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Free form amino acids

P Petkov, R Marinova, V Kochev, N Ilieva, E Lilkova, L Litov
Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defence against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defence mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
Denis Warshan, Anton Liaimer, Eric Pederson, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Bjørn Altermark, Katharina Pawlowski, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history...
March 15, 2018: Molecular Biology and Evolution
Yu-Hao Chu, Yuan Li, Yu-Tang Wang, Bin Li, Ying-Hua Zhang
Organophosphorus pesticides (OPPs) are widely used in agricultural production but cause serious pollution. Alkaline phosphatase (ALP) has been implemented to enhance the degradation of OPPs. Deciphering the structural and energetic determinants of OPPs-ALP interaction harbors the potential to understand key biodegradation processes of pesticides at the molecular level. With this aim, the binding modes of OPPs and ALP were studied using computational methods as molecular docking.The CASTp server was used to predict the active site residues...
July 15, 2018: Food Chemistry
Renyu Zhang, Michelle J Yoo, Jessica Gathercole, Mariza Gomes Reis, Mustafa M Farouk
Bresaola made from New Zealand mutton and lamb, were compared in quality attributes. Mutton bresaola had slightly lower protein and higher moisture contents, and similar amount of intramuscular fat and instrumental colour compared to that of the lamb. 36 and 80 unique endogenous peptides were observed in mutton and lamb, respectively. Proteolysis during dry-curing was affected by the age of the animal and has resulted in softer and easier to chew textural properties to the mutton bresaola. Significantly higher amounts of total free amino acids and higher proportion of essential amino acids were detected in the mutton bresaola from digestion simulation compared to that from lamb...
July 15, 2018: Food Chemistry
Noorakmar Jusoh, Hasanuddin Zainal, Azzmer Azzar Abdul Hamid, Noraslinda M Bunnori, Khairul Bariyyah Abd Halim, Shafida Abd Hamid
Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites...
March 15, 2018: Journal of Molecular Modeling
Prakash Chandra, Alain M Jonas, Antony E Fernandes
Confinement and cooperativity are important design principles used by Nature to optimize catalytic activity in enzymes. In these biological systems, the precise sequence of the protein encodes for specific chain folding to preorganize critical amino acid side chains within defined binding pockets, allowing to express and trigger synergistic catalytic activation pathways. Here we show that short synthetic precision oligomers with the optimal sequence of catalytic units, spatially arranged by dense surface grafting to form confined cooperative "pockets", display an up to 5-fold activity improvement compared to a "mismatched" sequence or free oligomers using the (pyta)Cu/TEMPO/NMI-catalyzed aerobic selective oxidation of alcohols as a model reaction...
March 15, 2018: Journal of the American Chemical Society
Jaya Kumar, Srijit Das, Seong Lin Teoh
Acrylamide (AA) is a water soluble white crystalline solid commonly used in industries. It was listed as an industrial chemical with potential carcinogenic properties. However to date, AA was used to produce polyacrylamide polymer, which was widely used as a coagulant in water treatment; additives during papermaking; grouting material for dams, tunnels, and other underground building constructions. AA in food could be formed during high-temperature cooking via several mechanisms, i.e., formation via acrylic acid which may be derived from the degradation of lipid, carbohydrates, or free amino acids; formation via the dehydration/decarboxylation of organic acids (malic acid, lactic acid, and citric acid); and direct formation from amino acids...
2018: Frontiers in Nutrition
Dohyun Im, Daisuke Matsui, Takatoshi Arakawa, Kimiyasu Isobe, Yasuhisa Asano, Shinya Fushinobu
l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition...
March 2018: FEBS Open Bio
Georgia C Boles, Randy L Hightower, Rebecca A Coates, Christopher P McNary, Giel Berden, Jos Oomens, Peter B Armentrout
Complexes of aspartic acid (Asp) cationized with Zn2+: Zn(Asp H)+, Zn(Asp H)+(ACN) where ACN = acetonitrile, and Zn(Asp H)+(Asp), as well as with Cd2+, CdCl+(Asp), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. A series of low-energy conformers for each complex was found using quantum chemical calculations in order to identify the structures formed experimentally. The main binding motif observed for the heavy metal complex, CdCl+(Asp)[N,CO,COs], is a charge solvated, tridentate structure where the metal center binds to the backbone amino group and carbonyl oxygens of the backbone and side-chain carboxylic acids...
March 4, 2018: Journal of Physical Chemistry. B
Guang Huang, Ping Jiang, Lindsay K Jmaiff Blackstock, Dayong Tian, Xing-Fang Li
Iodinated disinfection byproducts (I-DBPs) are highly toxic, but few precursors of I-DBPs have been investigated. Tyrosine containing biomolecules are ubiquitous in surface water. Here we investigated the formation of I-DBPs from the chloramination of seven tyrosyl dipeptides (i.e., tyrosylglycine, tyrosylalanine, tyrosylvaline, tyrosylhistidine, tyrosylglutamine, tyrosylglutamic acid, and tyrosylphenylalanine) in the presence of potassium iodide. High resolution mass spectrometry (HRMS) and tandem mass spectrometry (MS/MS) analyses of the benchtop reaction solutions found all seven precursors formed both I- and Cl- substituted tyrosyl dipeptide products...
February 28, 2018: Environmental Science & Technology
Ahmed A Abd-Rabou, Dhruba J Bharali, Shaker A Mousa
PURPOSE: Breast cancer is the second most common cause of mortality in women in the United States. Targeted delivery of antitumor breast cancer drugs as a drug-delivery strategy may allow direct delivery into the tumor. Currently, chemotherapy is one of the principle strategies for cancer treatment, but it can have toxic side effects. Nanotechnology attempts to resolve these challenges by loading drugs in nanoparticles, such as solid lipid nanoparticles (SLN). In response to the breast cancer drug 5-fluorouracil (5-FU), p38MAPK signaling has been investigated since the 1990s...
February 27, 2018: Pharmaceutical Research
Attia Anwar, Provvidenza Maria Abruzzo, Sabah Pasha, Kashif Rajpoot, Alessandra Bolotta, Alessandro Ghezzo, Marina Marini, Annio Posar, Paola Visconti, Paul J Thornalley, Naila Rabbani
Background: Clinical chemistry tests for autism spectrum disorder (ASD) are currently unavailable. The aim of this study was to explore the diagnostic utility of proteotoxic biomarkers in plasma and urine, plasma protein glycation, oxidation, and nitration adducts, and related glycated, oxidized, and nitrated amino acids (free adducts), for the clinical diagnosis of ASD. Methods: Thirty-eight children with ASD (29 male, 9 female; age 7.6 ± 2.0 years) and 31 age-matched healthy controls (23 males, 8 females; 8...
2018: Molecular Autism
Sihui Liang, Hanh Lan Tran, Lilian Were
Lowering of greening formed from oxidized chlorogenic acid (CGA) and amino groups, and favoured at alkaline pH, was investigated using acidic ingredients (sour cream, buttermilk, yoghurt, and honey) in sunflower butter cookies. Cookies with maple syrup added were used as a positive control. Changes in greening intensity, greening reactants (total phenols, CGA, protein), antioxidant capacity, tryptophan and Schiff base fluorescence were measured. Percentage greening, pH and aw of cookies followed the same order: maple syrup > sour cream ≥ buttermilk > yoghurt > honey...
June 30, 2018: Food Chemistry
Naila Rabbani, Paul J Thornalley
Advanced glycation end products (AGEs) are stable posttranslational modifications of proteins formed by the spontaneous reaction with glucose and related metabolites. Important AGEs quantitatively are methylglyoxal (MG)-derived hydroimidazolone MG-H1, Nε -carboxymethyl-lysine (CML), and glucosepane. They contribute to the development of chronic kidney disease (CKD). Cellular proteolysis of AGE-modified proteins forms AGE free adducts, glycated amino acids, which are cleared by the kidneys and excreted in urine...
February 22, 2018: Kidney International
João César N Santos, Isabella M da Silva, Taniris C Braga, Ângelo de Fátima, Isis M Figueiredo, Josué Carinhanha Caldas Santos
The interaction between bovine serum albumin (BSA) and thimerosal (TM), an organomercury compound widely employed as a preservative in vaccines, was investigated simulating physiological conditions and using different spectroscopic techniques. The results, employing molecular fluorescence showed the interaction occurs by static quenching through electrostatic forces (ΔH < 0 and ΔS > 0), spontaneously (ΔG = -4.40 kJ mol-1 ) and with a binding constant of 3.24 × 103  M-1 . Three-dimensional fluorescence studies indicated that TM causes structural changes in the polypeptide chain of the BSA, confirmed by circular dichroism that showed an increase in α-helix (from 43...
February 21, 2018: International Journal of Biological Macromolecules
Takayoshi Matsuda, Takuhiro Ito, Chie Takemoto, Kazushige Katsura, Mariko Ikeda, Motoaki Wakiyama, Mutsuko Kukimoto-Niino, Shigeyuki Yokoyama, Yoshikazu Kurosawa, Mikako Shirouzu
Growing numbers of therapeutic antibodies offer excellent treatment strategies for many diseases. Elucidation of the interaction between a potential therapeutic antibody and its target protein by structural analysis reveals the mechanism of action and offers useful information for developing rational antibody designs for improved affinity. Here, we developed a rapid, high-yield cell-free system using dialysis mode to synthesize antibody fragments for the structural analysis of antibody-antigen complexes. Optimal synthesis conditions of fragments (Fv and Fab) of the anti-EGFR antibody 059-152 were rapidly determined in a day by using a 30-μl-scale unit...
2018: PloS One
Shengwei Zhang, Qi Cheng, Chenxi Luo, Lei Yin, Yali Qin, Mingzhou Chen
The phosphoprotein (P) of human parainfluenza virus type 3 (HPIV3) plays a pivotal role in viral RNA synthesis, which interacts with the nucleoprotein (N) to form a soluble N0 -P complex (N0 , free of RNAs) to prevent the nonspecific RNA binding and illegitimate aggregation of N. Functional regions within P have been studied intensively. However, the precise site (s) within P directly involved in N0 -P interaction still remains unclear. In this study, using a series of deleted and truncated mutants of P of HPIV3, we demonstrate that amino-terminal 40 amino acids (aa) of P restrict and regulate N0 -P interaction...
February 15, 2018: Virology
Timothy H Bertram, Richard E Cochran, Vicki H Grassian, Elizabeth A Stone
Sea spray aerosol particles (SSA), formed through wave breaking at the ocean surface, contribute to natural aerosol particle concentrations in remote regions of Earth's atmosphere, and alter the direct and indirect effects of aerosol particles on Earth's radiation budget. In addition, sea spray aerosol serves as suspended surface area that can catalyze trace gas reactions. It has been shown repeatedly that sea spray aerosol is heavily enriched in organic material compared to the surface ocean. The selective enrichment of organic material complicates the selection of representative molecular mimics of SSA for laboratory or computational studies...
February 16, 2018: Chemical Society Reviews
Yoann Cote, Patrice Delarue, Harold A Scheraga, Patrick Senet, Gia G Maisuradze
α-Synuclein (αS) is a major constituent of Lewy bodies, the insoluble aggregates that are the hallmark of one of the most prevalent neurodegenerative disorders, Parkinson's disease (PD). The vast majority of experiments in vitro and in vivo provide extensive evidence that a disordered monomeric form is the predominant state of αS in water solution, and it undergoes a large-scale disorder-to-helix transition upon binding to vesicles of different types. Recently, another form, tetrameric, of αS with a stable helical structure was identified experimentally...
February 26, 2018: ACS Chemical Neuroscience
Anna Ciarkowska, Maciej Ostrowski, Anna Jakubowska
Indole-3-acetic acid (IAA) conjugation is one of mechanisms responsible for regulation of free auxin levels in plants. A new member of the serine carboxypeptidase-like (SCPL) acyltransferases family from Oryza sativa has been cloned and characterized. 1-O-indole-3-acetyl-β-D-glucose (1-O-IAGlc): myo-inositol acyltransferase (IAInos synthase) is an enzyme of IAA ester conjugates biosynthesis pathway that catalyzes transfer of IAA moiety from 1-O-IAGlc to myo-inositol forming IA-myo-inositol (IAInos). The OsIAA-At cDNA has been cloned and expressed using yeast and bacterial expression systems...
February 9, 2018: Plant Physiology and Biochemistry: PPB
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