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https://www.readbyqxmd.com/read/28729559/effects-of-poly-%C3%AE-glutamic-acid-%C3%AE-pga-on-plant-growth-and-its-distribution-in-a-controlled-plant-soil-system
#1
Lei Zhang, Xueming Yang, Decai Gao, Lingli Wang, Jie Li, Zhanbo Wei, Yuanliang Shi
To demonstrate the responses of plant (Pakchoi) and soil to poly-γ-glutamic acid (γ-PGA) is essential to better understand the pathways of the promotional effect of γ-PGA on plant growth. In this study, the effects of γ-PGA on soil nutrient availability, plant nutrient uptake ability, plant metabolism and its distribution in a plant-soil system were tested using labeled γ-PGA synthesized from (13)C1-(15)N-L-glutamic acid (L-Glu). γ-PGA significantly improved plant uptake of nitrogen (N), phosphorus (P), and potassium (K) and hence increased plant biomass...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729386/dormancy-in-embryos-insight-from-hydrated-encysted-embryos-of-an-aquatic-invertebrate
#2
Tamar Ziv, Vered Chalifa-Caspi, Nadav Denekamp, Inbar Plaschkes, Sylwiya Sylwia Kierszniowska, Idit Blais, Arie Admon, Esther Lubzens
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with non-dormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilis</p> <p>A total of 2,631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p=0...
July 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#3
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28723063/using-cooperatively-folded-peptides-to-measure-interaction-energies-and-conformational-propensities
#4
Maziar S Ardejani, Evan T Powers, Jeffery W Kelly
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities...
July 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28710924/identification-of-new-bace1-inhibitors-using-pharmacophore-and-molecular-dynamics-simulations-approach
#5
Anantha Krishnan Dhanabalan, Manish Kesherwani, Devadasan Velmurugan, Krishnasamy Gunasekaran
Inhibition of β-Secretase (BACE1) is crucial for the treatment of Alzheimer's disease (AD). Availability of BACE1 crystal structures in both apo and complexed forms enables to find structure-based BACE1 inhibitors for controlling AD. There are two catalytic aspartates (ASP32 and ASP228) presents in the active domain of BACE1. In order to understand the binding mechanism and structure-activity relationship of amidine-containing BACE1 inhibitors, molecular docking, and pharmacophore and 3D-QSAR studies have been carried out with 34 amidine derivatives to develop a pharmacophore model...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28700717/integrated-analysis-of-zone-specific-protein-and-metabolite-profiles-within-nitrogen-fixing-medicago-truncatula-sinorhizobium-medicae-nodules
#6
Aaron J Ogden, Mahmoud Gargouri, JeongJin Park, David R Gang, Michael L Kahn
Symbiotic nitrogen fixation (SNF) between rhizobia and legumes requires metabolic coordination within specialized root organs called nodules. Nodules formed in the symbiosis between S. medicae and barrel medic (M. truncatula) are indeterminate, cylindrical, and contain spatially distinct developmental zones. Bacteria in the infection zone II (ZII), interzone II-III (IZ), and nitrogen fixation zone III (ZIII) represent different stages in the metabolic progression from free-living bacteria into nitrogen fixing bacteroids...
2017: PloS One
https://www.readbyqxmd.com/read/28697887/molecular-origins-of-the-compatibility-between-glycosaminoglycans-and-a%C3%AE-40-amyloid-fibrils
#7
Katie L Stewart, Eleri Hughes, Edwin A Yates, David A Middleton, Sheena E Radford
The Aβ peptide forms extracellular plaques associated with Alzheimer's disease. In addition to protein fibrils, amyloid plaques also contain non-proteinaceous components, including glycosaminoglycans (GAGs). We have shown previously that the GAG low molecular weight heparin (LMWH) binds to Aβ40 fibrils with a three-fold-symmetric (3Q) morphology with higher affinity than Aβ40 fibrils in alternative structures, Aβ42 fibrils, or amyloid fibrils formed from other sequences. Solid-state NMR (SSNMR) analysis of the GAG-3Q fibril complex revealed an interaction site at the corners of the 3Q fibril structure, but the origin of the binding specificity remained obscure...
July 8, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28686288/distribution-of-cyp2c8-and-cyp2c9-amino-acid-substitution-alleles-in-south-indian-diabetes-patients-a-genotypic-and-computational-protein-phenotype-study
#8
Durga Koteswara Rao, Dwarakanath K Murthy, Nazia Sultana Shaik, Babajan Banaganapalli, Kumar Swami Konda, Hanumantha P Rao, Eswar Ganti, Ahmed A Zuheir, Ashraf El-Harouni, Ramu Elango, Imran Ali Khan, Noor Ahmad Shaik
The CYP2C8 and CYP2C9 are two major isoforms of the cytochrome P450 enzyme family, which is involved in drug response, detoxification, and disease development. This study describes the differential distribution of amino acid substitution variants of CYP2C8 (*2-I269F & *3-R139K) and CYP2C9 (*2-C144R & *3-L359A) genes in 234 type 2 diabetes mellitus (T2DM) patients and 218 healthy controls from Andhra Pradesh, South India. Single locus genotype analysis has revealed that homozygous recessive genotypes of 2C8*2-TT (p=<0...
July 7, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28680440/vaccatides-antifungal-glutamine-rich-hevein-like-peptides-from-vaccaria-hispanica
#9
Ka H Wong, Wei Liang Tan, Shruthi G Kini, Tianshu Xiao, Aida Serra, Sui Kwan Sze, James P Tam
Hevein and hevein-like peptides are disulfide-constrained chitin-binding cysteine-rich peptides. They are divided into three subfamilies, 6C-, 8C-, and 10C-hevein-like peptides, based on the number of cysteine residues. In addition, hevein-like peptides can exist in two forms, short and long. The long C-terminal form found in hevein and 10C-hevein-like peptides contain a C-terminal protein cargo. In contrast, the short form without a protein cargo is found in all three subfamilies. Here, we report the discovery and characterization of two novel glutamine-rich and protein cargo-free 8C-hevein-like peptides, vaccatides vH1 and vH2, from Vaccaria hispanica of the Caryophyllaceae family...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28677335/substrate-specificity-and-reaction-mechanism-of-human-prolidase
#10
Piotr Wilk, Monika Uehlein, Jacquelin Kalms, Holger Dobbek, Uwe Mueller, Manfred S Weiss
Prolidase is a ubiquitously distributed dipeptidase and the only dipeptidase in humans capable of cleaving the peptide bond preceding the amino acids proline (Pro) or hydroxyproline (Hyp). It is mainly implicated in the degradation of dietary and endogenous proteins. It is also involved in the terminal steps of collagen catabolism by hydrolyzing Pro and Hyp-containing dipeptides. Finally, it is believed to play a role in the regulation of peptidic hormones. Diminished or absent prolidase activity is related to a rare autosomal disease, referred to as prolidase deficiency (PD)...
July 4, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28676723/analysis-of-reactive-oxygen-and-nitrogen-species-generated-in-three-liquid-media-by-low-temperature-helium-plasma-jet
#11
Julie Chauvin, Florian Judée, Mohammed Yousfi, Patricia Vicendo, Nofel Merbahi
In order to identify aqueous species formed in Plasma activated media (PAM), quantitative investigations of reactive oxygen and nitrogen species (ROS, RNS) were performed and compared to Milli-Q water and culture media without and with Fetal Calf Serum. Electron paramagnetic resonance, fluorometric and colorimetric analysis were used to identify and quantify free radicals generated by helium plasma jet in these liquids. Results clearly show the formation of ROS such as hydroxyl radical, superoxide anion radical and singlet oxygen in order of the micromolar range of concentrations...
July 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28655155/evolution-of-cytochrome-c-oxidase-in-hypoxia-tolerant-sculpins-cottidae-actinopterygii
#12
Gigi Y Lau, Milica Mandic, Jeffrey G Richards
Vertebrate hypoxia tolerance can emerge from modifications to the oxygen (O2) transport cascade, but whether there is adaptive variation to O2 binding at the terminus of this cascade, mitochondrial cytochrome c oxidase (COX), is not known. In order to address the hypothesis that hypoxia tolerance is associated with enhanced O2 binding by mitochondria we undertook a comparative analysis of COX O2 kinetics across species of intertidal sculpins (Cottidae, Actinopterygii) that vary in hypoxia tolerance. Our analysis revealed a significant relationship between hypoxia tolerance (critical O2 tension of O2 consumption rate; Pcrit), mitochondrial O2 binding affinity (O2 tension at which mitochondrial respiration was half maximal; P50), and COX O2-binding affinity (apparent Michaelis-Menten constant for O2 binding to COX; Km,app O2)...
June 24, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28646115/genome-analysis-of-endomicrobium-proavitum-suggests-loss-and-gain-of-relevant-functions-during-the-evolution-of-intracellular-symbionts
#13
Hao Zheng, Carsten Dietrich, Andreas Brune
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates...
June 23, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28643343/alpha-beta-hydrolases-a-unique-structural-motif-coordinates-catalytic-acid-residue-in-40-protein-fold-families
#14
Polytimi S Dimitriou, Alexander Denesyuk, Seiji Takahashi, Satoshi Yamashita, Mark S Johnson, Toru Nakayama, Konstantin Denessiouk
The alpha/beta-hydrolases (ABH) are a family of acid-base-nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28636317/downsizing-proto-oncogene-cfos-to-short-helix-constrained-peptides-that-bind-jun
#15
Daniel Baxter, Samuel R Perry, Timothy A Hill, W Mei Kok, Nathan R Zaccai, R Leo Brady, David P Fairlie, Jody M Mason
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components...
June 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28627455/gemcitabine-vitamin-e-conjugates-synthesis-characterization-entrapment-into-nanoemulsions-and-in-vitro-deamination-and-antitumor-activity
#16
Ahmed Abu-Fayyad, Sami Nazzal
Gemcitabine is the first line therapy for pancreatic cancer. It is, however, extensively metabolized to the inactive form by deamination enzymatic reaction. Conjugation of gemcitabine with fatty acids on its 4-amino group was found to protect it from deamination deactivation reaction. The objective of the present study was to test the in-vitro anticancer activity of gemcitabine conjugated to the γ-tocotrienol isomer of vitamin E against pancreatic tumor cells. This objective was based on reported studies in which it was demonstrated that free tocotrienol isomers of vitamin E can potentiate the anticancer activity of gemcitabine...
June 13, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28611396/coupling-neutron-reflectivity-with-cell-free-protein-synthesis-to-probe-membrane-protein-structure-in-supported-bilayers
#17
Thomas Soranzo, Donald K Martin, Jean-Luc Lenormand, Erik B Watkins
The structure of the p7 viroporin, an oligomeric membrane protein ion channel involved in the assembly and release of the hepatitis C virus, was determined from proteins expressed and inserted directly into supported model lipid membranes using cell-free protein expression. Cell-free protein expression allowed (i ) high protein concentration in the membrane, (ii ) control of the protein's isotopic constitution, and (iii ) control over the lipid environment available to the protein. Here, we used cell-free protein synthesis to directly incorporate the hepatitis C virus (HCV) p7 protein into supported lipid bilayers formed from physiologically relevant lipids (POPC or asolectin) for both direct structural measurements using neutron reflectivity (NR) and conductance measurements using electrical impedance spectroscopy (EIS)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607419/two-step-atp-driven-opening-of-cohesin-head
#18
Íñigo Marcos-Alcalde, Jesús I Mendieta-Moreno, Beatriz Puisac, María Concepción Gil-Rodríguez, María Hernández-Marcos, Diego Soler-Polo, Feliciano J Ramos, José Ortega, Juan Pié, Jesús Mendieta, Paulino Gómez-Puertas
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606519/folate-conjugated-thermosensitive-o-maleoyl-modified-chitosan-micellar-nanoparticles-for-targeted-delivery-of-erlotinib
#19
Marziyeh Fathi, Parham Sahandi Zangabad, Ayuob Aghanejad, Jaleh Barar, Hamid Erfan-Niya, Yadollah Omidi
In the present work, new self-assembled nanoparticles (NPs) were engineered using biocompatible and biodegradable natural polymer, chitosan (CS). The complexation of CS with sodium dodecyl sulfate (SDS) facilitated the regioselective chemical modification of CS hydroxyl groups with maleic anhydride, and produced polymerizable precursor of CS that was further grafted with N-isopropylacrylamide (NIPAAm) as temperature-sensitive moiety and oleic acid (OA) as hydrophobic monomer. After removal of SDS complex, the free amino groups were functionalized with folic acid (FA) to form folate-(PNIPAAm-co-OA)-g-CS micellar NPs...
September 15, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28596363/polymeric-peptide-pigments-with-sequence-encoded-properties
#20
Ayala Lampel, Scott A McPhee, Hang-Ah Park, Gary G Scott, Sunita Humagain, Doeke R Hekstra, Barney Yoo, Pim W J M Frederix, Tai-De Li, Rinat R Abzalimov, Steven G Greenbaum, Tell Tuttle, Chunhua Hu, Christopher J Bettinger, Rein V Ulijn
Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence...
June 9, 2017: Science
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