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Joseph R Sachleben, Aashish N Adhikari, Grzegorz Gawlak, Robert J Hoey, Gaohua Liu, Andrzej Joachimiak, Gaetano T Montelione, Tobin R Sosnick, Shohei Koide
We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus. The unusual sequence of this protein has a tryptophan content 5 times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet with a novel fold that we have termed an Aromatic Claw...
October 17, 2016: Protein Science: a Publication of the Protein Society
Maximiliano L Agazzi, M Belén Ballatore, Eugenia Reynoso, Ezequiel D Quiroga, Edgardo N Durantini
Two cationic BODIPYs 3 and 4 were synthesized by acid-catalyzed condensation of the corresponding pyrrole and benzaldehyde, followed by complexation with boron and methylation. Compound 3 contains methyl at the 1,3,5 and 7 positions of the s-indacene ring and a N,N,N-trimethylamino group attached to the phenylene unit, while 4 is not substituted by methyl groups and the cationic group is bound by an aliphatic spacer. UV-visible absorption spectra of these BODIPYs show an intense band at ∼500 nm in solvents of different polarities and n-heptane/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/water reverse micelles...
October 3, 2016: European Journal of Medicinal Chemistry
Luisa Matos Do Canto, Catalin Marian, Rency S Varghese, Jaeil Ahn, Patricia A Da Cunha, Shawna Willey, Mary Sidawy, Janice D Rone, Amrita K Cheema, George Luta, Mohammad R Nezami Ranjbar, Habtom W Ressom, Bassem R Haddad
Identification of new biomarkers for breast cancer remains critical in order to enhance early detection of the disease and improve its prognosis. Towards this end, we performed an untargeted metabolomic analysis of breast ductal fluid using an ultra-performance liquid chromatography coupled with a quadrupole time-of-light (UPLC-QTOF) mass spectrometer. We investigated the metabolomic profiles of breast tumors using ductal fluid samples collected by ductal lavage (DL). We studied fluid from both the affected breasts and the unaffected contralateral breasts (as controls) from 43 women with confirmed unilateral breast cancer...
October 13, 2016: International Journal of Oncology
Heike Hevekerl, Johan Tornmalm, Jerker Widengren
Tryptophan fluorescence is extensively used for label-free protein characterization. Here, we show that by analyzing how the average tryptophan fluorescence intensity varies with excitation modulation, kinetics of tryptophan dark transient states can be determined in a simple, robust and reliable manner. Thereby, highly environment-, protein conformation- and interaction-sensitive information can be recorded, inaccessible via traditional protein fluorescence readouts. For verification, tryptophan transient state kinetics were determined under different environmental conditions, and compared to literature data...
October 17, 2016: Scientific Reports
Inseyah Bagasrawala, Nada Zecevic, Nevena V Radonjić
Kynurenic acid (KYNA), a neuroactive metabolite of tryptophan degradation, acts as an endogenous N-methyl-D-aspartate receptor (NMDAR) antagonist. Elevated levels of KYNA have been observed in pregnant women after viral infections and are considered to play a role in neurodevelopmental disorders. However, the consequences of KYNA-induced NMDAR blockade in human cortical development still remain elusive. To study the potential impact of KYNA on human neurodevelopment, we used an in vitro system of multipotent cortical progenitors, i...
2016: Frontiers in Neuroscience
Bo Sun, Xubin Wang, Ruili Cao, Qi Zhang, Qiao Liu, Meifeng Xu, Ming Zhang, Xiangbo Du, Fangting Dong, Xianzhong Yan
ETHNOPHARMACOLOGICAL RELEVANCE: Fuzi, the processed lateral root of Aconitum carmichaelii Debeaux, is a traditional Chinese medicine used for its analgesic, antipyretic, anti-rheumatoid arthritis and anti-inflammation effects; however, it is also well known for its toxicity. Gancao, the root of Glycyrrhiza uralensis Fisch., is often used concurrently with Fuzi to alleviate its toxicity. However, the mechanism of detoxication is still not well clear. AIM OF THE STUDY: In this study, the effect of Gancao on the metabolic changes induced by Fuzi was investigated by NMR-based metabonomic approaches...
October 13, 2016: Journal of Ethnopharmacology
Naoya Fukui, Kiho Araki, Kunihiro Hongo, Tomohiro Mizobata, Yasushi Kawata
The isolated apical domain of the E. coli GroEL subunit displays the ability to suppress the irreversible fibrillation of numerous amyloid-forming polypeptides. In previous experiments, we have shown that mutating Gly192 (located at hinge II that connects the apical domain and the intermediate domain) to a tryptophan results in an inactive chaperonin whose apical domain is disoriented. In this study, we have utilized this disruptive effect of Gly192 mutation to our advantage, by substituting this residue with amino acid residues of varying Van der Waals volumes with the intent to modulate the affinity of GroEL toward fibrillogenic peptides...
October 14, 2016: Journal of Biological Chemistry
Shrestha Priyadarsini, Tina B McKay, Akhee Sarker-Nag, Jeremy Allegood, Charles Chalfant, Jian-Xing Ma, Dimitrios Karamichos
Prolonged hyperglycemia during diabetes mellitus can cause severe ophthalmic complications affecting both the anterior and posterior ocular segments leading to impaired vision or blindness. Diabetes-induced corneal pathologies are associated with decreased wound healing capacity, corneal edema, and altered epithelial basement membrane. The mechanism by which diabetes modulates structure and function within the corneal stroma are unknown. In our study, we characterized the effects of diabetes on extracellular matrix, lipid transport, and cellular metabolism by defining the entire metabolome and lipidome of Type 1 and Type 2 human diabetic corneal stroma...
October 11, 2016: Experimental Eye Research
B Barman, M Lyngdoh, K G Lynrah, S B Warjri
The purple urine bag syndrome (PUBS) i.e. purple discolouration of urine, is an uncommon and alarming condition in patients with long term urinary catheterisation. Though the condition is benign, it should draw immediate attention to the possibility of an underlying urinary tract infection. The postulated hypothesis for this unusual event is probably a chemical reaction involving tryptophan from food in the gut. We report a case with this unusual and interesting phenomenon in a 65 year old female.
June 2016: Journal of the Association of Physicians of India
Andrea von Zadow, Elisabeth Ignatz, Richard Pokorny, Lars-Oliver Essen, Gabriele Klug
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers (CPD) or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions, instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition...
October 14, 2016: FEBS Journal
Akimasa Fujihara, Naoto Maeda, Thuc N Doan, Shigeo Hayakawa
Chiral transmission between monosaccharides and amino acids via photodissociation in the gas phase was examined using a tandem mass spectrometer fitted with an electrospray ionization source and a cold ion trap in order to investigate the origin of the homochirality of biomolecules in molecular clouds. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of the monosaccharide enantiomers glucose (Glc) and galactose (Gal) with protonated L-tryptophan H(+)(L-Trp) were obtained by photoexcitation of the indole ring of L-Trp...
October 13, 2016: Journal of the American Society for Mass Spectrometry
G Oxenkrug, J Cornicelli, M van der Hart, J Roeser, P Summergrad
Obesity is an increasingly urgent global problem and the molecular mechanisms of obesity are not fully understood. Dysregulation of the tryptophan (Trp) - kynurenine (Kyn) metabolic pathway (TKP) have been suggested as a mechanism of obesity and described in obese humans and in animal models of obesity. However, to the best of our knowledge, TKP metabolism has not been studied in leptin-receptor-deficient Zucker fatty rats (ZFR) (fa/fa), the best-known and most widely used rat model of obesity. We were interested to determine if there are any deviations of TKP in ZFR...
2016: Integrative Molecular Medicine
Ilya A Osterman, Ekaterina S Komarova, Dmitry I Shiryaev, Ilya A Korniltsev, Irina M Khven, Dmitry A Lukyanov, Vadim N Tashlitsky, Marina V Serebryakova, Olga V Efremenkova, Yan A Ivanenkov, Alexey A Bogdanov, Petr V Sergiev, Olga A Dontsova
In order to accelerate drug discovery, a simple, reliable and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double reporter system for not only antimicrobial activity detection, but also for simultaneous sorting of potential antimicrobials into those that cause ribosome stalling, and others that induce SOS response due to DNA damage. In this reporter system the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter...
October 10, 2016: Antimicrobial Agents and Chemotherapy
A Mangas, J Yajeya, N González, S Duleu, M Geffard, R Coveñas
A highly specific monoclonal antibody directed against nitric oxide-tryptophan (NO-W) with good affinity (10-9 M) and specificity was developed. In the rat brain, using an indirect immunoperoxidase technique, cell bodies containing NO-W were exclusively found in the intermediate and dorsal parts of the lateral septal nucleus. No immunoreactive fibres were found in the rat brain. This work reports the first visualization and the morphological characteristics of cell bodies containing NO-W in the mammalian brain...
September 22, 2016: European Journal of Histochemistry: EJH
Vinodhkumar Vijayakumar, Ramadoss Vijayaraj, Günther H Peters
The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(D-Trp-L-Gln-D-Trp-L-Glu)2], and hereafter is referred to as (WQWE)8...
November 2016: Journal of Molecular Modeling
Kim Ve Braun, Nicole S Erler, Jessica C Kiefte-de Jong, Vincent Wv Jaddoe, Edith H van den Hooven, Oscar H Franco, Trudy Voortman
BACKGROUND: High protein intake in infancy might lead to a higher body mass index (BMI) in childhood. However, whether these associations differ between different sources of protein is unclear. OBJECTIVE: We investigated associations between the intake of total protein, protein from different sources, and individual amino acids in early childhood and repeatedly measured height, weight, and BMI up to the age of 9 y. METHODS: This study was performed in 3564 children participating in the Generation R Study, a population-based prospective cohort study in Rotterdam, Netherlands...
October 12, 2016: Journal of Nutrition
Arunima Chaudhuri, Xavier Prasanna, Priyanka Agiru, Hirak Chakraborty, Anna Rydström, James C S Ho, Catharina Svanborg, Durba Sengupta, Amitabha Chattopadhyay
Bovine α-lactalbumin (BLA) forms cytotoxic complexes with oleic acid (OA) that perturbs tumor cell membranes, but molecular determinants of these membrane-interactions remain poorly understood. Here, we aim to obtain molecular insights into the interaction of BLA/BLA-OA complex with model membranes. We characterized the folding state of BLA-OA complex using tryptophan fluorescence and resolved residue-specific interactions of BLA with OA using molecular dynamics simulation. We integrated membrane-binding data using a voltage-sensitive probe and molecular dynamics (MD) to demonstrate the preferential interaction of the BLA-OA complex with negatively charged membranes...
October 12, 2016: Scientific Reports
Brendan F O'Connor, Philip M Cummins
Most proteins and large polypeptides have hydrophobic regions at their surface. These hydrophobic "patches" are due to the presence of the side chains of hydrophobic or nonpolar amino acids such as phenylalanine, tryptophan, alanine, and methionine. These surface hydrophobic regions are interspersed between more hydrophilic or polar regions and the number, size, and distribution of them is a specific characteristic of each individual protein. Hydrophobic Interaction Chromatography (HIC) is a commonly used technique that exploits these hydrophobic features of proteins as a basis for their separation even in complex biological mixtures (Queiroz et al...
2017: Methods in Molecular Biology
Sally A Abuelezz, Nevien Hendawy, Yosra Magdy
Depression is a major health problem in which oxidative stress and inflammation are inextricably connected in its pathophysiology. Coenzyme Q10 (CoQ10) is an important anti-oxidant compound with anti-inflammatory and neuro-protective properties. This study was designed to investigate the hypothesis that CoQ10 by its anti-oxidant and anti-inflammatory potentials can alleviate depressive- like behavior by restoring the balance of the tryptophan catabolites kynurenine/serotonin toward the serotonin pathway by down-regulation of hippocampal indoleamine 2,3-dioxygenase 1 (IDO-1)...
October 11, 2016: Journal of Neuroimmune Pharmacology: the Official Journal of the Society on NeuroImmune Pharmacology
Makedonka Gulcev, Cavan Reilly, Timothy J Griffin, Corey D Broeckling, Brian J Sandri, Bruce A Witthuhn, Shane W Hodgson, Prescott G Woodruff, Chris H Wendt
INTRODUCTION: Exacerbations are a leading cause of morbidity in COPD. The objective of this study was to identify metabolomic biomarkers of acute exacerbations of COPD (AECOPD). METHODS: We measured metabolites via mass spectrometry (MS) in plasma drawn within 24 hours of admission to the hospital for 33 patients with an AECOPD (day 0) and 30 days later and for 65 matched controls. Individual metabolites were measured via selective reaction monitoring with mass spectrometry...
2016: International Journal of Chronic Obstructive Pulmonary Disease
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