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https://www.readbyqxmd.com/read/29138501/targeting-sxip-eb1-interaction-an-integrated-approach-to-the-discovery-of-small-molecule-modulators-of-dynamic-binding-sites
#1
T B Almeida, A J Carnell, I L Barsukov, N G Berry
End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule (MT) growing ends, which has a fundamental role in MT polymerisation. EB1 is an important protein target as it is involved in regulating MT dynamic behaviour, and has been associated with several disease states, such as cancer and neuronal diseases. Diverse EB1 binding partners are recognised through a conserved four amino acid motif, (serine-X-isoleucine-proline) which exists within an intrinsically disordered region...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29131604/from-zn-ii-carboxylate-to-double-walled-zn-ii-carboxylato-phosphate-mof-change-in-the-framework-topology-capture-and-conversion-of-co2-and-catalysis-of-strecker-reaction
#2
Mayank Gupta, Dinesh De, Kapil Tomar, Parimal K Bharadwaj
The ligand H2L has been built by linking an imidazole moiety to the 5-position of isophthalic acid. It forms two types of porous frameworks, {[Zn(L)]·2DMF·2H2O}n (1) and {[(CH3)2NH2][Zn2(L)(H2O)PO4]·2DMF}n (2). 1 is a porous neutral framework and has rtl rutile 3,6-conn topology, while 2 is an organo-metallophosphate anionic porous framework with double-walled hexagonal channels. Framework 1' (desolvated) exhibits moderate CO2 adsorption (58 cc g(-1) at 273 K, 1 bar), whereas 2' (desolvated) shows a microporous nature with a high adsorption of CO2 (111...
November 13, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29130419/recapitulation-of-native-dermal-tissue-in-a-full-thickness-human-skin-model-using-human-collagens
#3
Arnout Mieremet, Marion Rietveld, Rianne van Dijk, Joke A Bouwstra, Abdoelwaheb El Ghalbzouri
OBJECTIVE: Full thickness skin models are comprised of a three dimensional dermal equivalent based on an animal derived collagen matrix that harbours fibroblasts and an epidermal equivalent formed by keratinocytes. The functionality of both equivalents is influenced by many factors, including extracellular matrix composition and resident cell type. Animal-derived collagens differ in amino acid composition and physico-chemical properties from human collagens. This composition could alter the functionality of the dermal equivalent and epidermal morphogenesis with the barrier formation in full thickness models (FTMs)...
November 12, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/29126984/osteopontin-as-a-novel-substrate-for-the-proprotein-convertase-5-6-pcsk5-in-bone
#4
Betty Hoac, Delia Susan-Resiga, Rachid Essalmani, Edwige Marcinkiweicz, Nabil G Seidah, Marc D McKee
Seven proprotein convertases cleave the basic amino acid consensus sequence K/R-Xn-K/R↓ (where n=0, 2, 4 or 6 variable amino acids) to activate precursor proteins. Despite similarities in substrate specificity, basic amino acid-specific proprotein convertases have a distinct tissue distribution allowing for enzymatic actions on tissue-resident substrates. Proprotein convertase 5/6 (PC5/6) has two splice variants - soluble PC5/6A and membrane-bound PC5/6B - and is expressed during mouse development in many tissues including bone and tooth, but little is known about the substrates for PC5/6 therein...
November 7, 2017: Bone
https://www.readbyqxmd.com/read/29096508/links-between-the-charge-model-and-bonded-parameter-force-constants-in-biomolecular-force-fields
#5
David S Cerutti, Karl T Debiec, David A Case, Lillian T Chong
The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model...
October 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29089759/in-vitro-and-in-vivo-protein-release-and-anti-ischemia-reperfusion-injury-properties-of-bone-morphogenetic-protein-2-loaded-glycyrrhetinic-acid-poly-ethylene-glycol-b-poly-l-lysine-nanoparticles
#6
Fang Shan, YuJuan Liu, Haiying Jiang, Fei Tong
Here, we describe a bone morphogenetic protein-2 (BMP-2) nanocarrier based on glycyrrhetinic acid (GA)-poly(ethylene glycol) (PEG)-b-poly(l-lysine) (PLL). A protein nanocarrier was synthesized, characterized and evaluated as a BMP-2 delivery system. The designed nanocarrier was synthesized based on the ring-opening polymerization of amino acid N-carboxyanhydride. The final product was measured with (1)H nuclear magnetic resonance. GA-PEG-b-PLL nanocarrier could combine with BMP-2 through electrostatic interaction to form polyion complex (PIC) micelles...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29065265/energetics-of-glutamate-binding-to-an-ionotropic-glutamate-receptor
#7
Alvin Yu, Albert Y Lau
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are responsible for the majority of excitatory transmission at the synaptic cleft. Mechanically speaking, agonist binding to the ligand binding domain (LBD) activates the receptor by triggering a conformational change that is transmitted to the transmembrane region, opening the ion channel pore. We use fully atomistic molecular dynamics simulations to investigate the binding process in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, an iGluR subtype...
November 9, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29062311/production-of-high-amounts-of-hepatotoxin-nodularin-and-new-protease-inhibitors-pseudospumigins-by-the-brazilian-benthic-nostoc-sp-cena543
#8
Jouni Jokela, Lassi M P Heinilä, Tânia K Shishido, Matti Wahlsten, David P Fewer, Marli F Fiore, Hao Wang, Esa Haapaniemi, Perttu Permi, Kaarina Sivonen
Nostoc is a cyanobacterial genus, common in soils and a prolific producer of natural products. This research project aimed to explore and characterize Brazilian cyanobacteria for new bioactive compounds. Here we report the production of hepatotoxins and new protease inhibitors from benthic Nostoc sp. CENA543 isolated from a small, shallow, saline-alkaline lake in the Nhecolândia, Pantanal wetland area in Brazil. Nostoc sp. CENA543 produces exceptionally high amounts of nodularin-R. This is the first free-living Nostoc that produces nodularin at comparable levels as the toxic, bloom-forming, Nodularia spumigena...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29061807/molecular-interactions-of-carcinogenic-aromatic-amines-4-aminobiphenyl-and-4-4-diaminobiphenyl-with-lactoperoxidase-insight-to-breast-cancer
#9
Ishfaq Ahmad Sheikh, Mohd Amin Beg, Muhammad Yasir
BACKGROUND/AIM: Lactoperoxidase (LPO) is an antimicrobial protein present in milk, saliva, gastric secretions, tears and upper respiratory tract secretions. LPO constitutes an important enzyme of the human immune defense system. However, LPO has also been suggested to be involved in breast cancer etiology through production of reactive free radicals and activation of carcinogenic aromatic compounds. Aromatic compounds are generally highly lipophilic and thus accumulate in highly fatty breast tissues...
November 2017: Anticancer Research
https://www.readbyqxmd.com/read/29059579/metabolic-solutions-to-the-biosynthesis-of-some-diaminomonocarboxylic-acids-in-nature-formation-in-cyanobacteria-of-the-neurotoxins-3-n-methyl-2-3-diaminopropanoic-acid-bmaa-and-2-4-diaminobutanoic-acid-2-4-dab
#10
REVIEW
Peter B Nunn, Geoffrey A Codd
The non-encoded diaminomonocarboxylic acids, 3-N-methyl-2,3-diaminopropanoic acid (syn: α-amino-β-methylaminopropionic acid, MeDAP; β-N-methylaminoalanine, BMAA) and 2,4-diaminobutanoic acid (2,4-DAB), are distributed widely in cyanobacterial species in free and bound forms. Both amino acids are neurotoxic in whole animal and cell-based bioassays. The biosynthetic pathway to 2,4-DAB is well documented in bacteria and in one higher plant species, but has not been confirmed in cyanobacteria. The biosynthetic pathway to BMAA is unknown...
October 20, 2017: Phytochemistry
https://www.readbyqxmd.com/read/29050977/prophylactic-role-of-taurine-and-its-derivatives-against-diabetes-mellitus-and-its-related-complications
#11
REVIEW
Poulami Sarkar, Priyanka Basak, Sumit Ghosh, Mousumi Kundu, Parames C Sil
Taurine is a conditionally essential amino acid present in the body in free form. Mammalian taurine is synthesized in the pancreas via the cysteine sulfinic acid pathway. Anti-oxidation and anti-inflammation are two main properties through which it exerts its therapeutic effects. Many studies have shown its excellent therapeutic potential against diabetes mellitus and related complications like diabetic neuropathy, retinopathy, nephropathy, hematological dysfunctions, reproductive dysfunctions, liver and pancreas related complications etc...
October 16, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29046620/the-dental-calculus-metabolome-in-modern-and-historic-samples
#12
Irina M Velsko, Katherine A Overmyer, Camilla Speller, Lauren Klaus, Matthew J Collins, Louise Loe, Laurent A F Frantz, Krithivasan Sankaranarayanan, Cecil M Lewis, Juan Bautista Rodriguez Martinez, Eros Chaves, Joshua J Coon, Greger Larson, Christina Warinner
INTRODUCTION: Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29040803/synthesis-and-characterization-of-fatty-acid-grafted-chitosan-polymer-and-their-nanomicelles-for-nonviral-gene-delivery-applications
#13
Divya Sharma, Jagdish Singh
The aim of this study was to synthesize and characterize fatty acid-grafted-chitosan (fatty acid-g-CS) polymer and their nanomicelles for use as carriers for gene delivery. CS was hydrophobically modified using saturated fatty acids of increasing fatty acyl chain length. Carbodiimide along with N-hydroxysuccinimide was used for coupling carboxyl group of fatty acids with amine groups of CS. Proton nuclear magnetic resonance and Fourier transform infrared spectroscopy were used to quantify fatty acyl substitution onto CS backbone...
October 23, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29037698/rapid-and-sensitive-detection-of-free-fatty-acids-in-edible-oils-based-on-chemical-derivatization-coupled-with-electrospray-ionization-tandem-mass-spectrometry
#14
Ming Liu, Fang Wei, Xin Lv, Xu-Yan Dong, Hong Chen
In this study, a strategy based on chemical derivatization coupled with electrospray ionizationtandem quadrupole mass spectrometry (ESI-MS/MS) for rapid and sensitive detection of FFAs in edible oils was developed. A derivative reagent (N,N-diethyl-1,2-ethanediamine, DEEA) was employed to selectively label carboxyl groups of FFAs to form an amino compound with a tertiary amino group. The DEEA derivative products could lose a characteristic neutral loss fragment of 73Da in collision-induced dissociation (CID), which enabled to discriminate and analyze the DEEA derived FFAs with neutral loss scan (NLS 73Da)under the positive ion mode of mass spectrometry...
March 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29037139/analysis-of-free-amino-acids-in-mammalian-brain-extracts
#15
A L Ksenofontov, A I Boyko, G V Mkrtchyan, V N Tashlitsky, A V Timofeeva, A V Graf, V I Bunik, L A Baratova
An optimized method for analysis of free amino acids using a modified lithium-citrate buffer system with a Hitachi L-8800 amino acid analyzer is described. It demonstrates clear advantages over the sodium-citrate buffer system commonly used for the analysis of protein hydrolysates. A sample pretreatment technique for amino acid analysis of brain extracts is also discussed. The focus has been placed on the possibility of quantitative determination of the reduced form of glutathione (GSH) with simultaneous analysis of all other amino acids in brain extracts...
October 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29019072/mass-spectrometry-based-metabolomics-to-identify-taurine-modified-metabolites-in-heart
#16
Takashi Ito, Koei Okazaki, Daisuke Nakajima, Daisuke Shibata, Shigeru Murakami, Stephen Schaffer
Taurine is an abundant beta-amino acid found in high concentration in mammalian tissues. Taurine possesses many beneficial functions in mammalian cells. There are also a variety of taurine-conjugated products formed between taurine and bile acids, fatty acids, chloramine, mitochondrial tRNA, etc., and some of these have been identified as functional compounds. In the present study, we identified taurine-conjugated metabolites using LC-MS-based metabolome analysis of heart extracts prepared from hearts of wild-type and taurine transporter-knockout (TauTKO) mice, the latter being severely taurine deficient...
October 10, 2017: Amino Acids
https://www.readbyqxmd.com/read/28975780/role-of-urea-aromatic-stacking-interactions-in-stabilizing-the-aromatic-residues-of-the-protein-in-urea-induced-denatured-state
#17
Siddharth Goyal, Aditya Chattopadhyay, Koushik Kasavajhala, U Deva Priyakumar
A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states. Experiments use thermal, chemical, or mechanical stress to perturb the folding equilibrium for examining protein stability and the protein folding process. Elucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explores the nature of urea-aromatic interactions relevant in urea-assisted protein denaturation. Free energy profiles corresponding to the unfolding of Trp-cage miniprotein in the presence and absence of urea at three different temperatures demonstrate the distortion of the hydrophobic core to be a crucial step...
October 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28974575/insights-into-the-roles-of-non-catalytic-residues-in-the-active-site-of-a-gh10-xylanase-with-activity-on-cellulose
#18
Yindi Chu, Tao Tu, Leena Penttinen, Xianli Xue, Xiaoyu Wang, Zhuolin Yi, Li Gong, Juha Rouvinen, Huiying Luo, Nina Hakulinen, Bin Yao, Xiaoyun Su
Bifunctional glycoside hydrolases have potential for cost saving in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme CbXyn10C/Cel48B from Caldicellulosiruptor bescii, is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of CbXyn10C would have at least six sugar binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cellooligosaccharides...
October 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28970921/near-uv-visible-electronic-absorption-originating-from-charged-amino-acids-in-a-monomeric-protein
#19
Saumya Prasad, Imon Mandal, Shubham Singh, Ashim Paul, Bhubaneswar Mandal, Ravindra Venkatramani, Rajaram Swaminathan
Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185-320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M(-1) cm(-1)] and 800 nm [ε = 501 M(-1) cm(-1)] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids...
August 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28970891/elucidating-the-3d-structures-of-al-iii-a%C3%AE-complexes-a-template-free-strategy-based-on-the-pre-organization-hypothesis
#20
Jon I Mujika, Jaime Rodríguez-Guerra Pedregal, Xabier Lopez, Jesus M Ugalde, Luis Rodríguez-Santiago, Mariona Sodupe, Jean-Didier Maréchal
Senile plaques are extracellular deposits found in patients with Alzheimer's Disease (AD) and are mainly formed by insoluble fibrils of β-amyloid (Aβ) peptides. The mechanistic details about how AD develops are not fully understood yet, but metals such as Cu, Zn, or Fe are proposed to have a non-innocent role. Many studies have also linked the non biological metal aluminum with AD, a species whose concentration in the environment and food has been constantly increasing since the industrial revolution. Gaining a molecular picture of how Al(iii) interacts with an Aβ peptide is of fundamental interest to improve understanding of the many variables in the evolution of AD...
July 1, 2017: Chemical Science
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