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https://www.readbyqxmd.com/read/28430446/piecing-together-the-allosteric-patterns-of-chaperonin-groel
#1
Jin Chen, Qian Zhang, Weitong Ren, Wenfei Li
Despite considerable effort, elucidating allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy and molecular simulations to characterize allosteric patterns of chaperonin GroEL, a ~800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429670/expression-of-dominant-negative-k6w-ubiquitin-in-the-lens-epithelium-via-an-adenoviral-vector-delays-posterior-capsule-opacification-in-a-rabbit-model
#2
Xuan Bao, Min Hou, Ruiping Peng, Furong Luo, Mingxing Wu
PURPOSE: Ubiquitin is involved in cell proliferation and differentiation, and the objective of this study is to investigate the potential of dominant negative Ubiquitin (Ub) with a lysine to tryptophan mutation at the 6 position (K6W) through an adenoviral expression vector in the prevention of posterior capsule opacification (PCO) in a rabbit PCO model. METHODS: Recombinant dominant negative K6W-Ub adenovirus (RAd-K6W-Ub) with green fluorescent protein (RAd-K6W-Ub/GFP) and RAd-GFP viruses (control) were generated with QBI-HEK 293A cells...
March 31, 2017: Current Molecular Medicine
https://www.readbyqxmd.com/read/28428084/metabolomics-of-fescue-toxicosis-in-grazing-beef-steers
#3
Ryan S Mote, Nicholas S Hill, Karan Uppal, ViLinh T Tran, Dean P Jones, Nikolay M Filipov
Fescue toxicosis (FT) results from consumption of tall fescue (Lolium arundinaceum) infected with an endophyte (Epichloë coenophiala) that produces ergot alkaloids (EA), which are considered key etiological agents of FT. Decreased weight gains, hormonal imbalance, circulating cholesterol disruption, and decreased volatile fatty acid absorption suggest toxic (E+) fescue-induced metabolic perturbations. Employing untargeted high-resolution metabolomics (HRM) to analyze E+ grazing-induced plasma and urine metabolome changes, fescue-naïve Angus steers were placed on E+ or non-toxic (Max-Q) fescue pastures and plasma and urine were sampled before, 1, 2, 14, and 28 days after pasture assignment...
April 18, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28426218/the-excited-state-triple-proton-transfer-reaction-of-2-6-diazaindoles-and-2-6-diazatryptophan-in-aqueous-solution
#4
Kun-You Chung, Yi-Han Chen, Yi-Ting Chen, Yen-Hao Hsu, Jiun-Yi Shen, Chi-Lin Chen, Yi-An Chen, Pi-Tai Chou
3-Me-2,6-diazaindole ((2,6-aza)Ind) was strategically designed and synthesized to probe water molecule catalyzed excited-state proton transfer in aqueous solution. Upon electronic excitation (λmax ~ 300 nm), (2,6-aza)Ind undergoes N(1)-H to N(6) long-distance proton transfer in neutral H2O, resulting in normal (340 nm) and proton-transfer tautomer (480 nm) emissions with an overall quantum yield of 0.25. The rate of the water-catalyzed proton transfer shows a prominent H/D kinetic isotope effect, which is determined to be 8...
April 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28425599/the-starch-binding-domain-family-cbm41-an-in-silico-analysis-of-evolutionary-relationships
#5
Štefan Janeček, Katarína Majzlová, Birte Svensson, E Ann MacGregor
Within the CAZy database, there are 81 carbohydrate-binding module (CBM) families. A CBM represents a non-catalytic domain in a modular arrangement of glycoside hydrolases (GHs). The present in silico study has been focused on starch-binding domains from the family CBM41 that are usually part of pullulanases from the α-amylase family GH13. Currently there are more than 1,600 sequences classified in the family CBM41, almost exclusively from Bacteria, and so a study was undertaken in an effort to divide the members into relevant groups (subfamilies) and also to contribute to the evolutionary picture of family CBM41...
April 20, 2017: Proteins
https://www.readbyqxmd.com/read/28425050/oxidative-protein-modification-alters-proteostasis-under-acute-hypobaric-hypoxia-in-skeletal-muscles-a-comprehensive-in-vivo-study
#6
Akanksha Agrawal, Richa Rathor, Geetha Suryakumar
While numerous maladies are associated with hypobaric hypoxia, muscle protein loss is an important under studied topic. Hence, the present study was designed to investigate the mechanism of muscle protein loss at HH. SD rats were divided into normoxic rats, while remaining rats were exposed to simulated hypoxia equivalent to 282-torr pressure (equal to an altitude of 7620 m, 8% oxygen), at 25 °C for 6, 12, and 24 h. Post-exposure rats were sacrificed and analysis was performed. Ergo, muscle loss-related changes were observed at 12 and 24 h post-HH exposure...
April 19, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28424423/the-antidepressant-like-effect-of-trans-astaxanthin-involves-the-serotonergic-system
#7
Xi Jiang, Keqi Zhu, Quanyi Xu, Guokang Wang, Jiajia Zhang, Rongrong Cao, Jiang Ye, Xuefeng Yu
The antidepressant-like effect of trans-astaxanthin, a compound present rich in algae, was evaluated through behavioral and neurochemical methods. Results showed that trans-astaxanthin treatment significantly decreased the immobility time in force swim test and tail suspension test, but did not influence locomotor activity. Trans-astaxanthin treatment did not effectively antagonize hypothermia and ptosis induced by reserpine. However, pre-treatment with para-chlorophenylalanine abolished the anti-immobility effect of trans-astaxanthin in force swim and tail suspension test...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424186/circulating-concentrations-of-biomarkers-and-metabolites-related-to-vitamin-status-one-carbon-and-the-kynurenine-pathways-in-us-nordic-asian-and-australian-populations
#8
Øivind Midttun, Despoina Theofylaktopoulou, Adrian McCann, Anouar Fanidi, David C Muller, Klaus Meyer, Arve Ulvik, Wei Zheng, Xiao-Ou Shu, Yong-Bing Xiang, Ross Prentice, Cynthia A Thomson, Mary Pettinger, Graham G Giles, Allison Hodge, Qiuyin Cai, William J Blot, Jie Wu, Mikael Johansson, Johan Hultdin, Kjell Grankvist, Victoria L Stevens, Marjorie L McCullough, Stephanie J Weinstein, Demetrius Albanes, Arnulf Langhammer, Kristian Hveem, Marit Næss, Howard D Sesso, J Michael Gaziano, Julie E Buring, I-Min Lee, Gianluca Severi, Xuehong Zhang, Jiali Han, Meir J Stampfer, Stephanie A Smith-Warner, Anne Zeleniuch-Jacquotte, Loic le Marchand, Jian-Min Yuan, Lesley M Butler, Woon-Puay Koh, Renwei Wang, Yu-Tang Gao, Ulrika Ericson, Emily Sonestedt, Regina G Ziegler, Neal D Freedman, Kala Visvanathan, Miranda R Jones, Caroline Relton, Paul Brennan, Mattias Johansson, Per M Ueland
Background: Circulating concentrations of biomarkers that are related to vitamin status vary by factors such as diet, fortification, and supplement use. Published biomarker concentrations have also been influenced by the variation across laboratories, which complicates a comparison of results from different studies.Objective: We robustly and comprehensively assessed differences in biomarkers that are related to vitamin status across geographic regions.Design: The trial was a cross-sectional study in which we investigated 38 biomarkers that are related to vitamin status and one-carbon and tryptophan metabolism in serum and plasma from 5314 healthy control subjects representing 20 cohorts recruited from the United States, Nordic countries, Asia, and Australia, participating in the Lung Cancer Cohort Consortium...
April 19, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28422069/protein-stability-and-unfolding-following-glycine-radical-formation
#9
Michael C Owen, Imre G Csizmadia, Béla Viskolcz, Birgit Strodel
Glycine (Gly) residues are particularly susceptible to hydrogen abstraction; which results in the formation of the capto-dative stabilized Cα-centered Gly radical (GLR) on the protein backbone. We examined the effect of GLR formation on the structure of the Trp cage; tryptophan zipper; and the villin headpiece; three fast-folding and stable miniproteins; using all-atom (OPLS-AA) molecular dynamics simulations. Radicalization changes the conformation of the GLR residue and affects both neighboring residues but did not affect the stability of the Trp zipper...
April 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28421413/substrate-induced-conformational-changes-of-the-tyrocidine-synthetase-1-adenylation-domain-probed-by-intrinsic-trp-fluorescence
#10
Matilda Šprung, Barbara Soldo, Stjepan Orhanović, Viljemka Bučević-Popović
Nonribosomal peptide synthetases (NRPS) are multifunctional proteins that catalyze the synthesis of the peptide products with enormous biological potential. The process of biosynthesis starts with the adenylation (A) domain, which during the catalytic cycle undergoes extensive structural rearrangements. In this paper, we present the first study of the tyrocidine synthetase 1 A-domain (TycA-A) fluorescence properties. The TycA-A protein contains five potentially fluorescent Trp residues at positions 227, 301, 323, 376 and 406...
April 18, 2017: Protein Journal
https://www.readbyqxmd.com/read/28421297/suppression-of-th1-differentiation-by-tryptophan-supplementation-in-vivo
#11
Tobias V Lanz, Simon Becker, Soumya R Mohapatra, Christiane A Opitz, Wolfgang Wick, Michael Platten
Metabolism of the essential amino acid tryptophan (trp) is a key endogenous immunosuppressive pathway restricting inflammatory responses. Tryptophan metabolites promote regulatory T cell (Treg) differentiation and suppress proinflammatory T helper cell (Th)1 and Th17 phenotypes. It has been shown that treatment with natural and synthetic tryptophan metabolites can suppress autoimmune neuroinflammation in preclinical animal models. Here, we tested if oral intake of tryptophan would increase immunosuppressive tryptophan metabolites and ameliorate autoimmune neuroinflammation as a safe approach to treat autoimmune disorders like multiple sclerosis (MS)...
April 18, 2017: Amino Acids
https://www.readbyqxmd.com/read/28419153/biochemical-and-structural-investigations-on-phosphoribosylpyrophosphate-synthetase-from-mycobacterium-smegmatis
#12
Stefano Donini, Silvia Garavaglia, Davide M Ferraris, Riccardo Miggiano, Shigetarou Mori, Keigo Shibayama, Menico Rizzi
Mycobacterium smegmatis represents one model for studying the biology of its pathogenic relative Mycobacterium tuberculosis. The structural characterization of a M. tuberculosis ortholog protein can serve as a valid tool for the development of molecules active against the M. tuberculosis target. In this context, we report the biochemical and structural characterization of M. smegmatis phosphoribosylpyrophosphate synthetase (PrsA), the ortholog of M. tuberculosis PrsA, the unique enzyme responsible for the synthesis of phosphoribosylpyrophosphate (PRPP)...
2017: PloS One
https://www.readbyqxmd.com/read/28419111/time-resolved-and-label-free-monitoring-of-extracellular-metabolites-by-surface-enhanced-raman-spectroscopy
#13
Victoria Shalabaeva, Laura Lovato, Rosanna La Rocca, Gabriele C Messina, Michele Dipalo, Ermanno Miele, Michela Perrone, Francesco Gentile, Francesco De Angelis
Metabolomics is an emerging field of cell biology that aims at the comprehensive identification of metabolite levels in biological fluids or cells in a specific functional state. Currently, the major tools for determining metabolite concentrations are mass spectrometry coupled with chromatographic techniques and nuclear magnetic resonance, which are expensive, time consuming and destructive for the samples. Here, we report a time resolved approach to monitor metabolite dynamics in cell cultures, based on Surface Enhanced Raman Scattering (SERS)...
2017: PloS One
https://www.readbyqxmd.com/read/28418760/aromatic-dipeptide-trp-ala-can-be-transported-by-arabidopsis-peptide-transporters-atptr1-and-atptr5
#14
Diyang Qiu, Rui Hu, Ying Li, Mingyong Zhang
Dipeptides with an aromatic residue at the N-terminal position induced lower inward currents or blocked leak currents in Xenopus oocytes expressing the proton-coupled peptide transporter AtPTR1 or AtPTR5 of Arabidopsis thaliana compared with dipeptides with an aromatic residue at the C-terminal position. Here, AtPTR1 and AtPTR5 were expressed in a yeast mutant of peptide transporter (ptr2) with tryptophan auxotrophy. Growth assays showed that Trp-Ala could be transported by both AtPTR1 and AtPTR5 as efficiently as Ala-Trp...
April 18, 2017: Channels
https://www.readbyqxmd.com/read/28418661/systematic-dissociation-pathway-searches-guided-by-principal-component-modes
#15
Zhiye Tang, Chia-En A Chang
We introduce a novel method, Pathway Search guided by Internal Motions (PSIM), that efficiently finds molecular dissociation pathways of a ligand-receptor system with guidance from principal component (PC) modes obtained from molecular dynamics (MD) simulations. Modeling ligand-receptor dissociation pathways can provide insights into molecular recognition and has practical applications, including understanding kinetic mechanisms and barriers to binding/unbinding as well as design of drugs with desired kinetic properties...
April 18, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28417340/preconditioning-of-primary-human-renal-proximal-tubular-epithelial-cells-without-tryptophan-increases-survival-under-hypoxia-by-inducing-autophagy
#16
Theodoros Eleftheriadis, Georgios Pissas, Maria Sounidaki, Nikolaos Antoniadis, Georgia Antoniadi, Vassilios Liakopoulos, Ioannis Stefanidis
PURPOSE: Hypoxia plays a significant role in the pathogenesis of acute kidney injury (AKI). Autophagy protects from AKI. Amino acid deprivation induces autophagy. The effect of L-tryptophan depletion on survival and autophagy in cultures of renal proximal tubular epithelial cells (RPTECs) under hypoxia was evaluated. METHODS: RPTECs were preconditioned in a medium containing or not tryptophan, following culture under hypoxia and treatment with or without the autophagy inhibitor chloroquine...
April 17, 2017: International Urology and Nephrology
https://www.readbyqxmd.com/read/28416218/dummy-molecularly-imprinted-microbeads-as-solid-phase-extraction-material-for-selective-determination-of-phthalate-esters-in-water
#17
Elif Tümay Özer, Bilgen Osman, Tuğçe Yazıcı
The aim of this study was to investigate the usability of newly synthesized dummy molecularly imprinted microbeads (DMIMs) as a solid phase extraction (SPE) material to determine six phthalate esters (PEs) in water by GC-MS analysis. Diethyl phthalate (DEP) was used as a dummy template to prepare poly(ethylene glycol dimethacrylate N-methacryloyl-l-tryptophan methyl ester) [PEMATrp)] DMIMs by using suspension polymerization. The PEMATrp DMIMs were characterized by using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM)...
April 9, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28415022/simultaneous-determination-of-tryptophan-and-8-metabolites-in-human-plasma-by-liquid-chromatography-tandem-mass-spectrometry
#18
Lysiane Boulet, Patrice Faure, Patrice Flore, Julien Montérémal, Véronique Ducros
Tryptophan (Trp) is an essential amino-acid and the precursor of many biologically active substances such as kynurenine (KYN) and serotonin (5HT). Its metabolism is involved in different physiopathological states, such as cardiovascular diseases, cancer, immunomodulation or depression. Hence, the quantification of Trp catabolites, from both KYN and 5HT pathways, might be usefulfor the discovery of novel diagnostic and follow-up biomarkers. We have developed a simple method for quantification of Trp and 8 of its metabolites,involved in both KYN and 5HT pathways, using liquid chromatography coupled to tandem mass spectrometry...
April 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28414980/fluorescence-and-circular-dichroism-studies-on-the-accessibility-of-tryptophan-residues-and-unfolding-of-a-jacalin-related-%C3%AE-d-galactose-specific-lectin-from-mulberry-morus-indica
#19
Debparna Datta, Musti J Swamy
MLGL (Mulberry Latex Galactose-specific Lectin) is an α-d-galactose binding lectin isolated from the latex of mulberry (Morus indica) tree and contains two tryptophan residues in each of its subunits. The fluorescence emission maximum of native MLGL seen at 326nm shifts to 350nm upon incubation with 6M guanidinium thiocyanate (Gdn.SCN), suggesting that the tryptophans are located inside the hydrophobic core of the protein and become fully exposed upon denaturation. Fluorescence quenching studies revealed that the neutral acrylamide exhibits the highest quenching, with ~33% of total fluorescence in the native protein being quenched at a quencher concentration of 0...
April 1, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28414589/progesterone-decreases-in-vitro-indoleamine-2-3-dioxygenase-expression-in-dendritic-and-cd4-cells-from-maternal-fetal-interface-of-rats
#20
Pedro Kastein Faria da Cunha Bianchi, Rafael Magdanelo Leandro, Aline Nayara Poscai, Tulio Yoshinaga, Patrícia Orlandini Gonçalez, José Roberto Kfoury Junior
PROBLEM: Several mechanisms contribute to the tolerogenic state observed during pregnancy, such as the activity of the enzyme indoleamine 2, 3-dioxygenase (IDO). This initializes the catabolism of tryptophan, inducing T cells to apoptosis due to its deprivation and by the action of its catabolites in the placental microenvironment. Progesterone plays an important part on immunological tolerance mechanisms during pregnancy; however, there is no evidence it is related to IDO activity. Thus, this study aimed to investigate progesterone influence on the maternal-fetal interface of pregnant Wistar rats, by identifying IDO positive cells by immunophenotyping and flow cytometry under exogenous progesterone supplementation...
April 17, 2017: Immunological Investigations
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