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https://www.readbyqxmd.com/read/29346724/structural-and-biophysical-characterization-of-human-extl3-domain-organisation-glycosylation-and-solution-structure
#1
Wael Awad, Sven Kjellstrom, Gabriel Svensson Birkedal, Katrin Mani, Derek Thomas Logan
Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular communication and signaling. The exostosin (EXT) proteins are glycosyltransferases in the Golgi apparatus that assemble HS chains on HSPGs. The EXTL3 enzyme mainly works as an initiator in HS biosynthesis. In this work, human lumenal N-glycosylated EXTL3 (EXTL3ΔN) was cloned, expressed in human embryonic kidney cells and purified...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29346611/combined-roles-of-atp-and-small-hairpin-rna-in-the-activation-of-rig-i-revealed-by-solution-based-analysis
#2
Neelam Shah, Simone A Beckham, Jacqueline A Wilce, Matthew C J Wilce
RIG-I (retinoic acid inducible gene-I) is a cytosolic innate immune protein that senses viral dsRNA with a 5'-triphosphate overhang. Upon interaction with dsRNA a de-repression of the RIG-I CARD domains takes place that ultimately leads to the production of type I interferons and pro-inflammatory cytokines. Here we investigate the RIG-I conformational rearrangement upon interaction with an activating 5'-triphosphate-10-base pair dsRNA hairpin loop (10bp) compared with a less active 5'-triphosphate-8-base pair dsRNA hairpin loop (8bp)...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346393/computational-study-of-hiv-gp120-as-a-target-for-polyanionic-entry-inhibitors-exploiting-the-v3-loop-region
#3
Louis R Hollingsworth, Anne M Brown, Richard D Gandour, David R Bevan
Multiple approaches are being utilized to develop therapeutics to treat HIV infection. One approach is designed to inhibit entry of HIV into host cells, with a target being the viral envelope glycoprotein, gp120. Polyanionic compounds have been shown to be effective in inhibiting HIV entry, with a mechanism involving electrostatic interactions with the V3 loop of gp120 being proposed. In this study, we applied computational methods to elucidate molecular interactions between the repeat unit of the precisely alternating polyanion, Poly(4,4'-stilbenedicarboxylate-alt-maleic acid) (DCSti-alt-MA) and the V3 loop of gp120 from strains of HIV against which these polyanions were previously tested (IIIb, BaL, 92UG037, JR-CSF) as well as two strains for which gp120 crystal structures are available (YU2, 2B4C)...
2018: PloS One
https://www.readbyqxmd.com/read/29346116/4d-computed-tomography-scans-for-conformal-thoracic-treatment-planning-is-a-single-scan-sufficient-to-capture-thoracic-tumor-motion
#4
Yolanda D Tseng, Landon Wootton, Matthew Nyflot, Smith Apisarnthanarax, Ramesh Rengan, Charles Bloch, George Sandison, Sara St James
Four dimensional computed tomography (4DCT) scans are routinely used in radiation therapy to determine the internal treatment volume for targets that are moving (e.g. lung tumors). The use of these studies has allowed clinicians to create target volumes based upon the motion of the tumor during the imaging study. The purpose of this work is to determine if a target volume based on a single 4DCT scan at simulation is sufficient to capture thoracic motion. Phantom studies were performed to determine expected differences between volumes contoured on 4DCT scans and those on the evaluation CT scans (slow scans)...
January 18, 2018: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29345991/collapse-transitions-of-proteins-and-the-interplay-among-backbone-sidechain-and-solvent-interactions
#5
Alex S Holehouse, Rohit V Pappu
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures...
January 18, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345988/measuring-entropy-in-molecular-recognition-by-proteins
#6
A Joshua Wand, Kim A Sharp
Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Here, we review the relationship between measures of fast side-chain motion and the underlying conformational entropy...
January 18, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345941/dual-signaling-dna-electrochemistry-an-approach-to-understand-dna-interfaces
#7
Saimon Moraes Silva, Roya Tavallaie, Vinicius R Gonçales, Robert H Utama, Mehran B Kashi, D Brynn Hibbert, Richard D Tilley, J Justin Gooding
Electrochemical DNA biosensors composed of a redox marker modified nucleic acid probe tethered to a solid electrode is a common experimental construct for detecting DNA and RNA targets, proteins, inorganic ions, and even small molecules. This class of biosensors generally relies on the binding-induced conformational changes in the distance of the redox marker relative to the electrode surface such that the charge transfer is altered. The conventional design is to attach the redox species to the distal end of a surface-bound nucleic acid strand...
January 18, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29345906/prediction-of-hot-spots-at-myeloid-cell-leukemia-1-inhibitors-interface-using-energy-estimation-and-alanine-scanning-mutagenesis
#8
Parthiban Marimuthu, Kalaimathy Singaravelu
Myeloid cell leukemia 1 (Mcl1) is an anti-apoptotic protein that plays central role in apoptosis regulation. Also, Mcl1 has the potency to resist apoptotic cues resulting in up-regulation and cancer cell protection. A molecular probe that has the potential to specifically target Mcl1, and thereby provoke its down-regulatory activity is very essential. The aim of the current study is to probe the internal conformational dynamics of protein motions and potential binding mechanism in response to a series of picomolar range Mcl1 inhibitors using explicit-solvent molecular dynamics (MD) simulations...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345905/chelate-assisted-ring-closing-metathesis-a-strategy-for-accelerated-macrocyclization-at-ambient-temperatures
#9
Carolyn S Higman, Daniel Luis do Nascimento, Benjamin J Ireland, Stephan Audörsch, Gwendolyn A Bailey, Robert McDonald, Deryn Elizabeth Fogg
Ring-closing metathesis (RCM) offers versatile catalytic routes to macrocycles, with applications ranging from perfumery to production of antiviral drugs. Unwanted oligomerization, however, is a long-standing challenge. Oligomers can be converted into the cyclic targets by catalysts that are sufficiently reactive to promote backbiting (e.g. Ru complexes of N-heterocyclic carbenes; NHCs), but catalyst decomposition limits yields and selectivity. Incorporation of a hemilabile o-dianiline (ODA) chelate into new catalysts of the form RuCl2(NHC)(ODA)(=CHPh) accelerates macrocyclization, particularly for dienes bearing polar sites capable of H-bonding: it may also inhibit catalyst decomposition during metathesis...
January 18, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29345807/targeting-a-dark-excited-state-of-hiv-1-nucleocapsid-by-anti-retroviral-thioesters-revealed-by-nmr
#10
Lalit Deshmukh, Vitali Tugarinov, Daniel H Appella, G Marius Clore
HIV-1 nucleocapsid (NCp7) is a two Cys2HisCys zinc knuckle (N-Zn and C-Zn) protein that plays a key role in viral replication. Here we characterize NCp7 conformational dynamics by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N-Zn knuckle is conformationally stable, the C-Zn knuckle interconverts on the millisecond time scale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1%) in which one of the coordination bonds (Cys413-S---Zn or His421-N2---Zn) is hydrolysed...
January 18, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29345709/chain-conformation-of-poly-acrylic-acid-graft-poly-ethylene-oxide-graft-dodecyl-in-solution-an-anomalous-counter-ions-condensation
#11
Xinlu Zhou, Kongshuang Zhao
A dielectric spectroscopy study on a polyelectrolyte in aqueous solutions, which contains hydrophobic groups in part of the side chains poly(acrylic acid)-graft-poly(ethylene oxide)-graft-dodecyl (PAA-g-PEO-g-dodecyl) is reported. A refined double layer polarization model was proposed to analyze the double dielectric relaxations in the dielectric spectra. Various electrical and structural parameters of the copolymers were obtained. Besides the crossover concentration, another turning point around 4 mg mL-1 was identified through the analysis of all the dielectrical parameters including dielectric increment, relaxation time and correlation length...
January 18, 2018: Soft Matter
https://www.readbyqxmd.com/read/29345618/necaps-are-negative-regulators-of-the-ap2-clathrin-adaptor-complex
#12
Gwendolyn M Beacham, Edward A Partlow, Jeffrey J Lange, Gunther Hollopeter
Eukaryotic cells internalize transmembrane receptors via clathrin-mediated endocytosis, but it remains unclear how the machinery underpinning this process is regulated. We recently discovered that membrane-associated muniscin proteins such as FCHo and SGIP initiate endocytosis by converting the AP2 clathrin adaptor complex to an open, active conformation that is then phosphorylated (Hollopeter et al., 2014). Here we report that loss of ncap-1, the sole C. elegans gene encoding an adaptiN Ear-binding Coat-Associated Protein (NECAP), bypasses the requirement for FCHO-1...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29345430/wearable-wireless-tyrosinase-bandage-and-microneedle-sensors-toward-melanoma-screening
#13
Bianca Ciui, Aida Martin, Rupesh K Mishra, Barbara Brunetti, Tatsuo Nakagawa, Thomas J Dawkins, Mengjia Lyu, Cecilia Cristea, Robert Sandulescu, Joseph Wang
Wearable bendable bandage-based sensor and a minimally invasive microneedle biosensor are described toward rapid screening of skin melanoma. These wearable electrochemical sensors are capable of detecting the presence of the tyrosinase (TYR) enzyme cancer biomarker in the presence of its catechol substrate, immobilized on the transducer surface. In the presence of the surface TYR biomarker, the immobilized catechol is rapidly converted to benzoquinone that is detected amperometrically, with a current signal proportional to the TYR level...
January 18, 2018: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29345424/a-fluorescence-based-sensor-assay-that-monitors-general-protein-aggregation-in-human-cells
#14
Marisa Pereira, Diogo Tomé, Ana S Domingues, Ana S Varanda, Cristiana Paulo, Manuel A S Santos, Ana R Soares
Protein conformational disorders are characterized by disruption of protein folding and toxic accumulation of protein aggregates. Here we describe a sensitive and simple method to follow and monitor general protein aggregation in human cells. Heat shock protein 27 (HSP27) is an oligomeric small heat shock protein that binds and keeps unfolded proteins in a folding competent state. This high specificity of HSP27 for aggregated proteins can be explored to monitor aggregation in living cells by fusing it to a fluorescent protein as Green Fluorescent Protein (GFP)...
January 18, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29345292/preparation-and-characterization-of-the-antibody-recognizing-amacr-inside-its-catalytic-center
#15
Boris V Popov, Gleb I Sutula, Nikolay S Petrov, Ximing J Yang
Alpha-methylacyl-CoA racemase (AMACR) catalyzes the β-oxidation of fatty acids and is overexpressed in carcinomas in various organs, while its inactivation results in the inhibition of cancer growth. In the present study, we prepared and characterized 20 different mouse monoclonal antibodies against human AMACR. In the course of biopanning of a phage peptide commercial library against in-house prepared 6H9 and 2A5, and commercial 13H4 antibodies, 10 phage mimotopes recognized by each type of the antibody were selected...
February 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29345225/indications-for-the-surgical-management-of-benign-goiter-in-adults
#16
Detlef K Bartsch, Markus Luster, Heinz J Buhr, Dietmar Lorenz, Christoph-Thomas Germer, Peter E Goretzki
BACKGROUND: Thyroidectomy is still three to six times more common in Germany than in the USA, Great Britain, and the Scandinavian countries. Thus, the question is often asked whether thyroidectomy in Germany is being performed for the correct indications. METHODS: This review is based on studies and guidelines containing information on the indications for surgery in benign goiter and Graves' disease; these publications were retrieved by a systematic literature search in the Medline and Cochrane Library databases (1990-2016)...
January 8, 2018: Deutsches Ärzteblatt International
https://www.readbyqxmd.com/read/29345110/remarkable-similarity-in-plasmodium-falciparum-and-plasmodium-vivax-geranylgeranyl-diphosphate-synthase-ggpps-dynamics-and-its-implication-for-anti-malarial-drug-design
#17
Aishwarya Venkatramani, Clarisse G Ricci, Eric Oldfield, J Andrew McCammon
Malaria, mainly caused by Plasmodium falciparum and Plasmodium vivax, has been a growing cause of morbidity and mortality. P. falciparum is more lethal than is P. vivax, but there is a vital need for effective drugs against both species. Geranylgeranyl diphosphate synthase (GGPPS) is an enzyme involved in the biosynthesis of quinones and in protein prenylation, and has been proposed to be a malaria drug target. However, the structure of P. falciparum GGPPS (PfGGPPS) has not been determined, due to difficulties in crystallization...
January 18, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29345075/genetic-analyses-of-linear-profiling-data-on-3-year-old-swedish-warmblood-horses
#18
Å Viklund, S Eriksson
A linear profiling protocol was introduced in 2013 at tests for 3-year-old Swedish Warmblood horses. In this protocol, traits are subjectively described on a nine-point linear scale from one biological extreme to the other. This complements the traditional scoring where horses are evaluated in relation to the breeding objective. This study aimed to investigate the suitability of the linear information for genetic evaluation. Data on 22 conformation traits, 17 movement traits, 14 jumping traits and one temperament trait from 3,410 horses tested between 2013 and 2016 were analysed using an animal model...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29345033/total-synthesis-and-conformational-study-of-the-anti-tubercular-cyclic-peptide-callyaerin-a-bearing-a-rare-rigidifying-z-2-3-diaminoacrylamide-moiety
#19
Margaret Anne Brimble, Shengping Zhang, Luis De Leon Rodriguez, Ivanhoe Leung, Greg Cook, Paul Harris
The first synthesis of the anti-TB cyclic peptide callyaerin A containing a rare (Z)-2,3-diaminoacrylamide bridging motif is reported. Fmoc-formylglycine-diethylacetal was used as a masked equivalent of formylglycine in the synthesis of the linear precursor of callyaerin A. Intramolecular cyclization between the formylglycine residue and the N-terminal amine in the linear peptide precursor afforded the macrocyclic natural product callyaerin A. Synthetic callyaerin A possessed potent anti-TB activity (MIC100 = 32 µM) while its all-amide congener was inactive...
January 18, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29344998/role-of-ap-endonuclease-ape1-active-site-residues-in-stabilization-of-the-reactant-enzyme-dna-complex
#20
Hossein Batebi, Jovan Dragelj, Petra Imhof
Apurinic/apyrimidinic endonuclease 1 (Ape1) is an important metal-dependent enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction. Molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing one or two Mg2+ -ions as cofactor located at different positions show a complex with one metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction-competent conformation...
January 18, 2018: Proteins
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