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Protein chemistry

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https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#1
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28811882/seasonal-changes-in-leaf-chemistry-and-leaf-selection-of-the-japanese-giant-flying-squirrel-upon-two-tree-species
#2
Mutsumi Ito, Noriko Tamura, Fumio Hayashi
Tree leaves are important food sources for arboreal herbivores, such as primates, rodents, and marsupials. These animals do not eat leaves randomly in habitats with many tree species but rather choose based on the chemical components of leaves, such as sugars, fibers, proteins, and toxins. However, the effects of the microscale distribution of these chemicals within each leaf have not been examined for these animals. The giant flying squirrels Petaurista leucogenys are entirely arboreal, nocturnal herbivores, usually feeding on leaves and dropping leaf debris on the ground after partially consuming them...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811262/probe-microscopy-methods-and-applications-in-imaging-of-biological-materials
#3
REVIEW
Alper D Ozkan, Ahmet E Topal, Fatma B Dikecoglu, Mustafa O Guler, Aykutlu Dana, Ayse B Tekinay
Atomic force microscopy is an emerging tool for investigating the biomolecular aspects of cellular interactions; however, cell and tissue analyses must frequently be performed in aqueous environment, over rough surfaces, and on complex adhesive samples that complicate the imaging process and readily facilitate the blunting or fouling of the AFM probe. In addition, the shape and surface chemistry of the probe determine the quality and types of data that can be acquired from biological materials, with certain information becoming available only within a specific range of tip lengths or diameters, or through the assistance of specific chemical or biological functionalization procedures...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28807864/reducing-diagnostic-turnaround-times-of-exome-sequencing-for-families-requiring-timely-diagnoses
#4
Aurélie Bourchany, Christel Thauvin-Robinet, Daphné Lehalle, Ange-Line Bruel, Alice Masurel-Paulet, Nolwenn Jean, Sophie Nambot, Marjorie Willems, Laetitia Lambert, Salima El Chehadeh-Djebbar, Elise Schaefer, Aurélia Jaquette, Judith St-Onge, Charlotte Poe, Thibaud Jouan, Martin Chevarin, Patrick Callier, Anne-Laure Mosca-Boidron, Nicole Laurent, Mathilde Lefebvre, Frédéric Huet, Nada Houcinat, Sébastien Moutton, Christophe Philippe, Frédéric Tran-Mau-Them, Antonio Vitobello, Paul Kuentz, Yannis Duffourd, Jean-Baptiste Rivière, Julien Thevenon, Laurence Faivre
BACKGROUND AND OBJECTIVE: Whole-exome sequencing (WES) has now entered medical practice with powerful applications in the diagnosis of rare Mendelian disorders. Although the usefulness and cost-effectiveness of WES have been widely demonstrated, it is essential to reduce the diagnostic turnaround time to make WES a first-line procedure. Since 2011, the automation of laboratory procedures and advances in sequencing chemistry have made it possible to carry out diagnostic whole genome sequencing from the blood sample to molecular diagnosis of suspected genetic disorders within 50 h...
August 11, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28807652/severity-indices-in-rheumatoid-arthritis-a-systematic-review
#5
Esther Toledano, M Jesús García de Yébenes, Isidoro González-Álvaro, Loreto Carmona
OBJECTIVE: To identify tools designed to evaluate the severity of patients with rheumatoid arthritis (RA) in order to use them in the investigation of prognostic markers in early arthritis. METHODS: We conducted a systematic review of studies that developed/validated an index for RA disease severity. They were analyzed using the COSMIN checklist to assess their methodological quality. In addition, all the variables included were evaluated for their clarity of definition, feasibility and probability of being present in each outcome during the first 2 years of the disease course...
August 11, 2017: Reumatología Clinica
https://www.readbyqxmd.com/read/28805222/heme-isomers-substantially-affect-heme-s-electronic-structure-and-function
#6
Kasper P Kepp
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol(-1)) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28804948/nelumbo-nucifera-leaf-extract-treatment-attenuated-preneoplastic-lesions-and-oxidative-stress-in-the-livers-of-diethylnitrosamine-treated-rats
#7
Chi-Ting Horng, Chien-Wei Huang, Mon-Yuan Yang, Tzu-Hsin Chen, Yun-Ching Chang, Chau-Jong Wang
Lotus (Nelumbo nucifera Gaertn) possesses antioxidant, hepatoprotective, and anticancer potential. This study determined the protective role of aqueous extract from Nelumbo nucifera leaves (NLE) against N-diethylnitrosamine (DEN)-induced oxidative stress and hepatocellular carcinogenesis in a sample of Sprague-Dawley rats. NLE was fed orally to rats in which hepatic carcinoma was induced with DEN for 12 weeks. Five groups of 12 rats each were used for the study: Group I (control group) rats received distilled water; Group II rats were induced with DEN; Group III rats were induced with DEN and cotreated with 0...
August 14, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/28804798/probing-biological-redox-chemistry-with-large-amplitude-fourier-transformed-ac-voltammetry
#8
Hope Adamson, Alan M Bond, Alison Parkin
Biological electron-exchange reactions are fundamental to life on earth. Redox reactions underpin respiration, photosynthesis, molecular biosynthesis, cell signalling and protein folding. Chemical, biomedical and future energy technology developments are also inspired by these natural electron transfer processes. Further developments in techniques and data analysis are required to gain a deeper understanding of the redox biochemistry processes that power Nature. This review outlines the new insights gained from developing Fourier transformed ac voltammetry as a tool for protein film electrochemistry...
August 14, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28803466/deciphering-the-fluorine-code-the-many-hats-fluorine-wears-in-a-protein-environment
#9
Allison Ann Berger, Jan-Stefan Völler, Nediljko Budisa, Beate Koksch
Deciphering the fluorine code is how we describe not only the focus of this Account, but also the systematic approach to studying the impact of fluorine's incorporation on the properties of peptides and proteins used by our groups and others. The introduction of fluorine has been shown to impart favorable, but seldom predictable, properties to peptides and proteins, but up until about two decades ago the outcomes of fluorine modification of peptides and proteins were largely left to chance. Driven by the motivation to extend the application of the unique properties of the element fluorine from medicinal and agro chemistry to peptide and protein engineering we have established extensive research programs that enable the systematic investigation of effects that accompany the introduction of fluorine into this class of biopolymers...
August 12, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28803046/design-synthesis-and-biological-evaluation-of-novel-pyrazolochalcones-as-potential-modulators-of-pi3k-akt-mtor-pathway-and-inducers-of-apoptosis-in-breast-cancer-cells
#10
Anver Basha Shaik, Garikapati Koteswara Rao, G Bharath Kumar, Nibeditha Patel, Vangala Santhosh Reddy, Irfan Khan, Sunitha Rani Routhu, C Ganesh Kumar, Immadi Veena, Kunta Chandra Shekar, Madan Barkume, Shailesh Jadhav, Aarti Juvekar, Jyoti Kode, Manika Pal-Bhadra, Ahmed Kamal
Cancer has been established as the "Emperor of all maladies". In recent years, medicinal chemistry has focused on identifying novel anti-cancer compounds; though discovery of these compounds appears to be a herculean task. In present study, we synthesized forty pyrazolochalcone conjugates and explored their cytotoxic activity against a panel of sixty cancer cell lines. Fifteen conjugates of the series showed excellent growth inhibition (13b-e, 13h-j, 14c-d, 15 a, 15 c-d, 16b, 16d and 18f; GI50 for MCF-7: 0...
July 25, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28801573/a-structural-and-mechanistic-study-of-%C3%AF-clamp-mediated-cysteine-perfluoroarylation
#11
Peng Dai, Jonathan K Williams, Chi Zhang, Matthew Welborn, James J Shepherd, Tianyu Zhu, Troy Van Voorhis, Mei Hong, Bradley L Pentelute
Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800395/using-chemistry-to-target-neuroblastoma
#12
Jeanne N Hansen, Xingguo Li, Y George Zheng, Louis T Lotta, Abhishek Dedhe, Nina F Schor
Neuroblastoma is a cancer of the neural crest almost exclusively seen in childhood. While children with single, small primary tumors are often cured with surgery alone, the 65% of children with neuroblastoma whose disease has metastasized have less than a 50% chance of surviving five years after diagnosis. Innovative pharmacological strategies are critically needed for these children. Efforts to identify novel targets that afford ablation of neuroblastoma with minimal toxicity to normal tissues are underway...
August 11, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28799461/preparation-and-characterization-of-protein-resistant-hydrogels-for-soft-contact-lens-applications-via-radical-copolymerization-involving-a-zwitterionic-sulfobetaine-comonomer
#13
Wanlu Zhang, Guangji Li, Yinlei Lin, Liying Wang, Shuqing Wu
We aimed to introduce hydrophilic sulfobetaine-type zwitterionic groups to macromolecular chains of copolymers to construct novel copolymer hydrogels with anti-protein-fouling performance that could be used as soft contact lens (SCL) materials. Using hydroxyethyl methacrylate (HEMA), N-vinyl pyrrolidinone (NVP) and sulfobetaine methacrylate (SBMA) as comonomers, several copolymer hydrogels with different SBMA contents, poly(HEMA-NVP-SBMA), are synthesized via radical copolymerization in an aqueous phase. Surface chemistry, structural morphologies, water contact angle (WCA), equilibrium water content (EWC), visible light transmittance and tensile mechanical properties are investigated...
August 11, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/28796164/enzymatic-synthesis-of-n-acetyllactosamine-lacnac-type-1-oligomers-and-characterization-as-multivalent-galectin-ligands
#14
Thomas Fischöder, Dominic Laaf, Carina Dey, Lothar Elling
Repeats of the disaccharide unit N-acetyllactosamine (LacNAc) occur as type 1 (Galβ1, 3GlcNAc) and type 2 (Galβ1, 4GlcNAc) glycosylation motifs on glycoproteins and glycolipids. The LacNAc motif acts as binding ligand for lectins and is involved in many biological recognition events. To the best of our knowledge, we present, for the first time, the synthesis of LacNAc type 1 oligomers using recombinant β1,3-galactosyltransferase from Escherichia coli and β1,3-N-acetylglucosaminyltranferase from Helicobacter pylori...
August 10, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28795351/advancements-in-understanding-immunogenicity-of-biotherapeutics-in-the-intraocular-space
#15
Eric Wakshull, Valerie Quarmby, Hanns-Christian Mahler, Hongwen Rivers, Dhananjay Jere, Meg Ramos, Piotr Szczesny, Karoline Bechtold-Peters, Sharmila Masli, Swati Gupta
Therapeutic breakthroughs in a number of retinal degenerative diseases have come about through the development of biotherapeutics administered directly into the eye. As a consequence of their use, we have gained more insight into the immune privileged status of the eye and the various considerations that development, manufacturing, and use of these drugs require. It has been observed that therapeutic proteins injected into the vitreous can elicit an immune response resulting in the production of anti-drug antibodies (ADAs) which can have clinical consequences...
August 9, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28795044/n-glycoproteomic-analysis-of-human-follicular-fluid-during-natural-and-stimulated-cycles-in-patients-undergoing-in-vitro-fertilization
#16
Hee-Joung Lim, Ae Eun Seok, Jiyou Han, Jiyeong Lee, Sungeun Lee, Hee-Gyoo Kang, Byung Heun Cha, Yunseok Yang
OBJECTIVE: Hyperstimulation methods are broadly used for in vitro fertilization (IVF) in patients with infertility; however, the side effects associated with these therapies, such as ovarian hyperstimulation syndrome (OHSS), have not been well studied. N-glycoproteomes are subproteomes used for the remote sensing of ovarian stimulation in follicular growth. Glycoproteomic variation in human follicular fluid (hFF) has not been evaluated. In this study, we aimed to identify and quantify the glycoproteomes and N-glycoproteins (N-GPs) in natural and stimulated hFF using label-free nano-liquid chromatography/electrospray ionization-quad time-of-flight mass spectrometry...
June 2017: Clinical and Experimental Reproductive Medicine
https://www.readbyqxmd.com/read/28793839/roughness-and-hydrophilicity-as-osteogenic-biomimetic-surface-properties
#17
Barbara Boyan, Ethan Major Lotz, Zvi Schwartz
Successful dental and orthopaedic implant outcomes are determined by the degree of osseointegration. Over the last 60 years, endosseous implants have evolved to stimulate osteogenesis without the need for exogenous biologics like bone morphogenetic proteins. An understanding of the interaction between cells and how cells interact with the physical features characteristics of their environments have has led to the development ofse bioactive implants. Implant surfaces that mimic the inherent chemistry, topography, and hydrophilicity wettability of native bone have been shown to provide cells in the osteoblast lineage cells with the structural cues to promote tissue regeneration and net new bone formation...
August 10, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28792736/chemical-synthesis-of-oligosaccharides-related-to-the-cell-walls-of-plants-and-algae
#18
Christine Kinnaert, Mathilde Daugaard, Faranak Nami, Mads H Clausen
Plant cell walls are composed of an intricate network of polysaccharides and proteins that varies during the developmental stages of the cell. This makes it very challenging to address the functions of individual wall components in cells, especially for highly complex glycans. Fortunately, structurally defined oligosaccharides can be used as models for the glycans, to study processes such as cell wall biosynthesis, polysaccharide deposition, protein-carbohydrate interactions, and cell-cell adhesion. Synthetic chemists have focused on preparing such model compounds, as they can be produced in good quantities and with high purity...
August 9, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28791911/targeting-species-specific-trace-amine-associated-receptor-1-ligands-to-date-perspective-of-the-rational-drug-design-process
#19
Elena Cichero, Michele Tonelli
G-protein-coupled receptors represent main targets of several clinically relevant drugs, playing nowadays a leading part for further drug discovery process. Trace amine-associated receptor's family (TAARs) assumed an intriguing role as druggable target in medicinal chemistry, being TAAR1 the most investigated. Indeed, related ligands proved to be intertwined in several circuits involved in pathological pathways or therapeutic routes. Herein, we highlight relevant efforts in the search of novel agonists, focusing on responsiveness featured by different chemotypes toward rodent and human TAAR1, in order to explore species-specificity preferences...
August 9, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28783866/hematologic-and-plasma-chemistry-ris-for-cultured-striped-catfish-pangasius-hypophthalmus-in-recirculating-aquaculture-systems
#20
Oscar A Galagarza, David D Kuhn, Stephen A Smith, Terry C Hrubec
BACKGROUND: Striped catfish (Pangasius hypophthalmus) is a valuable aquaculture fish species produced primarily in Southeast Asia. In the United States, it is bred as an ornamental species. Striped catfish has high productivity and great demand in numerous countries around the world, yet little is known about its normal physiology. OBJECTIVES: The objective of this study was to establish hematologic and blood chemistry RIs for healthy juvenile Striped catfish. METHODS: Blood samples were collected from 70 Striped catfish raised in recirculating aquaculture systems...
August 7, 2017: Veterinary Clinical Pathology
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