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https://www.readbyqxmd.com/read/29224103/sex-differences-and-role-of-estradiol-in-hypoglycemia-associated-counter-regulation
#1
Karen P Briski, Hussain N Alhamami, Ayed Alshamrani, Santosh K Mandal, Manita Shakya, Mostafa H H Ibrahim
Vital nerve cell functions, including maintenance of transmembrane voltage and information transfer, occur at high energy expense. Inadequate provision of the obligate metabolic fuel glucose exposes neurons to risk of dysfunction or injury. Clinical hypoglycemia rarely occurs in nondiabetic individuals but is an unfortunate regular occurrence in patients with type 1 or advanced insulin-treated type 2 diabetes mellitus. Requisite strict glycemic control, involving treatment with insulin, sulfonylureas, or glinides, can cause frequent episodes of iatrogenic hypoglycemia due to defective counter-regulation, including reduced glycemic thresholds and diminished magnitude of motor responses...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29224093/sex-effects-at-the-ramparts-nutrient-and-microbe-mediated-regulation-of-the-immune-metabolic-interface
#2
Nyrie Israelian, Jayne S Danska
The relationships between dietary compounds, derivative metabolites, and host metabolism and immunity are controlled by diverse molecular mechanisms. Essential contributions to these dynamics come from the community of microbes (the microbiome) inhabiting the human digestive tract. The composition and function of the microbiome are shaped by available nutrients, and reciprocally, these organisms produce an as yet poorly defined repertoire of molecules that communicate with the epithelial barrier and the mucosal immune system...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29223917/molecular-dynamics-simulations-suggest-changes-in-electrostatic-interactions-as-a-potential-mechanism-through-which-serine-phosphorylation-inhibits-dna-polymerase-%C3%AE-s-activity
#3
Dirar Homouz, Kwee Hong Joyce-Tan, Mohd Shahir Shamsir, Ibrahim M Moustafa, Haitham Idriss
DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics...
November 7, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29223802/proteogenomic-insights-into-uranium-tolerance-of-a-chernobyl-s-microbacterium-bacterial-isolate
#4
Gallois Nicolas, Alpha-Bazin Béatrice, Ortet Philippe, Barakat Mohamed, Piette Laurie, Long Justine, Berthomieu Catherine, Armengaud Jean, Chapon Virginie
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29223157/self-organization-of-recombinant-membrane-porin-ompf-from-yersinia-pseudotuberculosis-in-aqueous-environments
#5
E V Sidorin, V A Khomenko, N Yu Kim, P S Dmitrenok, A M Stenkova, O D Novikova, T F Solov'eva
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223097/recent-advances-in-microtubule-stabilizing-agents
#6
REVIEW
Ya-Nan Cao, Ling-Li Zheng, Dan Wang, Xiao-Xia Liang, Feng Gao, Xian-Li Zhou
Highly dynamic mitotic spindle microtubules are superb therapeutic targets for a group of chemically diverse and clinically successful anticancer drugs. Microtubule-targeted drugs disrupt microtubule dynamics in distinct ways, and they are primarily classified into two groups: microtubule destabilizing agents (MDAs), such as vinblastine, colchicine, and combretastatin-A4, and microtubule stabilizing agents (MSAs), such as paclitaxel and epothilones. Systematic discovery and development of new MSAs have been aided by extensive research on paclitaxel, yielding a large number of promising anticancer compounds...
November 24, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29223088/probing-molecular-interaction-mechanisms-of-organic-fouling-on-polyamide-membrane-using-a-surface-forces-apparatus-implication-for-wastewater-treatment
#7
Qingye Lu, Jun Huang, Omar Maan, Yang Liu, Hongbo Zeng
Surface fouling is the dominant fouling mechanism of thin-film composite (TFC) membranes used in reverse osmosis (RO) technology. Understanding the complex interactions between foulant-membrane which drive the attachment and growth of foulants on membrane surface is of both fundamental and practical importance. This work aims to understand the molecular interaction mechanisms of organic fouling on RO-TFC membranes. A surface forces apparatus (SFA) was employed to directly measure the interaction forces and time-dependent adsorption behaviors between model organic foulants: humic acid (HA), bovine serum albumin (BSA), and lipopolysaccharides (LPS) and a polyamide (PA) thin film...
December 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29222836/biochemical-and-structural-insights-into-a-thermostable-cellobiohydrolase-from-myceliophthora-thermophila
#8
Marco Antonio Seiki Kadowaki, Paula Higasi, Mariana Ortiz de Godoy, Rolf A Prade, Igor Polikarpov
Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by β-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent the access of hydrolytic enzymes and water molecules. The most abundant enzyme secreted by Myceliophthora thermophila M77 in response to the presence of biomass is the cellobiohydrolase MtCel7A, which is composed by a GH7-catalytic domain (CD), a linker and a CBM1-type carbohydrate binding module...
December 8, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29222784/methods-for-quantitative-analysis-of-axonal-cargo-transport
#9
Matias Alloatti, Luciana Bruno, Tomas L Falzone
Neurons rely on complex axonal transport mechanisms that mediate the intracellular dynamics of proteins, vesicles, and mitochondria along their high polarized structure. The fast improvement of live imaging techniques of fluorescent cargos allowed the identification of the diverse motion properties of different transported molecules. These properties arise as the result of molecular interactions between many players involved in axonal transport. Motor proteins, microtubule tracks, cargo association, and even axonal viscosity contribute to the proper axonal dynamics of different cargos...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#10
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222528/structure-and-dynamics-of-cas9-hnh-domain-catalytic-state
#11
Zhicheng Zuo, Jin Liu
The bacterial CRISPR-Cas9 immune system has been harnessed as a powerful and versatile genome-editing tool and holds immense promise for future therapeutic applications. Despite recent advances in understanding Cas9 structures and its functional mechanism, little is known about the catalytic state of the Cas9 HNH nuclease domain, and identifying how the divalent metal ions affect the HNH domain conformational transition remains elusive. A deeper understanding of Cas9 activation and its cleavage mechanism can enable further optimization of Cas9-based genome-editing specificity and efficiency...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222519/virtual-screening-for-inhibitors-of-the-human-tslp-tslpr-interaction
#12
Dries Van Rompaey, Kenneth Verstraete, Frank Peelman, Savvas N Savvides, Koen Augustyns, Pieter Van Der Veken, Hans De Winter
The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) plays a pivotal role in the pathophysiology of various allergy disorders that are mediated by type 2 helper T cell (Th2) responses, such as asthma and atopic dermatitis. TSLP forms a ternary complex with the TSLP receptor (TSLPR) and the interleukin-7-receptor subunit alpha (IL-7Rα), thereby activating a signaling cascade that culminates in the release of pro-inflammatory mediators. In this study, we conducted an in silico characterization of the TSLP:TSLPR complex to investigate the drugability of this complex...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222455/binding-modes-of-teixobactin-to-lipid-ii-molecular-dynamics-study
#13
Yang Liu, Yaxin Liu, Mary B Chan-Park, Yuguang Mu
Teixobactin (TXB) is a newly discovered antibiotic targeting the bacterial cell wall precursor Lipid II (LII). In the present work, four binding modes of TXB on LII were identified by a contact-map based clustering method. The highly flexible binary complex ensemble was generated by parallel tempering metadynamics simulation in a well-tempered ensemble (PTMetaD-WTE). In agreement with experimental findings, the pyrophosphate group and the attached first sugar subunit of LII are found to be the minimal motif for stable TXB binding...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222439/alloy-assisted-deposition-of-three-dimensional-arrays-of-atomic-gold-catalyst-for-crystal-growth-studies
#14
Yin Fang, Yuanwen Jiang, Mathew J Cherukara, Fengyuan Shi, Kelliann Koehler, George Freyermuth, Dieter Isheim, Badri Narayanan, Alan W Nicholls, David N Seidman, Subramanian K R S Sankaranarayanan, Bozhi Tian
Large-scale assembly of individual atoms over smooth surfaces is difficult to achieve. A configuration of an atom reservoir, in which individual atoms can be readily extracted, may successfully address this challenge. In this work, we demonstrate that a liquid gold-silicon alloy established in classical vapor-liquid-solid growth can deposit ordered and three-dimensional rings of isolated gold atoms over silicon nanowire sidewalls. We perform ab initio molecular dynamics simulation and unveil a surprising single atomic gold-catalyzed chemical etching of silicon...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222424/structural-insight-into-a-ce15-esterase-from-the-marine-bacterial-metagenome
#15
Concetta De Santi, Osman Absm Gani, Ronny Helland, Adele Williamson
The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising the catalytic triad differ from previously-characterized fungal homologs, and resolves three large loop regions that are unique to this bacterial sub-clade. The catalytic triad of the bacterial CE15, which includes Asp 332 as its third member, closely resembles that of family 1 carbohydrate esterases (CE1), despite the overall lower structural similarity with members of this family...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222417/insulin-in-motion-the-a6-a11-disulfide-bond-allosterically-modulates-structural-transitions-required-for-insulin-activity
#16
Bianca van Lierop, Shee Chee Ong, Alessia Belgi, Carlie Delaine, Sofianos Andrikopoulos, Naomi L Haworth, John G Menting, Michael C Lawrence, Andrea J Robinson, Briony E Forbes
The structural transitions required for insulin to activate its receptor and initiate regulation of glucose homeostasis are only partly understood. Here, using ring-closing metathesis, we substitute the A6-A11 disulfide bond of insulin with a rigid, non-reducible dicarba linkage, yielding two distinct stereo-isomers (cis and trans). Remarkably, only the cis isomer displays full insulin potency, rapidly lowering blood glucose in mice (even under insulin-resistant conditions). It also posseses reduced mitogenic activity in vitro...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222414/structural-dynamics-of-the-mscl-c-terminal-domain
#17
Navid Bavi, Adam D Martinac, D Marien Cortes, Omid Bavi, Pietro Ridone, Takeshi Nomura, Adam P Hill, Boris Martinac, Eduardo Perozo
The large conductance mechanosensitive channel (MscL), acts as an osmoprotective emergency valve in bacteria by opening a large, water-filled pore in response to changes in membrane tension. In its closed configuration, the last 36 residues at the C-terminus form a bundle of five α-helices co-linear with the five-fold axis of symmetry. Here, we examined the structural dynamics of the C-terminus of EcMscL using site-directed spin labelling electron paramagnetic resonance (SDSL EPR) spectroscopy. These experiments were complemented with computational modelling including molecular dynamics (MD) simulations and finite element (FE) modelling...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221989/differential-targeting-of-membrane-lipid-domains-by-caffeic-acid-and-its-ester-derivatives
#18
Hugo A L Filipe, Carla Sousa, Joaquim T Marquês, Diogo Vila-Viçosa, António de Granada Flor, Ana S Viana, M Soledade C S Santos, Miguel Machuqueiro, Rodrigo F M de Almeida
Phenolic acids have been associated to a wide range of important health benefits underlain by a common molecular mechanism of action. Considering that significant membrane permeation is prevented by their hydrophilic character, we hypothesize that their main effects result from the interplay with cell membrane surface. This hypothesis was tested using the paradigmatic caffeic acid (CA) and two of its ester derivatives, rosmarinic (RA) and chlorogenic (CGA) acids, for which we predict, based on molecular dynamics simulations, a shallow location in phospholipid bilayers dependent on the protonation-state...
December 5, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29221897/comparative-mechanical-unfolding-studies-of-spectrin-domains-r15-r16-and-r17
#19
Anna V Glyakina, Ilya V Likhachev, Nikolay K Balabaev, Oxana V Galzitskaya
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1Å·ps-1) and constant forces (700 and900pN) using molecular dynamics (MD) simulations at T = 300K...
December 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29221677/epigenetic-regulation-of-biological-rhythms-an-evolutionary-ancient-molecular-timer
#20
REVIEW
Tyler J Stevenson
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms...
December 5, 2017: Trends in Genetics: TIG
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