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https://www.readbyqxmd.com/read/29925592/functionally-specific-binding-regions-of-microtubule-associated-protein-2c-exhibit-distinct-conformations-and-dynamics
#1
Kateřina Melková, Vojtěch Zapletal, Séverine Jansen, Erik Nomilner, Milan Zachrdla, Jozef Hritz, Jiří Nováček, Markus Zweckstetter, Malene R Jensen, Martin Blackledge, Lukas Zidek
Microtubule-associated protein 2c (MAP2c)1 is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c...
June 20, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29922770/how-low-resolution-structural-data-predict-the-conformational-changes-of-a-protein-a-study-on-data-driven-molecular-dynamics-simulations
#2
Ryuhei Harada, Yasuteru Shigeta
Parallel cascade selection molecular dynamics (PaCS-MD) is a conformational sampling method for generating transition pathways between a given reactant and a product. PaCS-MD repeats the following two steps: (1) selections of initial structures relevant to transitions and (2) their conformational resampling. When selecting the initial structures, several measures are utilized to identify their potential to undergo transitions. In the present study, low-resolution structural data obtained from small angle scattering (SAXS) and cryo-electron microscopy (EM) are adopted as the measures in PaCS-MD to promote the conformational transitions of proteins, which is defined as SAXS-/EM-driven targeted PaCS-MD...
June 20, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29920363/wounding-induced-upregulation-of-the-bone-morphogenic-protein-signaling-pathway-in-drosophila-promotes-survival-against-parasitic-nematode-infection
#3
Jelena Patrnogic, Christa Heryanto, Ioannis Eleftherianos
The common fruit fly, Drosophila melanogaster is an outstanding model to analyze the regulation of conserved signaling pathways. In this study, we examined whether signaling components in the Bone Morphogenic Protein (BMP) branch of the TGF-β signaling pathway are involved in the response to wounding caused by either sterile injury or infection by parasitic nematodes in D. melanogaster adult flies. We found that following sterile injury, the BMP pathway Type I receptor sax and intracellular transcription factor Mad were substantially upregulated...
June 16, 2018: Gene
https://www.readbyqxmd.com/read/29911233/lysine-based-amino-functionalized-lipids-for-gene-transfection-3d-phase-behaviour-and-transfection-performance
#4
Stephanie Tassler, Dorota Pawlowska, Christopher Janich, Julia Giselbrecht, Simon Drescher, Andreas Langner, Christian Wölk, Gerald Brezesinski
Based on previous work, the influence of the chain composition on the physical-chemical properties of five new transfection lipids (TH10, TT10, OH10, OT10 and OO10) containing the same lysine-based head group has been investigated in aqueous dispersions. For this purpose, the chain composition has been gradually varied from saturated tetradecyl (T, C14:0) and hexadecyl (H, C16:0) chains to longer but unsaturated oleyl (O, C18:1) chains with double bonds in the cis configuration. In this work, the lipid dispersions have been investigated in the absence and presence of the helper lipid DOPE and calf thymus DNA by small-angle and wide-angle X-ray scattering (SAXS/WAXS) supplemented by differential scanning calorimetry (DSC), attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and Fourier-transform Raman spectroscopy (FTRS)...
June 18, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29909654/placing-plants-on-paper-lists-herbaria-and-tables-as-experiments-with-territorial-inventory-at-the-mid-seventeenth-century-gotha-court
#5
Alix Cooper
Over the past several decades, historians of science have come increasingly to focus on the role of so-called "paper technologies," reorganizing and transforming information through the use of paper and pen, in the emergence of modern science. Taking as a case study an effort by administrators in the seventeenth-century German princely state of Saxe-Gotha to enlist foresters and herb-women to catalog the medicinal plants of the territory, this article analyzes the varied forms of paperwork produced in the process, including an extremely unusual table, and argues that the table represented an effort to produce a synoptic visualization, akin to but not identical to a map, of the location of the territory's herbs...
June 1, 2018: History of Science; An Annual Review of Literature, Research and Teaching
https://www.readbyqxmd.com/read/29908915/recombinant-production-of-a1s_0222-from-acinetobacter-baumannii-atcc-17978-and-confirmation-of-its-dna-adenine-n6-methyltransferase-activity
#6
Ulrike Blaschke, Beneditta Suwono, Sachli Zafari, Ingo Ebersberger, Evelyn Skiebe, Cy M Jeffries, Dmitri I Svergun, Gottfried Wilharm
Acinetobacter baumannii appears as an often multidrug-resistant nosocomial pathogen in hospitals worldwide. Its remarkable persistence in the hospital environment is probably due to intrinsic and acquired resistance to disinfectants and antibiotics, tolerance to desiccation stress, capability to form biofilms, and is possibly facilitated by surface-associated motility. Our attempts to elucidate surface-associated motility in A. baumannii revealed a mutant inactivated in a putative DNA-(adenine N6)-methyltransferase, designated A1S_0222 in strain ATCC 17978...
June 14, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/29908816/structural-basis-of-pyrrole-polymerization-in-human-porphobilinogen-deaminase
#7
Paula Pluta, Pietro Roversi, Ganeko Bernardo-Seisdedos, Adriana L Rojas, Jonathan B Cooper, Shuang Gu, Richard W Pickersgill, Oscar Millet
Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor...
June 14, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29906562/amino-acid-conjugated-chitosan-nanoparticles-for-the-brain-targeting-of-a-model-dipeptidyl-peptidase-4-inhibitor
#8
Jessica Fernandes, M Vivek Ghate, Sanchari Basu Mallik, Shaila A Lewis
Saxagliptin (SAX) is dipeptidyl peptidase-4 enzyme inhibitor molecule now explored for its activity in the therapy of Alzheimer's disease. Being extremely hydrophilic, it is unable to permeate the blood-brain barrier by the conventional therapy modalities. Further repurposing the drug, SAX is associated with a reduction in the blood sugar level in the periphery. In the present study, the chitosan-L-valine conjugate was synthesized by carbodiimide chemistry. The conjugate was then used to prepare nanoparticles encapsulating SAX...
June 12, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29905462/the-human-biomolecular-corona-of-liposomal-doxorubicin-the-overlooked-factor-in-anticancer-drug-delivery
#9
Giulio Caracciolo, Sara Palchetti, Luca Digiacomo, Riccardo Zenezini Chiozzi, Anna Laura Capriotti, Heinz Amenitsch, Paolo Maria Tentori, Valentina Palmieri, Massimiliano Papi, Francesco Cardarelli, Daniela Pozzi, Aldo Laganà
More than twenty years after its approval by the Food and Drug Administration (FDA) liposomal doxorubicin (DOX) is still the drug of choice for the treatment of breast cancer and other conditions such as ovarian cancer and multiple myeloma. Yet, despite the efforts, liposomal DOX did not satisfy expectations at the clinical level. When liposomal drugs enter a physiological environment, their surface gets coated by a dynamic biomolecular corona (BC). The BC changes liposome's synthetic identity, providing it with a new one, referred to as 'biological identity' (size, aggregation state, and BC composition)...
June 15, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29904765/cationic-double-chained-metallosurfactants-synthesis-aggregation-cytotoxicity-antimicrobial-activity-and-their-impact-on-the-structure-of-bovine-serum-albumin
#10
Gurpreet Kaur, Preeti Garg, Baljinder Kaur, Ganga Ram Chaudhary, Sandeep Kumar, Neeraj Dilbaghi, P A Hassan, Santosh L Gawali
Bovine serum albumin (BSA) is one of the most copious and significant blood proteins with dynamic structure. The understanding of the structural functionality of BSA and its interaction with metal ions is desired for various biological functions. Herein, three different metallosurfactants containing different transition metals and the same hydrophobic tail were engaged to investigate the structural transition of BSA. The metallosurfactants have been prepared by a combination of metal ions (M = Fe, Co and Ni) with cetylpyridinium chloride surfactant via the ligand insertion method and were characterized by elemental, FTIR, 1H-NMR, and thermogravimetric analysis (TGA)...
June 15, 2018: Soft Matter
https://www.readbyqxmd.com/read/29895898/ncam2-fibronectin-type-iii-domains-form-a-rigid-structure-that-binds-and-activates-the-fibroblast-growth-factor-receptor
#11
Kim Krighaar Rasmussen, Maria Hansen Falkesgaard, Malene Winther, Nikolaj Kulahin Roed, Christine Louise Quistgaard, Marie Nygaard Teisen, Sofie Marie Edslev, David Leander Petersen, Ali Aljubouri, Claus Christensen, Peter Waaben Thulstrup, Leila Lo Leggio, Kaare Teilum, Peter Schledermann Walmod
NCAM1 and NCAM2 have ectodomains consisting of 5 Ig domains followed by 2 membrane-proximal FnIII domains. In this study we investigate and compare the structures and functions of these FnIII domains. The NCAM1 and -2 FnIII2 domains both contain a Walker A motif. In NCAM1 binding of ATP to this motif interferes with NCAM1 binding to FGFR. We obtained a structural model of the NCAM2 FnIII2 domain by NMR spectroscopy, and by titration with an ATP analogue we show that the NCAM2 Walker A motif does not bind ATP...
June 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29894936/cationic-polyacrylamide-induced-nanoparticles-assembly-in-a-cellulose-nanofiber-network
#12
Vikram Singh Raghuwanshi, Uthpala Manavi Garusinghe, Praveena Raj, Nigel Kirby, Armin Hoell, Warren Batchelor, Gil Garnier
Polyacrylamides of different molecular weight, charges and dosages allow to control the retention and distribution of nanoparticles (NPs) in composites, and optimise composite properties and functionality. Our aim is to evaluate the effect of high molecular weight (13 MDa) cationic polyacrylamide (CPAM) charge and dosage on SiO2 (74 nm) NP's assembly in cellulose nanofibers composites. Engineered cellulose/SiO2 composites were investigated by SEM, SAXS and DLS. SEM images show the local area retention of NPs into the cellulose matrix...
June 5, 2018: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/29891311/structural-characterization-and-in-vitro-antioxidant-activities-of-chondroitin-sulfate-purified-from-andrias-davidianus-cartilage
#13
Wenming Zhu, Yang Ji, Yi Wang, Dong He, Yishu Yan, Nan Su, Chong Zhang, Xin-Hui Xing
Origin and manufacturing process are key factors affecting the biological activities of chondroitin sulfate (CS), which can be utilized as a nutraceutical in dietary supplements. Herein, we extracted and purified CS from the cartilage of artificially breeding Andrias davidianus (ADCS), i.e., Chinese giant salamander (CGS), one of the prospective functional food source materials in China. Low molecular weight CS (LMWADCS) was then prepared by free radical depolymerization of ADCS. High-performance gel permeation chromatography (HPGPC) analysis showed that the average molecular weight (Mw) of ADCS was 49...
September 15, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29891297/chondroitin-sulfate-dermatan-sulfate-from-corb-sciaena-umbra-skin-purification-structural-analysis-and-anticoagulant-effect
#14
Hajer Bougatef, Fatma Krichen, Federica Capitani, Ikram Ben Amor, Francesca Maccari, Veronica Mantovani, Fabio Galeotti, Nicola Volpi, Ali Bougatef, Assaad Sila
In this study, chondroitin sulfate/dermatan sulfate was isolated and purified from the skin of corb (Sciaena umbra) (CSG) with a yield of 6.2%. Chemical and structural analysis showed that CSG consisted of high sulfate content 28.74% and an average molecular weight of 15.46 KDa. The separation of CSG by agarose-gel electrophoresis revealed the presence of DS and CS. Structural analysis of the purified CS/DS by means of SAX-HPLC after treatment with specific chondroitinases showed that this polymer was composed of nonsulfated disaccharide, monosulfated disaccharides and disulfated disaccharides in various percentages...
September 15, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29888371/kinetic-monitoring-of-glutathione-induced-silver-nanoparticle-disintegration
#15
Claudia Kästner, Patrick E J Saloga, Andreas F Thünemann
We report on etching of polyacrylic acid-stabilised silver nanoparticles in the presence of glutathione (GSH). The initial particles with a radius of 3.2 nm and consisting of ∼8100 silver atoms dissolve in a two-step reaction mechanism while in parallel smaller silver particles with a radius of 0.65 nm and consisting of 60 to 70 silver atoms were formed. The kinetics of the etching of the initial particles, accompanied by formation of smaller silver particles was interpreted based on in situ, time-resolved small-angle X-ray scattering (SAXS) experiments...
June 11, 2018: Nanoscale
https://www.readbyqxmd.com/read/29886536/noninvasive-structural-analysis-of-intermediate-species-during-fibrillation-an-application-of-small-angle-x-ray-scattering
#16
Annette Eva Langkilde, Fátima Herranz-Trillo, Pau Bernadó, Bente Vestergaard
Structural investigation of intermediately formed oligomers and pre-fibrillar species is of tremendous importance in order to elucidate the structural principles of fibrillation, and because intermediate species have been suggested as the pathogenic agents in several amyloid diseases. Structural investigations are however greatly complicated by the dynamic changes between structural states of very different sizes and life-times. Small angle X-ray scattering (SAXS) is an ideal method to handle this challenge...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29880640/structural-insight-into-the-human-mitochondrial-trna-purine-n1-methyltransferase-and-ribonuclease-p-complexes
#17
Stephanie Oerum, Martine Roovers, Robert P Rambo, Jola Kopec, Henry J Bailey, Fiona Fitzpatrick, Joseph A Newman, William G Newman, Albert Amberger, Johannes Zschocke, Louis Droogmans, Udo Oppermann, Wyatt W Yue
Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5'-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalysed by two proteinaceous complexes with overlapping subunit composition. The Mg2+-dependent ribonuclease P complex for 5'-end cleavage comprises the methyltransferase domain-containing protein TRMT10C/MRPP1, short-chain oxidoreductase HSD17B10/MRPP2, and metallonuclease KIAA0391/MRPP3...
June 7, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29874600/machine-learning-methods-for-x-ray-scattering-data-analysis-from-biomacromolecular-solutions
#18
Daniel Franke, Cy M Jeffries, Dmitri I Svergun
Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (Dmax ) as well as molecular mass directly from experimental scattering data...
June 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29873345/saxs-characterization-of-the-interactions-among-digested-food-compounds-and-the-anti-oxidant-and-anti-inflammatory-activities-of-the-formed-nanocomplexes
#19
Yingkang Yang, Xiaoqi Wang, Guijie Chen, Wenhua Zhou, Xiaoxiong Zeng, Bing Hu, Yunqi Li, Qingrong Huang
In the present study, small angle X-ray scattering (SAXS) is applied to investigate the interaction between caseinophosphopeptides (CPP), the major digested product of milk protein, and chitosan (CS) under simulated gastrointestinal (GI) pH conditions. The change in pH value from the gastric to small intestinal environment induces complexation between CPP and CS, which is mainly driven by electrostatic interactions. The fractal dimension (Df) value of the domains inside the CPP-CS complexes is greater than 3, indicating the formation of dense particles/aggregates at the nanoscale...
June 6, 2018: Food & Function
https://www.readbyqxmd.com/read/29869308/characterization-of-lipid-based-lyotropic-liquid-crystal-and-effects-of-guest-molecules-on-its-microstructure-a-systematic-review
#20
Xingqi Wang, Yong Zhang, Shuangying Gui, Jie Huang, Jiaojiao Cao, Zhengguang Li, Qian Li, Xiaoqin Chu
Liquid crystals (LCs) are conventionally divided into thermotropic or lyotropic, based on the organization and sequence of the controlled molecular system. Lipid-based lyotropic liquid crystal (LLC), such as lamellar (Lα), bicontinuous cubic (QII ), or hexagonal (HII ) phases, have attracted wide interest in the last few decades due to their practical potential in diverse applications and notable structural complexity. Various guest molecules, such as biopharmaceuticals, chemicals, and additives, can be solubilized in either aqueous or oily phase...
June 4, 2018: AAPS PharmSciTech
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