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Tryptophan

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https://www.readbyqxmd.com/read/28806086/role-of-electrostatics-in-protein-rna-binding-the-global-vs-the-local-energy-landscape
#1
Zhaleh Ghaemi, Irisbel Guzman, David Gnutt, Zaida Luthey-Schulten, Martin Gruebele
U1A protein - stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape towards a specific binding site...
August 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28802861/contrasting-effects-of-vortioxetine-and-paroxetine-on-pineal-gland-biochemistry-in-a-tryptophan-depletion-model-of-depression-in-female-rats
#2
M Franklin, N Hlavacova, Y Li, I Bermudez, A Csanova, C Sanchez, D Jezova
We studied the effects of the multi-modal antidepressant, vortioxetine and the SSRI, paroxetine on pineal melatonin and monoamine synthesis in a sub-chronic tryptophan (TRP) depletion model of depression based on a low TRP diet. Female Sprague-Dawley rats were randomised to groups a) control, b) low TRP diet, c) low TRP diet+paroxetine and d) low TRP diet+vortioxetine. Vortioxetine was administered via the diet (0.76mg/kg of food weight) and paroxetine via drinking water (10mg/kg/day) for 14days. Both drugs resulted in SERT occupancies >90%...
August 9, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28802845/fluorescence-quenching-structural-and-unfolding-studies-of-a-purified-cysteine-protease-zcpg-from-zingiber-montanum-rhizome
#3
Kizukala Jamir, Kottapalli Seshagirirao
A first attempt was made to study the fluorescence quenching, structure and unfolding nature of the purified Zingiber montanum (J.Koenig) Link ex A.Dietr. cysteine protease glycoprotein (ZCPG). ATR-IR spectra showed the presences of amide groups along with carbohydrate stretch indicating the glycoprotein nature. UV-vis spectra determined the presences of peptide groups and aromatic sidechains of tyrosine, tryptophan and phenylalanine. Far UV-Circular Dichroism spectrum revealed that the secondary structure consists of 47...
August 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28801970/lysozyme-oxidation-by-singlet-molecular-oxygen-peptides-characterization-using-18-o-labeling-oxygen-and-nlc-ms-ms
#4
Emerson Finco Marques, Marisa H G Medeiros, Paolo Di Mascio
Singlet molecular oxygen ((1) O2 ) is generated in biological systems and reacts with different biomolecules. Proteins are a major target for (1) O2 and His, Tyr, Met, Cys and Trp are oxidized at physiological pH. In the present study, the modification of lysozyme protein by (1) O2 was investigated using mass spectrometry approaches. The experimental findings showed methionine, histidine and tryptophan oxidation. The experiments were achieved using [(18) O]-labeled (1) O2 released from thermolabile endoperoxides in association with nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry, an UHR-ESI-Q-TOF...
August 11, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28801461/structural-basis-of-human-prdm9-allele-c-specific-recognition-of-its-cognate-dna-sequence
#5
Anamika Patel, Xing Zhang, Robert M Blumenthal, Xiaodong Cheng
PRDM9 is the only mammalian gene that has been associated with speciation. The PR/SET domain 9 (PRDM9) protein is a major determinant of meiotic recombination hotspots, and acts through sequence-specific DNA binding via its C2H2 zinc finger (ZF) tandem array, which is highly polymorphic within and between species. The most common human variant, PRDM9 allele A (PRDM9a), contains 13 fingers (ZF1-13). Allele C (PRDM9c) is the second-most common among African populations, and differs from PRDM9a by an arginine-to-serine change (R764S) in ZF9, and by replacement of ZF11 with two other fingers, yielding 14 fingers in PRDM9c...
August 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28801236/frailty-status-in-older-adults-is-related-to-alterations-in-indoleamine-2-3-dioxygenase-1-and-guanosine-triphosphate-cyclohydrolase-i%C3%A2-enzymatic-pathways
#6
Diego Marcos-Pérez, María Sánchez-Flores, Ana Maseda, Laura Lorenzo-López, José C Millán-Calenti, Barbara Strasser, Johanna M Gostner, Dietmar Fuchs, Eduardo Pásaro, Vanessa Valdiglesias, Blanca Laffon
BACKGROUND: Frailty is a multidimensional syndrome correlated to the loss of homeostasis and increased vulnerability to stressors, which is associated with increase in the risk of disability, comorbidity, hospitalization, and death in the elderly. It is based on the interplay of physiological, psychological, social, and environmental factors. OBJECTIVES: Because aging involves a detrimental immune response, this work aimed to assess the possible role of chronic low-grade immune stimulation on frailty status in the elderly...
August 8, 2017: Journal of the American Medical Directors Association
https://www.readbyqxmd.com/read/28800113/biomarker-research-in-parkinson-s-disease-using-metabolite-profiling
#7
REVIEW
Jesper F Havelund, Niels H H Heegaard, Nils J K Færgeman, Jan Bert Gramsbergen
Biomarker research in Parkinson's disease (PD) has long been dominated by measuring dopamine metabolites or alpha-synuclein in cerebrospinal fluid. However, these markers do not allow early detection, precise prognosis or monitoring of disease progression. Moreover, PD is now considered a multifactorial disease, which requires a more precise diagnosis and personalized medication to obtain optimal outcome. In recent years, advanced metabolite profiling of body fluids like serum/plasma, CSF or urine, known as "metabolomics", has become a powerful and promising tool to identify novel biomarkers or "metabolic fingerprints" characteristic for PD at various stages of disease...
August 11, 2017: Metabolites
https://www.readbyqxmd.com/read/28799778/how-important-is-tryptophan-in-human-health
#8
Joanna Kałużna-Czaplińska, Paulina Gątarek, Salvatore Chirumbolo, Max Stanley Chartrand, Geir Bjørklund
Tryptophan (Trp) is an amino acid and an essential component of the human diet. It plays a crucial role in many metabolic functions. Clinicians can use Trp levels in the course of diagnosing various metabolic disorders and the symptoms associated with those diseases. Furthermore, supplementation with this amino acid is considered in the treatment of depression and sleep disorders, mainly due to the Trp relationship with the synthesis of serotonin (5-HT) and melatonin. It is also used in helping to resolve cognitive disorders, anxiety, or neurodegenerative diseases...
August 11, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28799334/the-impact-of-commonly-used-alkylating-agents-on-artefactual-peptide-modification
#9
Peter G Hains, Phillip J Robinson
Iodoacetamide is by far the most commonly used agent for alkylation of cysteine during sample preparation for proteomics. An alternative, 2-chloroacetamide, has been recently suggested to reduce the alkylation of residues other than cysteine, such as the N-terminus, Asp, Glu, Lys, Ser, Thr and Tyr. Here, we show that although 2-chloroacetamide reduces the level of off-target alkylation, it exhibits a range of adverse effects. The most significant of these was methionine oxidation, which increases to a maximum of 40% of all Met containing peptides compared to 2-5% with iodoacetamide...
August 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28798976/5-ht-modulation-of-pain-perception-in-humans
#10
Sarah L Martin, Andrea Power, Yvonne Boyle, Ian M Anderson, Monty A Silverdale, Anthony K P Jones
INTRODUCTION: Although there is clear evidence for the serotonergic regulation of descending control of pain in animals, little direct evidence exists in humans. The majority of our knowledge comes from the use of serotonin (5-HT)-modulating antidepressants as analgesics in the clinical management of chronic pain. OBJECTIVES: Here, we have used an acute tryptophan depletion (ATD) to manipulate 5-HT function and examine its effects of ATD on heat pain threshold and tolerance, attentional manipulation of nociceptive processing and mood in human volunteers...
August 10, 2017: Psychopharmacology
https://www.readbyqxmd.com/read/28796377/tryptophan-and-cysteine-oxidation-products-dominate-in-%C3%AE-lactalbumin-derived-peptides-analyzed-with-lc-ms-n
#11
Tuuli P Koivumäki, Göker Gürbüz, I Marina Heinonen
α-Lactalbumin (α-La), a major milk whey protein, is comprised of several amino acids prone to metal-catalyzed oxidation (MCO) typical in processing and during storage of foods. New tools are needed for the detection of characteristic oxidation products especially from tryptophan and cysteine that often remain unrecognized when using the traditional methods of carbonyl formation monitoring. In this study, the oxidative changes in α-La were investigated through tryptic digestion and collection of 3 descriptive peptides fitted into a metal-catalyzed oxidation (Fenton reaction) model...
August 10, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28796169/cell-surface-and-nuclear-receptors-in-the-colon-as-targets-for-bacterial-metabolites-and-its-relevance-to-colon-health
#12
REVIEW
Sathish Sivaprakasam, Yangzom D Bhutia, Sabarish Ramachandran, Vadivel Ganapathy
The symbiotic co-habitation of bacteria in the host colon is mutually beneficial to both partners. While the host provides the place and food for the bacteria to colonize and live, the bacteria in turn help the host in energy and nutritional homeostasis, development and maturation of the mucosal immune system, and protection against inflammation and carcinogenesis. In this review, we highlight the molecular mediators of the effective communication between the bacteria and the host, focusing on selective metabolites from the bacteria that serve as messengers to the host by acting through selective receptors in the host colon...
August 10, 2017: Nutrients
https://www.readbyqxmd.com/read/28795267/cyp79-p450-monooxygenases-in-gymnosperms-cyp79a118-is-associated-with-the-formation-of-taxiphyllin-in-taxus-baccata
#13
Katrin Luck, Qidong Jia, Meret Huber, Vinzenz Handrick, Gane Ka-Shu Wong, David R Nelson, Feng Chen, Jonathan Gershenzon, Tobias G Köllner
Conifers contain P450 enzymes from the CYP79 family that are involved in cyanogenic glycoside biosynthesis. Cyanogenic glycosides are secondary plant compounds that are widespread in the plant kingdom. Their biosynthesis starts with the conversion of aromatic or aliphatic amino acids into their respective aldoximes, catalysed by N-hydroxylating cytochrome P450 monooxygenases (CYP) of the CYP79 family. While CYP79s are well known in angiosperms, their occurrence in gymnosperms and other plant divisions containing cyanogenic glycoside-producing plants has not been reported so far...
August 9, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28794205/the-human-serum-metabolome-of-vitamin-b-12-deficiency-and-repletion-and-associations-with-neurological-function-in-elderly-adults
#14
Alex Brito, Dmitry Grapov, Johannes Fahrmann, Danielle Harvey, Ralph Green, Joshua W Miller, Sergey N Fedosov, Setareh Shahab-Ferdows, Daniela Hampel, Theresa L Pedersen, Oliver Fiehn, John W Newman, Ricardo Uauy, Lindsay H Allen
Background: The specific metabolomic perturbations that occur in vitamin B-12 deficiency, and their associations with neurological function, are not well characterized.Objective: We sought to characterize the human serum metabolome in subclinical vitamin B-12 deficiency and repletion.Methods: A before-and-after treatment study provided 1 injection of 10 mg vitamin B-12 (with 100 mg pyridoxine and 100 mg thiamin) to 27 community-dwelling elderly Chileans (∼74 y old) with vitamin B-12 deficiency, as evaluated with serum vitamin B-12, total plasma homocysteine (tHcy), methylmalonic acid (MMA), and holotranscobalamin...
August 9, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28794173/glucose-potentiates-%C3%AE-cell-function-by-inducing-tph1-expression-in-rat-islets
#15
Yuqing Zhang, Ruyuan Deng, Xue Yang, Wan Xu, Yun Liu, Fengying Li, Juan Zhang, Hongju Tang, Xueying Ji, Yufang Bi, Xiao Wang, Libin Zhou, Guang Ning
Impaired pancreatic β-cell function is the primary defect in type 2 diabetes. Glucose is an important regulator of β-cell growth and function; however, the mechanisms that are involved in the chronic adaptation of β-cells to hyperglycemia remain largely unknown. In the present study, global gene expression patterns revealed that tryptophan hydroxylase 1 (Tph1) was the most profound of genes that are up-regulated in rat islets exposed to high glucose. Calcium and cAMP signals synergistically mediated glucose-stimulated Tph1 transcription in β-cells by activating cAMP-responsive element-binding protein and promoting its binding with a Tph1 promoter...
August 9, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28793366/cadmium-induced-melatonin-synthesis-in-rice-requires-light-hydrogen-peroxide-and-nitric-oxide-key-regulatory-roles-for-tryptophan-decarboxylase-and-caffeic-acid-o-methyltransferase
#16
Kyungjin Lee, Geun-Hee Choi, Kyoungwhan Back
In plants, melatonin production is induced by stimuli such as cold and drought, and cadmium (Cd) is the best elicitor of melatonin production in rice. However, the mechanism by which Cd induces melatonin synthesis in plants remains unknown. We challenged rice seedlings with Cd under different light conditions and found that continuous light produced the highest levels of melatonin, while continuous dark failed to induce melatonin production. Transcriptional and translational induction of tryptophan decarboxylase contributed to the light induction of melatonin during Cd treatment, whereas the protein level of light-induced caffeic acid O-methyltransferase (COMT) was decreased by Cd treatment...
August 9, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28792876/nad-deficiency-congenital-malformations-and-niacin-supplementation
#17
Hongjun Shi, Annabelle Enriquez, Melissa Rapadas, Ella M M A Martin, Roni Wang, Julie Moreau, Chai K Lim, Justin O Szot, Eddie Ip, James N Hughes, Kotaro Sugimoto, David T Humphreys, Aideen M McInerney-Leo, Paul J Leo, Ghassan J Maghzal, Jake Halliday, Janine Smith, Alison Colley, Paul R Mark, Felicity Collins, David O Sillence, David S Winlaw, Joshua W K Ho, Gilles J Guillemin, Matthew A Brown, Kazu Kikuchi, Paul Q Thomas, Roland Stocker, Eleni Giannoulatou, Gavin Chapman, Emma L Duncan, Duncan B Sparrow, Sally L Dunwoodie
BACKGROUND: Congenital malformations can be manifested as combinations of phenotypes that co-occur more often than expected by chance. In many such cases, it has proved difficult to identify a genetic cause. We sought the genetic cause of cardiac, vertebral, and renal defects, among others, in unrelated patients. METHODS: We used genomic sequencing to identify potentially pathogenic gene variants in families in which a person had multiple congenital malformations...
August 10, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28792629/alteration-of-cell-wall-xylan-acetylation-trigger-defense-responses-that-counterbalance-the-immune-deficiencies-of-plants-impaired-in-the-%C3%AE-subunit-of-the-heterotrimeric-g-protein
#18
Viviana Escudero, Lucía Jordá, Sara Sopeña-Torres, Hugo Mélida, Eva Miedes, Antonio Muñoz-Barrios, Sanjay Swami, Danny Alexander, Lauren S McKee, Andrea Sánchez-Vallet, Vincent Bulone, Alan M Jones, Antonio Molina
Arabidopsis heterotrimeric G protein complex modulates Pathogen Associated Molecular Pattern-triggered immunity (PTI) and disease resistance responses to different type of pathogens. It also plays a role in plant cell wall integrity as mutants impaired in the Gβ (agb1-2) or Gγ subunits have an altered wall composition compared to wild-type plants. Here we performed a mutant screen to identify suppressors of agb1-2 (sgb) that restore susceptibility to pathogens to wild-type levels. Out of the four sgb mutants (sgb10-sgb13) identified, sgb11 is a new mutant allele of ESKIMO1 (ESK1), which encodes a plant-specific polysaccharide O-acetyltransferase involved in xylan acetylation...
August 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28792588/immunosuppressive-enzymes-in-the-tumor-microenvironement
#19
REVIEW
Valérie Molinier-Frenkel, Flavia Castellano
Antigen encounter by T lymphocytes induces important metabolic changes. Anti-tumor T lymphocytes enter in a metabolic competition with tumors, which divert feedback mechanisms of the immune response. Immunosuppressive enzymes, modifying the nutrient availability and leading to the production of toxic catabolites, represent one of these mechanisms, contributing to the metabolic halo in which T lymphocytes evolve during immune responses. Two classes of immunosuppressive enzymes, expressed by the tumor cells or by cells of the microenvironment, have been described: those catabolizing essential or semi-essential amino acids, tryptophan, arginine and phenylalanine and the ectoenzymes, which degrade the ATP to produce adenosine...
August 9, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28792039/using-an-artificial-tryptophan-wire-in-cytochrome-c-peroxidase-for-oxidation-of-organic-substrates
#20
Mackenzie J Field, Rajneesh K Bains, Jeffrey J Warren
Lignolytic peroxidases use an electron transfer (ET) pathway that involves amino acid-mediated substrate oxidation at the surface of the protein rather than at an embedded heme site. In many of these peroxidases, redox catalysis takes place at a substrate accessible tyrosine or tryptophan (Trp) amino acid. Here, we describe new mutants of cytochrome c peroxidase (CcP) that were designed to incorporate a Trp-based "wire" that can move oxidizing equivalents from the heme to the protein surface. Three mutant CcP proteins were expressed and characterized: A193W, Y229W, and A193W/Y229W...
August 9, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
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