-structural-elucidation-and-anti-inflammatory-activity-of-xylosyl-galactofucan-from-armillariella-mellea
#5
Chia-Chuan Chang, Jing-Jy Cheng, I-Jung Lee, Mei-Kuang Lu
A xylosyl galactofucan (AMPS-III) was isolated and identified as a novel anti-inflammatory agent from an edible fungus, Armillariella mellea. The characteristics chemical structure of AMPS-III including the linkages of compositional monosaccharides and structure of the repeat unit were depicted and elucidated by proton, carbon and two-dimensional nuclear magnetic resonance techniques. AMPS-III was chemically proposed to have a partial 4‑O‑xylosylated 1,3-linked α‑d‑galactosyl-interlaced α‑l‑fucan composed of a pentadecasaccharide repeat unit with a molecular mass approximately 13 kDa, as shown below...
February 13, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29452157/hypertrophic-cardiomyopathy-mutation-r58q-in-the-myosin-regulatory-light-chain-perturbs-thick-filament-based-regulation-in-cardiac-muscle
#6
Thomas Kampourakis, Saraswathi Ponnam, Malcolm Irving
Hypertrophic cardiomyopathy (HCM) is frequently linked to mutations in the protein components of the myosin-containing thick filaments leading to contractile dysfunction and ultimately heart failure. However, the molecular structure-function relationships that underlie these pathological effects remain largely obscure. Here we chose an example mutation (R58Q) in the myosin regulatory light chain (RLC) that is associated with a severe HCM phenotype and combined the results from a wide range of in vitro and in situ structural and functional studies on isolated protein components, myofibrils and ventricular trabeculae to create an extensive map of structure-function relationships...
February 13, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29452143/unusual-self-assembly-of-the-recombinant-chlamydia-trachomatis-major-outer-membrane-protein-momp-based-fusion-antigen-cth522-into-protein-nanoparticles
#7
Fabrice Rose, Kasper Karlsen, Pernille Rønde Jensen, Rasmus Uffe Jakobsen, Grith Krøyer Wood, Kasper Dyrberg Rand, Helene Godiksen, Peter Andersen, Frank Follmann, Camilla Foged
Sexually transmitted Chlamydia trachomatis (Ct) infects more than 100 million people annually, and untreated chlamydia infections can cause severe complications. Therefore, there is an urgent need for a chlamydia vaccine. The Ct major outer membrane protein (MOMP) is highly immunogenic but is a challenging vaccine candidate by being an integral membrane protein, and the immunogenicity depends on a correctly folded structure. We investigated the biophysical properties of the recombinant MOMP-based fusion antigen CTH522, which is tested in early human clinical trials...
February 13, 2018: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29452110/exploring-the-impact-of-house-screening-intervention-on-entomological-indices-and-incidence-of-malaria-in-arba-minch-town-southwest-ethiopia-a-randomized-control-trial
#8
Solomon Kinde Getawen, Temesgen Ashine, Fekadu Massebo, Daniel Woldeyes, Bernt Lindtjørn
House is the major site for malaria infection where most human-vector contact takes place. Hence, improving housing might reduce the risk of malaria infection by limiting house entry of vectors. This study aimed to explore the impact of screening doors and windows with wire meshes on density and entomological inoculation rate (EIR) of malaria vector, and malaria incidence, and assess the acceptability, durability, and cost of the intervention. The susceptibility status of malaria vector was also assessed. A two-arm randomized trial was done in Arba Minch Town, southwest Ethiopia...
February 13, 2018: Acta Tropica
https://www.readbyqxmd.com/read/29452108/effect-of-brimonidine-an-%C3%AE-2-adrenergic-agonist-on-human-meibomian-gland-epithelial-cells
#9
Xi Han, Yang Liu, Wendy R Kam, David A Sullivan
We recently discovered that the anti-glaucoma pharmaceuticals timolol, a β adrenergic antagonist, and pilocarpine, a cholinergic compound, negatively influence the morphology, proliferative capacity and survival of human meibomian gland epithelial cells (HMGECs). We hypothesize that another class of anti-glaucoma drugs, the α2 adrenergic agonists, also acts directly on HMGECs to affect their structure and function. We tested this hypothesis. Immortalized (i) HMGECs were cultured with brimonidine, as well as clonidine (α2 agonist), phenylephrine (α1 agonist), RX821002 (inverse α2 agonist) and MK912 (neutral α2 agonist) for up to 7 days...
February 13, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29452030/comparative-phylogenetic-and-expression-analysis-of-small-gtpases-families-in-legume-and-non-legume-plants
#10
Ana Claudia Flores, Virginia Dalla Via, Virginia Savy, Ulises Mancini Villagra, María Eugenia Zanetti, Flavio Blanco
BACKGROUND: Small monomeric GTPases act as molecular switches in several processes that involve polar cell growth, participating mainly in vesicle trafficking and cytoskeleton rearrangements. This gene superfamily has largely expanded in plants through evolution as compared with other Kingdoms, leading to the suggestion that members of each subfamily might have acquired new functions associated to plant-specific processes. Legume plants engage in a nitrogen-fixing symbiotic interaction with rhizobia in a process that involves polar growth processes associated with the infection throughout the root hair...
February 16, 2018: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29451913/identification-of-the-s-transferase-like-superfamily-bacillithiol-transferases-encoded-by-bacillus-subtilis
#11
Varahenage R Perera, John D Lapek, Gerald L Newton, David J Gonzalez, Kit Pogliano
Bacillithiol is a low molecular weight thiol found in Firmicutes that is analogous to glutathione, which is absent in these bacteria. Bacillithiol transferases catalyze the transfer of bacillithiol to various substrates. The S-transferase-like (STL) superfamily contains over 30,000 putative members, including bacillithiol transferases. Proteins in this family are extremely divergent and are related by structural rather than sequence similarity, leaving it unclear if all share the same biochemical activity. Bacillus subtilis encodes eight predicted STL superfamily members, only one of which has been shown to be a bacillithiol transferase...
2018: PloS One
https://www.readbyqxmd.com/read/29451901/the-novel-antibiotic-rhodomyrtone-traps-membrane-proteins-in-vesicles-with-increased-fluidity
#12
Dennapa Saeloh, Varomyalin Tipmanee, Kin Ki Jim, Marien P Dekker, Wilbert Bitter, Supayang P Voravuthikunchai, Michaela Wenzel, Leendert W Hamoen
The acylphloroglucinol rhodomyrtone is a promising new antibiotic isolated from the rose myrtle Rhodomyrtus tomentosa, a plant used in Asian traditional medicine. While many studies have demonstrated its antibacterial potential in a variety of clinical applications, very little is known about the mechanism of action of rhodomyrtone. Preceding studies have been focused on intracellular targets, but no specific intracellular protein could be confirmed as main target. Using live cell, high-resolution, and electron microscopy we demonstrate that rhodomyrtone causes large membrane invaginations with a dramatic increase in fluidity, which attract a broad range of membrane proteins...
February 16, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29451898/integrating-linear-optimization-with-structural-modeling-to-increase-hiv-neutralization-breadth
#13
Alexander M Sevy, Swetasudha Panda, James E Crowe, Jens Meiler, Yevgeniy Vorobeychik
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods...
February 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29451808/implications-of-recent-research-on-microstructure-modifications-through-heat-related-processing-and-trait-alteration-to-bio-functions-molecular-thermal-stability-and-mobility-metabolic-characteristics-and-nutrition-in-cool-climate-cereal-grains-and-other-types
#14
Yuguang Ying, Huihua Zhang, Peiqiang Yu
The cutting-edge synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy have recently been developed. These novel techniques are able to reveal structure features at cellular and molecular levels with the tested tissues being intact. However, to date, the advanced techniques are unfamiliar or unknown to food and feed scientists and have not been used to study the molecular structure changes in cool-climate cereal grain seeds and other types of bio-oil and bioenergy seeds. This article aims to provide some recent research in cool-climate cereal grains and other types of seeds on molecular structures and metabolic characteristics of carbohydrate and protein, and implication of microstructure modification through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, and nutrition with advanced molecular techniques- synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy in the areas of (1) Inherent microstructure of cereal grain seeds; (2) The nutritional values of cereal grains; (3) Impact and modification of heat-related processing to cereal grain; (4) Conventional nutrition evaluation methodology; (5) Synchrotron radiation-based and globar-sourced vibrational (micro)-spectroscopy for molecular structure study and molecular thermal stability and mobility, and (6) Recent molecular spectroscopic technique applications in research on raw, traits altered and processed cool-climate cereal grains and other types of seeds...
February 16, 2018: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/29451771/structural-transformation-of-wireframe-dna-origami-via-dna-polymerase-assisted-gap-filling
#15
Nayan P Agarwal, Michael Matthies, Bastian Joffroy, Thorsten L Schmidt
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions...
February 16, 2018: ACS Nano
https://www.readbyqxmd.com/read/29451714/development-of-regenerative-and-flexible-fibroin-based-wound-dressings
#16
Angelica Panico, Federica Paladini, Mauro Pollini
Skin injuries represent a health problem with consequences in terms of morbidity, disability and life quality. Numerous strategies have been developed for the treatment of wounds, including skin substitutes, biomembranes, scaffolds, and smart dressings. The excellent properties of fibroin can be exploited for the development of advanced wound dressing biomaterials, aiming at promoting the wound healing process. In this work, silk fibroin films modified through the addition of glucose were developed to enhance flexibility of medical device without affecting the biocompatibility, to promote wound healing and to improve the patient well-being...
February 16, 2018: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
https://www.readbyqxmd.com/read/29451641/splenic-implant-preservation-after-conservation-in-lactated-ringer%C3%A2-s-solution
#17
Argos Soares DE Matos Filho, Andy Petroianu, Valbert Nascimento Cardoso, Paula Vieira Teixeira Vidigal
OBJECTIVE: to evaluate the morphology and function of autogenous splenic tissue implanted in the greater omentum, 24 hours after storage in Ringer-lactate solution. METHODS: we divided 35 male rats into seven groups (n=5): Group 1: no splenectomy; Group 2: total splenectomy without implant; Group 3: total splenectomy and immediate autogenous implant; Group 4: total splenectomy, preservation of the spleen in Ringer-lactate at room temperature, then sliced ​​and implanted; Group 5: total splenectomy, ​​spleen sliced and preserved in Ringer-lactate at room temperature before implantation; Group 6: total splenectomy with preservation of the spleen in Ringer-lactate at 4°C and then sliced ​​and implanted; Group 7: total splenectomy and the spleen sliced for preservation in Ringer-lactate at 4°C before implantation...
2018: Revista do Colégio Brasileiro de Cirurgiões
https://www.readbyqxmd.com/read/29451388/a-dual-inhibitor-of-staphylococcus-aureus-virulence-and-biofilm-attenuates-expression-of-major-toxins-and-adhesins
#18
Barbara Hofbauer, Jan Vomacka, Matthias Stahl, Vadim S Korotkov, Megan C Jennings, William Wuest, Stephan A Sieber
Staphylococcus aureus is a major bacterial pathogen that invades and damages host tissue by the expression of devastating toxins. We here performed a phenotypic screen of 35 molecules that were structurally inspired by previous hydroxyamide-based S. aureus virulence inhibitors compiled from commercial sources or designed and synthesized de novo. One of the most potent compounds, AV73, did not only reduce hemolytic alpha-hemolysin production in S. aureus but also impeded in vitro biofilm formation. The effect of AV73 on bacterial proteomes and extracellular protein levels were analyzed by quantitative proteomics and revealed a significant down-regulation of major virulence and biofilm promoting proteins...
February 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29451337/eosinophil-derived-exosomes-contribute-to-asthma-remodelling-by-activating-structural-lung-cells
#19
José A Cañas, Beatriz Sastre, José M Rodrigo-Muñoz, Mar Fernández-Nieto, Pilar Barranco, Santiago Quirce, Joaquín Sastre, Victoria Del Pozo
BACKGROUND: Eosinophils, a central factor in asthma pathogenesis, have the ability to secrete exosomes. However, the precise role played by exosomes in the biological processes leading up to asthma has not been fully defined. OBJECTIVE: We hypothesised that exosomes released by eosinophils contribute to asthma pathogenesis by activating structural lung cells. METHODS: Eosinophils from asthmatic patients and healthy volunteers were purified from peripheral blood, and exosomes were isolated from eosinophils of asthmatic and healthy individuals...
February 16, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29450991/mass-spectrometry-based-fast-photochemical-oxidation-of-proteins-fpop-for-higher-order-structure-characterization
#20
Ke Sherry Li, Liuqing Shi, Michael L Gross
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure...
February 16, 2018: Accounts of Chemical Research
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