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https://www.readbyqxmd.com/read/28448026/lerlic-ms-ms-for-in-depth-characterization-and-quantification-of-glutamine-and-asparagine-deamidation-in-shotgun-proteomics
#1
Xavier Gallart-Palau, Aida Serra, Siu Kwan Sze
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples...
April 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28443077/molecular-dynamics-simulation-of-the-influenza-a-h3n2-hemagglutinin-trimer-reveals-the-structural-basis-for-adaptive-evolution-of-the-recent-epidemic-clade-3c-2a
#2
Masaru Yokoyama, Seiichiro Fujisaki, Masayuki Shirakura, Shinji Watanabe, Takato Odagiri, Kimito Ito, Hironori Sato
Influenza A(H3N2) has been a major cause of seasonal influenza in humans since 1968, and has evolved by antigenic drift under the constantly changing human herd immunity. Increasing evidence suggests that the antigenic change occasionally occurred concomitant with the alterations of the N-glycosylation site profile and hemagglutination activity of the virion surface protein hemagglutinin (HA). However, the structural basis of these changes remains largely unclear. To address this issue, we performed molecular dynamics simulations of the glycosylated HA trimers of the A(H3N2), which has a novel pattern of Asn-X-Ser/Thr sequons unique in the new A(H3N2) epidemic clade 3C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28441623/identification-of-a-macrobrachium-nipponense-c-type-lectin-with-a-close-evolutionary-relationship-to-vertebrate-lectins
#3
Xin Huang, Tingting Li, Min Jin, Shaowu Yin, Wen Wang, Qian Ren
C-type lectins (CTLs) are involved in the innate immune defense of vertebrates and invertebrates against invading pathogens. This study cloned and characterized a novel C-type lectin (MnCTL) of the oriental river prawn, Macrobrachium nipponense. The cloned MnCTL cDNA encompasses an open reading frame of 774 nucleotides and encodes polypeptides of 257 residues. The deduced MnCTL protein contains a single carbohydrate recognition domain (CRD) with an EPN (Glu-Pro-Asn) motif in calcium-binding site 2. Phylogenetic analysis indicated that MnCTL has a closer evolutionary relationship with vertebrate lectins than with invertebrate lectins...
April 22, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28435822/targeted-intracellular-heat-transfer-in-cancer-therapy-assessment-of-asparagine-laminated-gold-nanoparticles-in-cell-model-of-t-cell-leukemia
#4
Shadab Shahriari, Maryam Bakhshi, Ahmad Reza Shahverdi, Azar Berahmeh, Farnaz Safavifar, Mohammad Reza Khorramizadeh
BACKGROUND: High temperatures have destructive effects on cancer cells by damaging proteins and structures within cells. Gold nanoparticles (AuNPs) can act as drug delivery vehicles, especially for cancer therapy. Due to the selective intake of asparagine molecules into malignant cells, AuNPs were coated with asparagine; and CCRF-CEM human T-cell leukemia cells were treated with the new combination, Asn-AuNPs, at 39 °C. METHODS: The co-authors from a number of collaborative labs located at Tehran University of Medical Sciences, Tehran, Iran, have initiated the idea and preliminary design of this study in 2011...
March 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/28435772/self-assembled-bifunctional-peptide-as-effective-drug-delivery-vector-with-powerful-antitumor-activity
#5
Rangrang Fan, Lan Mei, Xiang Gao, Yuelong Wang, Mingli Xiang, Yu Zheng, Aiping Tong, Xiaoning Zhang, Bo Han, Liangxue Zhou, Peng Mi, Chao You, Zhiyong Qian, Yuquan Wei, Gang Guo
E-cadherin/catenin complex is crucial for cancer cell migration and invasion. The histidine-alanine-valine (HAV) sequence has been shown to inhibit a variety of cadherin-based functions. In this study, by fusing HAV and the classical tumor-targeting Arg-Gly-Asp (RGD) motif and Asn-Gly-Arg (NGR) motif to the apoptosis-inducing peptide sequence-AVPIAQK, a bifunctional peptide has been constructed with enhanced tumor targeting and apoptosis effects. This peptide is further processed as a nanoscale vector to encapsulate the hydrophobic drug docetaxel (DOC)...
April 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28434792/cloning-and-expression-patterns-of-neuromedin-u-and-its-receptors-in-pigs
#6
Xiang Li, Mingfu Niu, Juan Su, Zhiyu Ma, Mengmeng Jin, Wenna Qiao, Ying Zhang, Yanyan Feng, Na An, Yuanlong Hou, Sheng Yang, Suo Chuan, Zhihai Lei
Neuromedin U (NMU) is a highly conserved neuropeptide that performs a variety of physiological functions in animals via neuromedin U receptor-1 (NMUR1) and neuromedin U receptor-2 (NMUR2). In this study, we cloned the pig NMU, NMUR1 and NMUR2 genes. Bioinformatics analysis demonstrated that the pig NMU cDNA encoded the amino acids Phe-Leu-Phe-Arg-Pro-Arg-Asn-NH2 at the C-terminus and that the NMU receptors, which are G-protein-coupled receptors (GPCRs), contained the seven transmembrane domains typical of GPCRs...
April 6, 2017: Neuropeptides
https://www.readbyqxmd.com/read/28434301/an-asp-to-asn-mutation-is-a-toxic-trigger-in-beta-2-microglobulin-structure-and-biophysics
#7
Matteo de Rosa, Levon Halabelian, Alberto Barbiroli, Martino Bolognesi, Vittorio Bellotti, Stefano Ricagno
No abstract text is available yet for this article.
March 2017: Amyloid: the International Journal of Experimental and Clinical Investigation
https://www.readbyqxmd.com/read/28433761/a-glycoproteomic-approach-reveals-that-the-s-layer-glycoprotein-of-lactobacillus-kefiri-cidca-83111-is-o-and-n-glycosylated
#8
Gustavo J Cavallero, Mariano Malamud, Adriana C Casabuono, M de Los Ángeles Serradell, Alicia S Couto
In Gram-positive bacteria, such as lactic acid bacteria, general glycosylation systems have not been documented so far. The aim of this work was to characterize in detail the glycosylation of the S-layer protein of Lactobacillus kefiri CIDCA 83111. A reductive β-elimination treatment followed by anion exchange high performance liquid chromatography analysis was useful to characterize the O-glycosidic structures. MALDI-TOF mass spectrometry analysis confirmed the presence of oligosaccharides bearing from 5 to 8 glucose units carrying galacturonic acid...
April 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28433609/hb-moncloa-a-new-variant-of-haemoglobin-that-interferes-in-the-quantification-of-hb-a1c
#9
Torrejón María Josefa, Ortíz-Cabrera N Valentina, M Nieto Jorge, González Fernández Fernando-Ataúlfo, Villegas Ana, Martínez Rafael, Ropero Paloma
BACKGROUND: In most routine laboratories in Spain, the commonly used method for evaluating HbA1c is ion-exchange high performance liquid chromatography (HPLC). The presence of a variant of Hb may interfere with the quantification of HbA1c. AIMS: Here, we report a novel haemoglobin variant, named Hb Moncloa, which was found during a routine health check at the Hospital Clínico San Carlos in Moncloa (Madrid), Spain. METHODS AND RESULTS: Molecular characterization of β gene identified a novel transversion mutation [β80(EF4)Asn>Ser; HBB:c...
April 19, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28428332/education-in-nephrology-fellowship-a-survey-based-needs-assessment
#10
Robert W Rope, Kurtis A Pivert, Mark G Parker, Stephen M Sozio, Sylvia Bereknyei Merell
Educational needs assessments for nephrology fellowship training are limited. This study assessed fellows' perceptions of current educational needs and interest in novel modalities that may improve their educational experience and quantified educational resources used by programs and fellows. We distributed a seven-question electronic survey to all United States-based fellows receiving complimentary American Society of Nephrology (ASN) membership at the end of the 2015-2016 academic year in conjunction with the ASN Nephrology Fellows Survey...
April 20, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28426790/lethality-of-mice-bearing-a-knockout-of-the-ngly1-gene-is-partially-rescued-by-the-additional-deletion-of-the-engase-gene
#11
Haruhiko Fujihira, Yuki Masahara-Negishi, Masaru Tamura, Chengcheng Huang, Yoichiro Harada, Shigeharu Wakana, Daisuke Takakura, Nana Kawasaki, Naoyuki Taniguchi, Gen Kondoh, Tadashi Yamashita, Yoko Funakoshi, Tadashi Suzuki
The cytoplasmic peptide:N-glycanase (Ngly1 in mammals) is a de-N-glycosylating enzyme that is highly conserved among eukaryotes. It was recently reported that subjects harboring mutations in the NGLY1 gene exhibited severe systemic symptoms (NGLY1-deficiency). While the enzyme obviously has a critical role in mammals, its precise function remains unclear. In this study, we analyzed Ngly1-deficient mice and found that they are embryonic lethal in C57BL/6 background. Surprisingly, the additional deletion of the gene encoding endo-β-N-acetylglucosaminidase (Engase), which is another de-N-glycosylating enzyme but leaves a single GlcNAc at glycosylated Asn residues, resulted in the partial rescue of the lethality of the Ngly1-deficient mice...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424964/pharmacodynamic-effects-in-the-cerebrospinal-fluid-of-rats-after-intravenous-administration-of-different-asparaginase-formulations
#12
Andrea Ballerini, Federico Moro, Ilaria Fuso Nerini, Claudio Marcello Marzo, Angelo Di Clemente, Mariella Ferrari, Maurizio D'Incalci, Andrea Biondi, Antonella Colombini, Valentino Conter, Luca Porcu, Luigi Cervo, Carmelo Rizzari, Massimo Zucchetti
PURPOSE: Asparaginase (ASNase) is used to treat various hematological malignancies for its capacity to deplete asparagine (ASN) in serum and cerebrospinal fluid (CSF). Since the biological mechanisms underlying CSF asparagine depletion in humans are not yet fully elucidated, this study compared, for the first time, the pharmacological properties of three clinically used ASNase formulations in a rodent model. METHODS: Male Wistar rats were treated with E.coli-ASNase, PEG-ASNase, or ERW-ASNase at different doses...
April 19, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28420706/common-structural-features-of-cholesterol-binding-sites-in-crystallized-soluble-proteins
#13
Anna N Bukiya, Alejandro M Dopico
Cholesterol-protein interactions are essential for the architectural organization of cell membranes and for lipid metabolism. While cholesterol-sensing motifs in transmembrane proteins have been identified, little is known about cholesterol recognition by soluble proteins. We reviewed the structural characteristics of binding sites for cholesterol and cholesterol sulfate from crystallographic structures available in the Protein Data Bank. This analysis unveiled key features of cholesterol-binding sites that are present in either all or the majority of sites: i) the cholesterol molecule is generally positioned between protein domains that have an organized secondary structure; ii) the cholesterol hydroxyl/sulfo group is often partnered by Asn, Gln and/or Tyr while the hydrophobic part of cholesterol interacts with Leu, Ile, Val and/or Phe; iii) cholesterol hydrogen-bonding partners are often found on alpha-helices while amino acids that interact with cholesterol hydrophobic core have a slight preference for beta-strands and secondary structure-lacking protein areas; iv) the steroid C21 and 26 constitute the ″hot spots″ most often seen for steroid-protein hydrophobic interactions; v) common ″cold spots″ are C8, 9, 10, 13 and 17, at which contacts with the proteins were not detected...
April 18, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28418051/a-structural-bioinformatics-investigation-on-protein-dna-complexes-delineates-their-modes-of-interaction
#14
Simone Gardini, Simone Furini, Annalisa Santucci, Neri Niccolai
The lifetimes of protein-DNA adducts are strictly related to the various protein functions. This feature must be encoded by the amino acids located at the protein-DNA interface. The large number of structurally characterized protein-DNA complexes now available from the Protein Data Bank (PDB) allows extensive structural bioinformatics investigations on protein-DNA interfaces. The modes of protein binding to DNA have been explored by dividing 629 non-redundant PDB files of protein-DNA complexes into separate classes for structural proteins, transcription factors and DNA-related enzymes...
April 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28393477/residues-at-a-single-site-differentiate-animal-cryptochromes-from-cyclobutane-pyrimidine-dimer-photolyases-by-affecting-the-proteins-preferences-for-reduced-fad
#15
Lei Xu, Bin Wen, Yuan Wang, Changqing Tian, Mingcai Wu, Guoping Zhu
Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state during illumination, which may induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed...
April 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28392772/the-tromso-infant-faces-database-tif-development-validation-and-application-to-assess-parenting-experience-on-clarity-and-intensity-ratings
#16
Jana K Maack, Agnes Bohne, Dag Nordahl, Lina Livsdatter, Åsne A W Lindahl, Morten Øvervoll, Catharina E A Wang, Gerit Pfuhl
Newborns and infants are highly depending on successfully communicating their needs; e.g., through crying and facial expressions. Although there is a growing interest in the mechanisms of and possible influences on the recognition of facial expressions in infants, heretofore there exists no validated database of emotional infant faces. In the present article we introduce a standardized and freely available face database containing Caucasian infant face images from 18 infants 4 to 12 months old. The development and validation of the Tromsø Infant Faces (TIF) database is presented in Study 1...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28391608/mechanistic-analysis-of-fluorescence-quenching-of-reduced-nicotinamide-adenine-dinucleotide-by-oxamate-in-lactate-dehydrogenase-ternary-complexes
#17
Huo-Lei Peng, Robert Callender
Fluorescence of Reduced Nicotinamide Adenine Dinucleotide (NADH) is extensively employed in studies of oxidoreductases. A substantial amount of static and kinetic work has focused on the binding of pyruvate or substrate mimic oxamate to LDH•NADH where substantial fluorescence quenching is typically observed. However, the quenching mechanism is not well understood limiting structural interpretation. Based on time-dependent density functional theory (TDDFT) computations with cam-B3LYP functional in conjunction with the analysis of previous experimental results, we propose that bound oxamate acts as an electron acceptor in the quenching of fluorescence of NADH in the ternary complex, where a charge transfer (CT) state characterized by excitation from the highest occupied molecular orbital (HOMO) of the nicotinamide moiety of NADH to the lowest unoccupied molecular orbital (LUMO) of oxamate exists close to the locally excited (LE) state involving only the nicotinamide moiety...
April 9, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28383883/the-proton-responsiveness-in-the-extracellular-domain-of-glic-differs-in-the-presence-of-the-elic-transmembrane-domain
#18
Mona A Alqazzaz, Kerry L Price, Sarah C R Lummis
Prokaryotic homologues of Cys-loop receptors have proven to be useful in understanding their eukaryotic counterparts, but even the best studied of these, Gloeobacter ligand-gated ion channel (GLIC), is still not yet fully understood. GLIC is activated by protons with a pH50 between 5 and 6, implicating a histidine residue in its activation, but although a histidine residue (His11') in the pore-forming α-helix (M2) is known to be involved in gating, the His in the extracellular domain (ECD), His127, is not...
April 6, 2017: Biochemistry
https://www.readbyqxmd.com/read/28383243/%C3%A3-rede-l%C3%A3-gestand
#19
Åsne Granlund
No abstract text is available yet for this article.
April 2017: Tidsskrift for Den Norske Lægeforening: Tidsskrift for Praktisk Medicin, Ny Række
https://www.readbyqxmd.com/read/28381551/production-of-homogeneous-glycoprotein-with-multi-site-modifications-by-an-engineered-n-glycosyltransferase-mutant
#20
Qitao Song, Zhigang Wu, Yueyuan Fan, Woran Song, Peiru Zhang, Li Wang, Faxing Wang, Yangyang Xu, Peng George Wang, Jiansong Cheng
Naturally occurring N- glycoproteins exhibit glycoform heterogeneity with respect to N-glycan sequon occupancy (macroheterogeneity) and glycan structure (microheterogeneity). However, access to well-defined glycoproteins is always important for both basic research and therapeutic purposes. As a result, there has been substantial effort to identify and understand the catalytic properties of N-glycosyltransferases, enzymes that install the first glycan on the protein chain. In this study, we found that ApNGT, a newly discovered cytoplasmic N- glycosyltransferase from Actinobacillus pleuropneumoniae, has strict selectivity towards the residues around the Asn of N-glycosylation sequon by screening a small library of synthetic peptides...
April 5, 2017: Journal of Biological Chemistry
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