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https://www.readbyqxmd.com/read/28346403/near-infrared-optogenetic-pair-for-protein-regulation-and-spectral-multiplexing
#1
Taras A Redchuk, Evgeniya S Omelina, Konstantin G Chernov, Vladislav V Verkhusha
Multifunctional optogenetic systems are in high demand for use in basic and biomedical research. Near-infrared-light-inducible binding of bacterial phytochrome BphP1 to its natural PpsR2 partner is beneficial for simultaneous use with blue-light-activatable tools. However, applications of the BphP1-PpsR2 pair are limited by the large size, multidomain structure and oligomeric behavior of PpsR2. Here, we engineered a single-domain BphP1 binding partner, Q-PAS1, which is three-fold smaller and lacks oligomerization...
March 27, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28346388/thermal-condensation-of-glycine-and-alanine-on-metal-ferrite-surface-primitive-peptide-bond-formation-scenario
#2
Md Asif Iqubal, Rachana Sharma, Sohan Jheeta, Kamaluddin
The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles...
March 27, 2017: Life
https://www.readbyqxmd.com/read/28346351/in-vitro-and-in-vivo-studies-on-the-structural-organization-of-chs3-from-saccharomyces-cerevisiae
#3
Simon Gohlke, Subbaratnam Muthukrishnan, Hans Merzendorfer
Chitin biosynthesis in yeast is accomplished by three chitin synthases (Chs) termed Chs1, Chs2 and Chs3, of which the latter accounts for most of the chitin deposited within the cell wall. While the overall structures of Chs1 and Chs2 are similar to those of other chitin synthases from fungi and arthropods, Chs3 lacks some of the C-terminal transmembrane helices raising questions regarding its structure and topology. To fill this gap of knowledge, we performed bioinformatic analyses and protease protection assays that revealed significant information about the catalytic domain, the chitin-translocating channel and the interfacial helices in between...
March 25, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28345931/predictable-conformational-diversity-in-foldamers-of-sugar-amino-acids
#4
Dora K Menyhard, Ilona Hudaky, Imre Jákli, György Juhász, András Perczel
Systematic conformational search was carried out for monomers and homohexamers of furanoid β-amino acids: cis-(S,R) and trans-(S,S) stereoisomers of aminocyclopentane carboxylic acid (ACPC), two different aminofuranuronic-acids (AFU(α) and AFU(β)), their isopropylidene derivatives (AFU(ip)) as well as the key intermediate β-aminotetrahydrofurancarboxylic acid (ATFC). Stereochemistry of the building blocks was chosen to match with that of natural sugar amino acid (xylose and ribose) precursors. Results show that hexamers of cis furanoid β-amino acids show great variability: while hydrophobic cyclopentane (cis(ACPC)6), and hydrophilic (cisXylAFU(α/β))6 foldamers favor two different zigzagged conformation as hexamers, the backbone fold turns into a helix in case of (cisATFC)6 (10-helix) and (cisAFU(ip))6 (14-helix)...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28345863/native-mass-spectrometry-of-recombinant-proteins-from-crude-cell-lysates
#5
Jinrui Gan, Gili Ben-Nissan, Galina Arkind, Mark Tarnavsky, Devin Trudeau, Lianet Noda Garcia, Dan Tawfik, Michal Sharon
Determining the properties of proteins prior to purification saves time and labor. Here, we demonstrate a native mass spectrometry approach for rapid characterization of overexpressed proteins directly in crude cell lysates. The method provides immediate information on the identity, solubility, oligomeric state, overall structure and stability, as well as ligand binding, without the need for purification.
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345702/the-role-of-conformational-heterogeneity-in-regulating-the-apoptotic-activity-of-bax-protein
#6
Te-Yu Kao, Chia-Jung Tsai, Yu-Jing Lan, Yun-Wei Chiang
While activation of BAX is required for initiating mitochondria-mediated apoptosis, the underlying mechanisms remain unsettled. We studied conformations of BAX protein using pressure- and temperature-resolved ESR techniques and obtained the thermodynamic properties of the conformations. We show that inactive BAX is structurally heterogeneous and exists in equilibrium between two major populations of the conformations, UM and UM', of which the former is thermodynamically favored at room temperature. An increase in the population of UM', induced by either pressure or point mutations of BAX, renders BAX susceptible to oligomerization, which leads to cell death...
March 27, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28345490/challenges-and-complexity-of-functionality-evaluation-of-flavan-3-ol-derivatives
#7
Akiko Saito
Flavan-3-ol derivatives are common plant-derived bioactive compounds. In particular, (-)-epigallocatechin-3-O-gallate shows various moderate biological activities without severe toxicity, and its health-promoting effects have been widely studied because it is a main ingredient in green tea and is commercially available at low cost. Although various biologically active flavan-3-ol derivatives are present as minor constituents in plants as well as in green tea, their biological activities have yet to be revealed, mainly due to their relative unavailability...
March 27, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28345259/the-role-of-complement-inhibitors-beyond-controlling-inflammation
#8
REVIEW
A M Blom
The complement system is an arm of innate immunity that aids in the removal of pathogens and dying cells. Due to its harmful, pro-inflammatory potential, complement is controlled by several soluble and membrane-bound inhibitors. This family of complement regulators has been recently extended by the discovery of several new members, and it is becoming apparent that these proteins harbour additional functions. In this review, the current state of knowledge of the physiological functions of four complement regulators will be described: cartilage oligomeric matrix protein (COMP), CUB and sushi multiple domains 1 (CSMD1), sushi domain-containing protein 4 (SUSD4) and CD59...
March 26, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28345116/oligomeric-state-and-thermal-stability-of-apo-and-holo-human-ornithine-%C3%AE-aminotransferase
#9
Riccardo Montioli, Carlotta Zamparelli, Carla Borri Voltattorni, Barbara Cellini
Human ornithine δ-aminotransferase (hOAT) (EC 2.6.1.13) is a mitochondrial pyridoxal 5'-phosphate (PLP)-dependent aminotransferase whose deficit is associated with gyrate atrophy, a rare autosomal recessive disorder causing progressive blindness and chorioretinal degeneration. Here, both the apo- and holo-form of recombinant hOAT were characterized by means of spectroscopic, kinetic, chromatographic and computational techniques. The results indicate that apo and holo-hOAT (a) show a similar tertiary structure, even if apo displays a more pronounced exposure of hydrophobic patches, (b) exhibit a tetrameric structure with a tetramer-dimer equilibrium dissociation constant about fivefold higher for the apoform with respect to the holoform, and (c) have apparent Tm values of 46 and 67 °C, respectively...
March 27, 2017: Protein Journal
https://www.readbyqxmd.com/read/28343346/molecularly-imprinted-polymer-prepared-with-polyhedral-oligomeric-silsesquioxane-through-reversible-addition-fragmentation-chain-transfer-polymerization
#10
Shu-Ping Gao, Xue Zhang, Li-Shun Zhang, Yan-Ping Huang, Zhao-Sheng Liu
Polyhedral oligomeric silsesquioxane (POSS) was utilized to prepare imprinted polymer through reversible addition-fragmentation chain transfer polymerization (RAFT) successfully. The imprinted polymer was made with a mixture of RAFT agent, 4-vinylpyridine (4-VP), POSS monomer [PSS-(1-propylmethacrylate)-heptaisobutyl substituted, MA 0702], and ethylene glycol dimethacrylate (EDMA), with ketoprofen (KET) as template. The influence of polymerization variables, the amount of RAFT agent and POSS monomer, the ratio of KET to 4-VP, and the ratio of 4-VP to EDMA, were investigated on the retention factor and imprinting effect...
March 25, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28343033/quinocetone-induces-mitochondrial-apoptosis-in-hepg2-cells-through-ros-dependent-promotion-of-vdac1-oligomerization-and-suppression-of-wnt1-%C3%AE-catenin-signaling-pathway
#11
Xiayun Yang, Shusheng Tang, Chongshan Dai, Daowen Li, Shen Zhang, Sijun Deng, Yan Zhou, Xilong Xiao
Quinocetone (QCT) has been used as an animal feed additive in China since 2003. However, investigations indicate that QCT has potential toxicity due to the fact that it shows cytotoxicity, genotoxicity, hepatotoxicity, nephrotoxicity and immunotoxicity in vitro and animal models. Although QCT-induced mitochondrial apoptosis has been established, the molecular mechanism remains unclear. This study was aimed to investigate the role of voltage-dependent anion channel 1 (VDAC1) oligomerization and Wnt/β-catenin pathway in QCT-induced mitochondrial apoptosis...
March 23, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28342582/simultaneous-determination-of-nitrated-and-oligomerized-proteins-by-size-exclusion-high-performance-liquid-chromatography-coupled-to-photodiode-array-detection
#12
Fobang Liu, Kathrin Reinmuth-Selzle, Senchao Lai, Michael G Weller, Ulrich Pöschl, Christopher J Kampf
Chemical modifications such as nitration and cross-linking may enhance the allergenic potential of proteins. The kinetics and mechanisms of the underlying chemical processes, however, are not yet well understood. Here, we present a size-exclusion chromatography/spectrophotometry method (SEC-HPLC-DAD) that allows a simultaneous detection of mono-, di-, tri-, and higher protein oligomers, as well as their individual nitration degrees (NDs). The ND results of proteins from this new method agree well with the results from an alternative well-established method, for the analysis of tetranitromethane (TNM)- and nitrogen dioxide and ozone (NO2/O3)-nitrated protein samples...
March 10, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28341845/the-trimer-interface-in-the-quaternary-structure-of-the-bifunctional-prokaryotic-fad-synthetase-from-corynebacterium-ammoniagenes
#13
Ana Serrano, María Sebastián, Sonia Arilla-Luna, Silvia Baquedano, Beatriz Herguedas, Adrián Velázquez-Campoy, Marta Martínez-Júlvez, Milagros Medina
Bifunctional FAD synthetases (FADSs) fold in two independent modules; The C-terminal riboflavin kinase (RFK) catalyzes the RFK activity, while the N-terminal FMN-adenylyltransferase (FMNAT) exhibits the FMNAT activity. The search for macromolecular interfaces in the Corynebacterium ammoniagenes FADS (CaFADS) crystal structure predicts a dimer of trimers organization. Within each trimer, a head-to-tail arrangement causes the RFK and FMNAT catalytic sites of the two neighboring protomers to approach, in agreement with active site residues of one module influencing the activity at the other...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341432/development-validation-and-evaluation-of-an-analytical-method-for-the-determination-of-monomeric-and-oligomeric-procyanidins-in-apple-extracts
#14
Wendy J Hollands, Stefan Voorspoels, Griet Jacobs, Kjersti Aaby, Ane Meisland, Rocio Garcia-Villalba, Francisco Tomas-Barberan, Mariusz K Piskula, Deborah Mawson, Irena Vovk, Paul W Needs, Paul A Kroon
There is a lack of data for individual oligomeric procyanidins in apples and apple extracts. Our aim was to develop, validate and evaluate an analytical method for the separation, identification and quantification of monomeric and oligomeric flavanols in apple extracts. To achieve this, we prepared two types of flavanol extracts from freeze-dried apples; one was an epicatechin-rich extract containing ∼30% (w/w) monomeric (-)-epicatechin which also contained oligomeric procyanidins (Extract A), the second was an oligomeric procyanidin-rich extract depleted of epicatechin (Extract B)...
March 18, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28341309/polymorphic-distribution-of-proteins-in-solution-by-mass-spectrometry-the-analysis-of-insulin-analogues
#15
Maely P Fávero-Retto, Luiz Henrique Guerreiro, Cássio M Pessanha, Leonardo C Palmieri, Luís Maurício T R Lima
The characterization of conformational and oligomeric distribution of proteins is of paramount importance for the understanding of the correlation between structure and function. Among the bioanalytical approaches currently available, the electrospray ionization-mass spectrometry (ESI-MS) coupled to ion mobility spectrometry (IMS) is the best suited for high resolution identification with high sensitivity, allowing the in situ separation of oligomeric and conformational species. We tested the performance of the ESI-MS technique along with the IMS separation approach on a broad variety of insulin and insulin analogues with distinct oligomeric distribution pattern...
January 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28339907/o-linked-%C3%AE-n-acetylglucosamine-modification-of-proteins-is-essential-for-foot-process-maturation-and-survival-in-podocytes
#16
Shinya Ono, Shinji Kume, Mako Yasuda-Yamahara, Kosuke Yamahara, Naoko Takeda, Masami Chin-Kanasaki, Hisazumi Araki, Osamu Sekine, Hideki Yokoi, Masashi Mukoyama, Takashi Uzu, Shin-Ichi Araki, Hiroshi Maegawa
Background.: O-linked β- N -acetylglucosamine modification O-GlcNAcylation) is a post-translational modification of intracellular proteins, serving as a nutrient sensor. Growing evidence has demonstrated its physiological and pathological importance in various mammalian tissues. This study examined the physiological role of O-GlcNAcylation in podocyte function and development. Methods.: O-GlcNAc transferase (Ogt) is a critical enzyme for O-GlcNAcylation and resides on the X chromosome...
February 27, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28339183/tunable-porosity-of-crosslinked-polyhedral-oligomeric-silsesquioxane-poss-supports-for-palladium-catalyzed-aerobic-alcohol-oxidation-in-water
#17
Preeyanuch Sangtrirutnugul, Thanawat Chaiprasert, Warodom Hunsiri, Thanudkit Jitjaroendee, Patsaya Songkhum, Kritapas Laohhasurayotin, Tanakorn Osotchan, Vuthichai Ervithayasuporn
Polyhedral oligomeric silsesquioxane (POSS)-based materials, poly-POSS-Tn [n = 8 (1), 10 (2), 12 (3), and mix (4)], were prepared in high yields via free radical polymerization of corresponding pure forms of methacrylate-functionalized POSS monomers, MMA-POSS-Tn (n = 8, 10, 12), and the mixture form, MMA-POSS-Tmix. Powder X-ray diffraction (XRD) spectra and BET analysis indicate that 1-4 are amorphous materials with high surface areas (683-839 m2•g-1). The surface areas and total pore volumes follow the trend: poly-POSS-T12 > poly-POSS-T10 > poly-POSS-Tmix > poly-POSS-T8...
March 24, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28338703/theoretical-investigation-of-proton-collisions-on-prebiotic-candidates-hydrogen-cyanide-polymers
#18
Marie-Christine Bacchus-Montabonel
One of the major concerns in prebiotic chemistry is the formation and destruction routes of prebiotic compounds in space. As detected for a long time, hydrogen cyanide (HCN) has been suggested to be a feedstock molecule at the origin of life driving easy oligomerization, in particular to form adenine. This may focus on its first oligomers because its dimer cyanomethanimine was recently observed in star-forming regions, or its trimer aminomalononitrile. With regard to the assumption of an extra-terrestrial origin of life, the stability of such species under ultraviolet radiation or in ion-collisions is an open question...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28338692/computational-design-of-self-assembling-cyclic-protein-homo-oligomers
#19
Jorge A Fallas, George Ueda, William Sheffler, Vanessa Nguyen, Dan E McNamara, Banumathi Sankaran, Jose Henrique Pereira, Fabio Parmeggiani, T J Brunette, Duilio Cascio, Todd R Yeates, Peter Zwart, David Baker
Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein-protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338017/a-role-of-the-sam-domain-in-epha2-receptor-activation
#20
Xiaojun Shi, Vera Hapiak, Ji Zheng, Jeannine Muller-Greven, Deanna Bowman, Ryan Lingerak, Matthias Buck, Bing-Cheng Wang, Adam W Smith
Among the 20 subfamilies of protein receptor tyrosine kinases (RTKs), Eph receptors are unique in possessing a sterile alpha motif (SAM domain) at their C-terminal ends. However, the functions of SAM domains in Eph receptors remain elusive. Here we report on a combined cell biology and quantitative fluorescence study to investigate the role of the SAM domain in EphA2 function. We observed elevated tyrosine autophosphorylation levels upon deletion of the EphA2 SAM domain (EphA2ΔS) in DU145 and PC3 prostate cancer cells and a skin tumor cell line derived from EphA1/A2 knockout mice...
March 24, 2017: Scientific Reports
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