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Protein chemistry

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https://www.readbyqxmd.com/read/28101863/lessons-from-animal-models-of-cytoplasmic-intermediate-filament-proteins
#1
Jamal-Eddine Bouameur, Thomas M Magin
Cytoplasmic intermediate filaments (IFs) represent a major cytoskeletal network contributing to cell shape, adhesion and migration as well as to tissue resilience and renewal in numerous bilaterians, including mammals. The observation that IFs are dispensable in cultured mammalian cells, but cause tissue-specific, life-threatening disorders, has pushed the need to investigate their function in vivo. In keeping with human disease, the deletion or mutation of murine IF genes resulted in highly specific pathologies...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28098177/an-extended-n-h-bond-driven-by-a-conserved-second-order-interaction-orients-the-flavin-n5-orbital-in-cholesterol-oxidase
#2
Emily Golden, Li-Juan Yu, Flora Meilleur, Matthew P Blakeley, Anthony P Duff, Amir Karton, Alice Vrielink
The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097901/skin-whitening-agents-medicinal-chemistry-perspective-of-tyrosinase-inhibitors
#3
Thanigaimalai Pillaiyar, Manoj Manickam, Vigneshwaran Namasivayam
Melanogenesis is a process to synthesize melanin, which is a primary responsible for the pigmentation of human skin, eye and hair. Although numerous enzymatic catalyzed and chemical reactions are involved in melanogenesis process, the enzymes such as tyrosinase and tyrosinase-related protein-1 (TRP-1) and TRP-2 played a major role in melanin synthesis. Specifically, tyrosinase is a key enzyme, which catalyzes a rate-limiting step of the melanin synthesis, and the downregulation of tyrosinase is the most prominent approach for the development of melanogenesis inhibitors...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28097602/dietary-supplementation-of-chromium-can-alleviate-negative-impacts-of-heat-stress-on-performance-carcass-yield-and-some-blood-hematology-and-chemistry-indices-of-growing-japanese-quail
#4
Mohamed Soliman El-Kholy, Mohamed Mohamed El-Hindawy, Mahmoud Alagawany, Mohamed Ezzat Abd El-Hack, Sabry Abd El-Gawad Abd El-Halim El-Sayed
The main objective of this work was to investigate the impact of dietary chromium supplementation on growth indices, carcass yield, and some hematological and biochemical blood parameters of growing Japanese quails subjected to heat stress. A total of 360 unsexed 2-week-old Japanese quail chicks were used in a 2 × 3 factorial arrangement that had two ambient temperatures (23 ± 2 and 33 ± 2 °C) and three dietary chromium (0.00, 500, and 1000 μg Cr/kg diet as chromium picolinate). For induction of heat stress, the room temperature was set at 33 ± 2 °C from 2 to 6 weeks of age...
January 17, 2017: Biological Trace Element Research
https://www.readbyqxmd.com/read/28097376/elemental-labelling-and-mass-spectrometry-for-the-specific-detection-of-sulfenic-acid-groups-in-model-peptides-a-proof-of-concept
#5
Mona Sharar, Essa M Saied, Mario C Rodriguez, Christoph Arenz, Maria Montes-Bayón, Michael W Linscheid
Oxidative transformation of cysteine thiol groups into different functional groups is considered a significant posttranslational modification of great importance in pathological and physiological processes. A cysteine sulfenic acid (SA) residue is the transient state for thiol group oxidation and it can react with free thiols to form disulfide bonds or can be further oxidized with reactive oxygen/reactive nitrogen species (ROS/RNS) to form sulfinic and sulfonic acids. The increase in ROS/RNS concentrations is correlated to age-related diseases such as cancer and Alzheimer's disease...
January 17, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28096391/network-based-integration-of-systems-genetics-data-reveals-pathways-associated-with-lignocellulosic-biomass-accumulation-and-processing
#6
Eshchar Mizrachi, Lieven Verbeke, Nanette Christie, Ana C Fierro, Shawn D Mansfield, Mark F Davis, Erica Gjersing, Gerald A Tuskan, Marc Van Montagu, Yves Van de Peer, Kathleen Marchal, Alexander A Myburg
As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28094987/crystal-engineering-of-self-assembled-porous-protein-materials-in-living-cells
#7
Satoshi Abe, Hiroyasu Tabe, Hiroshi Ijiri, Keitaro Yamashita, Kunio Hirata, Kohei Atsumi, Takuya Shimoi, Masaki Akai, Hajime Mori, Susumu Kitagawa, Takafumi Ueno
Crystalline porous materials have been investigated for development of important applications in molecular storage, separations, and catalysis. The potential of protein crystals is increasing as they become better understood. Protein crystals have been regarded as porous materials because they present highly ordered 3D arrangements of protein molecules with high porosity and wide range of pore sizes. However, it remains difficult to functionalize protein crystals in living cells. Here, we report that polyhedra, a natural crystalline protein assembly of polyhedrin monomer (PhM) produced in insect cells infected by cypovirus, can be engineered to extend porous networks by deleting selected amino acid residues located on the intermolecular contact region of PhM...
January 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28094985/beyond-the-hofmeister-series-ion-specific-effects-on-proteins-and-their-biological-functions
#8
Halil I Okur, Jana Hladílková, Kelvin B Rembert, Younhee Cho, Jan Heyda, Joachim Dzubiella, Paul S Cremer, Pavel Jungwirth
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting-out/salting-in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood...
January 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28094920/antifouling-thin-film-composite-membranes-by-controlled-architecture-of-zwitterionic-polymer-brush-layer
#9
Caihong Liu, Jongho Lee, Jun Ma, Menachem Elimelech
In this study, we demonstrate a highly antifouling thin-film-composite (TFC) membrane by grafting a zwitterionic polymer brush via atom-transfer radical-polymerization (ATRP), a controlled, environmentally benign chemical process. Initiator molecules for polymerization were immobilized on the membrane surface by bio-inspired catechol chemistry, leading to the grafting of a dense zwitterionic polymer brush layer. Surface characterization revealed that the modified membrane exhibits reduced surface roughness, enhanced hydrophilicity, and lower surface charge...
January 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28094501/artificial-cells-synthetic-compartments-with-life-like-functionality-and-adaptivity
#10
Bastiaan C Buddingh', Jan C M van Hest
Cells are highly advanced microreactors that form the basis of all life. Their fascinating complexity has inspired scientists to create analogs from synthetic and natural components using a bottom-up approach. The ultimate goal here is to assemble a fully man-made cell that displays functionality and adaptivity as advanced as that found in nature, which will not only provide insight into the fundamental processes in natural cells but also pave the way for new applications of such artificial cells. In this Account, we highlight our recent work and that of others on the construction of artificial cells...
January 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28093981/chemical-and-biological-aspects-of-the-natural-1-4-benzoquinone-embelin-and-its-semi-synthetic-derivatives
#11
Priti Singh Shuveksh, Subhash Padhye, Rainer Schobert, Bernhard Biersack
BACKGROUND: Like the impressive biological properties of embelin, its chemical aspects have raised the interest of scientists in the field as well. A detailed understanding of the chemistry of embelin is necessary to fully exploit it medicinally. METHODS: Search for embelin isolation and its chemical modifications was carried out using web-based literature searching tools such as Pubmed and Scifinder. Pertinent literature is covered up to 2016. Structures of bioactive embelin derivatives are provided...
January 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28092944/reaction-chemistry-to-characterize-the-molecular-initiating-event-in-skin-sensitization-a-journey-to-be-continued
#12
Andreas Natsch, Roger Emter
The publication by the OECD of the adverse outcome pathway (AOP) for skin sensitization has accelerated the development and validation of mechanistic tests and testing strategies to assess the potential of new molecules to trigger skin allergies. The molecular initiating event (MIE) in the AOP is reaction with skin peptides/proteins. It is followed by a number of cellular events. Currently, only one in chemico test to characterize the MIE was proposed to and underwent adoption by the OECD, while two cell-based assays have completed the process...
January 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28091754/a-new-look-at-the-role-of-thiolate-ligation-in-cytochrome-p450
#13
Timothy H Yosca, Aaron P Ledray, Joanna Ngo, Michael T Green
Protonated ferryl (or iron(IV)hydroxide) intermediates have been characterized in several thiolate-ligated heme proteins that are known to catalyze C-H bond activation. The basicity of the ferryl intermediates in these species has been proposed to play a critical role in facilitating this chemistry, allowing hydrogen abstraction at reduction potentials below those that would otherwise lead to oxidative degradation of the enzyme. In this contribution, we discuss the events that led to the assignment and characterization of the unusual iron(IV)hydroxide species, highlighting experiments that provided a quantitative measure of the ferryl basicity, the iron(IV)hydroxide pKa...
January 16, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28091665/trace-element-protein-interactions-in-endolymph-from-the-inner-ear-of-fish-implications-for-environmental-reconstructions-using-fish-otolith-chemistry
#14
Oliver R B Thomas, Katherine Ganio, Blaine R Roberts, Stephen E Swearer
Otoliths, the biomineralised hearing "ear stones" from the inner ear of fish, grow throughout the lifespan of an individual, with deposition of alternating calciferous and proteinaceous bands occurring daily. Trace element : calcium ratios within daily increments measured by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) are often used in fisheries science to reconstruct environmental histories. There is, however, considerable uncertainty as to which elements are interacting with either the proteinaceous or calciferous zones of the otolith, and thus their utility as indicators of environmental change...
January 16, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28090121/redox-signaling-through-dna
#15
Elizabeth O'Brien, Rebekah M B Silva, Jacqueline K Barton
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances...
October 2016: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/28088631/an-esipt-based-two-photon-fluorescent-probe-detection-of-hydrogen-peroxide-in-live-cells-and-tissues
#16
Liyi Zhou, Yongbo Peng, Qianqian Wang, Qinlu Lin
A variety of diseases associated with human aging, which have a strong oxidative stress, but connecting age-related diseases and oxidative stress of the basic molecular mechanisms still insufficiently understood. Oxidative stress origins from the unregulated production of reactive oxygen species (ROS), and oxidative damaging to tissues and organs from subsequent oxidation-reduction chemistry by cellular mismanagement. In particular, H2O2 is a major by-product of ROS in live organisms and a common marker for oxidative stress, and its dynamic equilibrium can have various physiological and pathological consequences...
January 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28088276/solid-supports-for-extraction-and-preconcentration-of-proteins-and-peptides-in-microfluidic-devices-a-review
#17
REVIEW
Szymon Dziomba, Monica Araya-Farias, Claire Smadja, Myriam Taverna, Benjamin Carbonnier, N Thuy Tran
Determination of proteins and peptides is among the main challenges of today's bioanalytical chemistry. The application of microchip technology in this field is an exhaustively developed concept that aims to create integrated and fully automated analytical devices able to quantify or detect one or several proteins from a complex matrix. Selective extraction and preconcentration of targeted proteins and peptides especially from biological fluids is of the highest importance for a successful realization of these microsystems...
February 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28078593/detection-of-s-acylated-cd95-by-acyl-biotin-exchange
#18
Aurelie Rossin, Anne-Odile Hueber
S-acylation is the covalent addition of a fatty acid, most generally palmitate onto cysteine residues of proteins through a labile thioester linkage. The death receptor CD95 is S-palmitoylated and this post-translational modification plays a crucial role on CD95 organization in cellular membranes and thus on CD95-mediated signaling. Here, we describe the nonradioactive detection of CD95 S-acylation by acyl-biotin exchange chemistry in which a biotin is substituted for the CD95-linked fatty acid. This sensitive technique, which depends on the ability of hydroxylamine to specifically cleave the thioester linkage between fatty acids and proteins, relies on three chemical steps: (1) blockage of free thiols of non-modified cysteine residues, (2) hydroxylamine-mediated cleavage of thioester-linked fatty acids to restore free thiols and (3) biotinylation of free thiols with a thiol reactive biotinylation agent...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28077807/folding-of-apomyoglobin-analysis-of-transient-intermediate-structure-during-refolding-using-quick-hydrogen-deuterium-exchange-and-nmr
#19
Chiaki Nishimura
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28076888/caspase-mediated-beclin-1-dependent-autophagy-tuning-activity-and-apoptosis-promotion-by-surface-modified-hausmannite-nanoparticle
#20
Souvik Mondal, Anupam Giri, Yunjiao Zhang, Samir Kumar Pal, Wei Zhou, Long-Ping Wen
Hidden effects of nano-materials to induced autophagy, a lysosomal degradative pathway, remain an exciting topic, in the level of material-protein interaction and subsequent cellular signaling features. Here, our studies show that surface modified hausmannite nanoparticles (Mn3 O4 NPs) can uniformly cleave/splice Beclin-1 protein and alter cellular mechanism on the emphasis of tuning autophagy and subsequently promote enhancement of apoptosis. Details investigation of Beclin-1 dependency and its uniform cleavage/splice pattern by surface modified Mn3 O4 NPs, shows tuning of cellular mechanism on emphasis of caspase mediated autophagy tuning...
January 11, 2017: Journal of Biomedical Materials Research. Part A
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