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https://www.readbyqxmd.com/read/29736537/effects-of-acceptor-doping-on-a-metalorganic-switch-dft-vs-model-analysis
#1
Tomasz Slusarski, Tomasz Kostyrko, V M García-Suárez
We propose a molecular switch based on copper dioxolene molecules with valence tautomeric properties. We study the system using density functional theory and a model Hamiltonian that can properly account for electronic correlations in these complex molecular systems. We compute the transport properties of the junction with a Cu-dioxolene unit sandwiched between gold electrodes and analyze its dependence on the valence tautomeric state of the molecule. We also study the effects of doping with ICl2 acceptor molecules on the magnetic and electronic features of the device...
May 8, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29697793/sequence-structure-and-expression-of-opsins-in-the-monochromatic-stomatopod-squilla-empusa
#2
Juan C Valdez-Lopez, Mary W Donohue, Michael J Bok, Julia Wolf, Thomas W Cronin, Megan L Porter
Most stomatopod crustaceans have complex retinas in their compound eyes, with up to 16 spectral types of photoreceptors, but members of the superfamily Squilloidea have much simpler retinas, thought to contain a single photoreceptor spectral class. In the Atlantic stomatopod Squilla empusa, microspectrophotometry shows that all photoreceptors absorb light maximally at 517 nm, indicating that a single visual pigment is present in all photoreceptors in the retina. However, six distinct, but partial, long wavelength sensitive (LWS) opsin transcripts, which encode the protein component of the visual pigment, have been previously isolated through RT-PCR...
April 25, 2018: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29695780/structural-basis-for-gpr40-allosteric-agonism-and-incretin-stimulation
#3
Joseph D Ho, Betty Chau, Logan Rodgers, Frances Lu, Kelly L Wilbur, Keith A Otto, Yanyun Chen, Min Song, Jonathan P Riley, Hsiu-Chiung Yang, Nichole A Reynolds, Steven D Kahl, Anjana Patel Lewis, Christopher Groshong, Russell E Madsen, Kris Conners, Jayana P Lineswala, Tarun Gheyi, Melbert-Brian Decipulo Saflor, Matthew R Lee, Jordi Benach, Kenton A Baker, Chahrzad Montrose-Rafizadeh, Michael J Genin, Anne R Miller, Chafiq Hamdouchi
Activation of free fatty acid receptor 1 (GPR40) by synthetic partial and full agonists occur via distinct allosteric sites. A crystal structure of GPR40-TAK-875 complex revealed the allosteric site for the partial agonist. Here we report the 2.76-Å crystal structure of human GPR40 in complex with a synthetic full agonist, compound 1, bound to the second allosteric site. Unlike TAK-875, which acts as a Gαq -coupled partial agonist, compound 1 is a dual Gαq and Gαs -coupled full agonist. compound 1 binds in the lipid-rich region of the receptor near intracellular loop 2 (ICL2), in which the stabilization of ICL2 by the ligand is likely the primary mechanism for the enhanced G protein activities...
April 25, 2018: Nature Communications
https://www.readbyqxmd.com/read/29645033/ion-pairing-in-1-butyl-3-methylpyridinium-halide-ionic-liquids-studied-using-nmr-and-dft-calculations
#4
Vincent P Swamy, Hirekodathakallu V Thulasiram, Federico Rastrelli, Giacomo Saielli
We present the 1H, 13C and 15N NMR chemical shifts of bulk ionic liquids based on 1-butyl-3-methylimidazolium (the cation also known as 1-butyl-3-picolinium) halides (Cl-, Br- and I-) and tribromide (Br3-) salts. A characterization in solution of the analogous ICl2- and I3- salts is also reported. A series of DFT calculations has been run to predict the features of the NMR spectra of the pure ILs based on a few selected supramolecular ionic aggregates. To test the effect of temperature, and vibrational and conformational motions, only for the chloride salt, we also run first-principles molecular dynamics simulations of the ion pair in the gas phase, using the ADMP scheme (Atom Centered Density Matrix Propagation molecular dynamics model)...
April 12, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29234476/syntheses-structures-and-stabilities-of-aliphatic-and-aromatic-fluorous-iodine-i-and-iodine-iii-compounds-the-role-of-iodine-lewis-basicity
#5
Tathagata Mukherjee, Soumik Biswas, Andreas Ehnbom, Subrata K Ghosh, Ibrahim El-Zoghbi, Nattamai Bhuvanesh, Hassan S Bazzi, John A Gladysz
The title molecules are sought in connection with various synthetic applications. The aliphatic fluorous alcohols Rf n CH2 OH (Rf n = CF3 (CF2 ) n -1 ; n = 11, 13, 15) are converted to the triflates Rf n CH2 OTf (Tf2 O, pyridine; 22-61%) and then to Rf n CH2 I (NaI, acetone; 58-69%). Subsequent reactions with NaOCl/HCl give iodine(III) dichlorides Rf n CH2 ICl2 ( n = 11, 13; 33-81%), which slowly evolve Cl2 . The ethereal fluorous alcohols CF3 CF2 CF2 O(CF(CF3 )CF2 O) x CF(CF3 )CH2 OH ( x = 2-5) are similarly converted to triflates and then to iodides, but efforts to generate the corresponding dichlorides fail...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29157227/metabolic-adaptation-of-two-in-silico-mutants-of-mycobacterium-tuberculosis-during-infection
#6
Víctor A López-Agudelo, Andres Baena, Howard Ramirez-Malule, Silvia Ochoa, Luis F Barrera, Rigoberto Ríos-Estepa
BACKGROUND: Up to date, Mycobacterium tuberculosis (Mtb) remains as the worst intracellular killer pathogen. To establish infection, inside the granuloma, Mtb reprograms its metabolism to support both growth and survival, keeping a balance between catabolism, anabolism and energy supply. Mtb knockouts with the faculty of being essential on a wide range of nutritional conditions are deemed as target candidates for tuberculosis (TB) treatment. Constraint-based genome-scale modeling is considered as a promising tool for evaluating genetic and nutritional perturbations on Mtb metabolic reprogramming...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29106998/antiapoptotic-serine-protease-inhibitors-contribute-to-survival-of-allergenic-t-h-2-cells
#7
Mohamed H Shamji, Jeff N Temblay, Wei Cheng, Susan M Byrne, Ellen Macfarlane, Amy R Switzer, Natalia D C Francisco, Fedina Olexandra, Fabian Jacubczik, Stephen R Durham, Philip G Ashton-Rickardt
BACKGROUND: The mechanisms that regulate maintenance of persistent TH 2 cells and potentiate allergic inflammation are not well understood. OBJECTIVE: The function of serine protease inhibitor 2A (Spi2A) was studied in mouse TH 2 cells, and the serine protease inhibitor B3 (SERPINB3) and SERPINB4 genes were studied in TH 2 cells from patients with grass pollen allergy. METHODS: Spi2A-deficient TH 2 cells were studied in in vitro culture or in vivo after challenge of Spi2A knockout mice with ovalbumin in alum...
October 26, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28694498/analysis-of-positive-and-negative-allosteric-modulation-in-metabotropic-glutamate-receptors-4-and-5-with-a-dual-ligand
#8
James A R Dalton, Jean-Philippe Pin, Jesús Giraldo
As class C GPCRs and regulators of synaptic activity, human metabotropic glutamate receptors (mGluRs) 4 and 5 are prime targets for allosteric modulation, with mGlu5 inhibition or mGlu4 stimulation potentially treating conditions like chronic pain and Parkinson's disease. As an allosteric modulator that can bind both receptors, 2-Methyl-6-(phenylethynyl)pyridine (MPEP) is able to negatively modulate mGlu5 or positively modulate mGlu4. At a structural level, how it elicits these responses and how mGluRs undergo activation is unclear...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679637/mechanism-based-inactivator-of-isocitrate-lyases-1-and-2-from-mycobacterium-tuberculosis
#9
Truc V Pham, Andrew S Murkin, Margaret M Moynihan, Lawrence Harris, Peter C Tyler, Nishant Shetty, James C Sacchettini, Hsiao-Ling Huang, Thomas D Meek
Isocitrate lyase (ICL, types 1 and 2) is the first enzyme of the glyoxylate shunt, an essential pathway for Mycobacterium tuberculosis (Mtb) during the persistent phase of human TB infection. Here, we report 2-vinyl-d-isocitrate (2-VIC) as a mechanism-based inactivator of Mtb ICL1 and ICL2. The enzyme-catalyzed retro-aldol cleavage of 2-VIC unmasks a Michael substrate, 2-vinylglyoxylate, which then forms a slowly reversible, covalent adduct with the thiolate form of active-site Cys191 2-VIC displayed kinetic properties consistent with covalent, mechanism-based inactivation of ICL1 and ICL2 with high efficiency (partition ratio, <1)...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28581512/structural-basis-for-the-cooperative-allosteric-activation-of-the-free-fatty-acid-receptor-gpr40
#10
Jun Lu, Noel Byrne, John Wang, Gerard Bricogne, Frank K Brown, Harry R Chobanian, Steven L Colletti, Jerry Di Salvo, Brande Thomas-Fowlkes, Yan Guo, Dawn L Hall, Jennifer Hadix, Nicholas B Hastings, Jeffrey D Hermes, Thu Ho, Andrew D Howard, Hubert Josien, Maria Kornienko, Kevin J Lumb, Michael W Miller, Sangita B Patel, Barbara Pio, Christopher W Plummer, Bradley S Sherborne, Payal Sheth, Sarah Souza, Srivanya Tummala, Clemens Vonrhein, Maria Webb, Samantha J Allen, Jennifer M Johnston, Adam B Weinglass, Sujata Sharma, Stephen M Soisson
Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle...
July 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28336329/an-aromatic-amino-acid-within-intracellular-loop-2-of-the-prostaglandin-ep2-receptor-is-a-prerequisite-for-selective-association-and-activation-of-g%C3%AE-s
#11
Akiko Yano, Yuko Takahashi, Hiromi Moriguchi, Tomoaki Inazumi, Tomoaki Koga, Akira Otaka, Yukihiko Sugimoto
We previously demonstrated that the aromatic moiety of Tyr(143) within the intracellular loop 2 (ICL2) region of the prostaglandin EP2 receptor plays a crucial role in Gs coupling. Here we investigated whether the ICL2 of the EP2 receptor directly binds to Gαs and whether an aromatic moiety affects this interaction. In Chinese hamster ovary cells, mutations of Tyr(143) reduced the ability of the EP2 receptor to interact with G proteins as demonstrated by GTPγS sensitivity, as well as the ability of agonist-induced cAMP formation, with the rank order of Phe>Tyr (wild-type)=Trp>Leu>Ala (=0)...
June 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28256674/piperazine-functionalized-c-60-and-diiodine-or-iodine-monochloride-as-components-in-forming-supramolecular-assemblies
#12
Amineh Aghabali, Sharon Jun, Marilyn M Olmstead, Alan L Balch
The reaction of the piperazine mono-adduct, N(CH2 CH2 )2 NC60 , with diiodine produced well ordered, black crystals of (I2 N(CH2 CH2 )2 NI2 )C60 ·2.884(C6 H6 )·0.116I2 , which contains two nearly linear N-I-I units. Reaction of N(CH2 CH2 )2 NC60 with iodine monochloride produced two materials: the dihalogen adduct, (ClIN(CH2 CH2 )2 NICl)C60 ·2.3(CS2 )·0.7(CH2 Cl2 ), when crystallization occurred rapidly from carbon disulfide/dichloromethane solution or the salt, [(N(CH2 CH2 )2 NH)C60 + ][ICl2 - ]·CS2 , when crystallization happened more slowly from toluene/dichloromethane solution where hydrolysis of the iodine monochloride by adventitious water presumably occurred...
March 14, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28213525/conformational-profiling-of-the-at1-angiotensin-ii-receptor-reflects-biased-agonism-g-protein-coupling-and-cellular-context
#13
Dominic Devost, Rory Sleno, Darlaine Pétrin, Alice Zhang, Yuji Shinjo, Rakan Okde, Junken Aoki, Asuka Inoue, Terence E Hébert
Here, we report the design and use of G protein-coupled receptor-based biosensors to monitor ligand-mediated conformational changes in receptors in intact cells. These biosensors use bioluminescence resonance energy transfer with Renilla luciferase (RlucII) as an energy donor, placed at the distal end of the receptor C-tail, and the small fluorescent molecule FlAsH as an energy acceptor, its binding site inserted at different positions throughout the intracellular loops and C-terminal tail of the angiotensin II type I receptor...
March 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28041939/involvement-of-the-coatomer-protein-complex-i-in-the-intracellular-traffic-of-the-delta-opioid-receptor
#14
Étienne St-Louis, Jade Degrandmaison, Sébastien Grastilleur, Samuel Génier, Véronique Blais, Christine Lavoie, Jean-Luc Parent, Louis Gendron
The delta opioid receptor (DOPr) is known to be mainly expressed in intracellular compartments. It remains unknown why DOPr is barely exported to the cell surface, but it seems that a substantial proportion of the immature receptor is trapped within the endoplasmic reticulum (ER) and the Golgi network. In the present study, we performed LC-MS/MS analysis to identify putative protein partners involved in the retention of DOPr. Analysis of the proteins co-immunoprecipitating with Flag-DOPr in transfected HEK293 cells revealed the presence of numerous subunits of the coatomer protein complex I (COPI), a vesicle-coating complex involved in recycling resident proteins from the Golgi back to the ER...
March 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27897283/identification-of-photofragmentation-patterns-in-trihalide-anions-by-global-analysis-of-vibrational-wavepacket-dynamics-in-broadband-transient-absorption-data
#15
Sebastian Schott, Lea Ress, Jan Hrušák, Patrick Nuernberger, Tobias Brixner
Trihalide anions are linear molecules that can be photodissociated with ultraviolet (UV) light. Whereas deep-UV excitation leads to three-body dissociation, for near-UV excitation just one molecular bond is cleaved, which notionally opens up the possibility for different fragmentation patterns. Here, we explore whether the dihalide fragment is formed as an anionic or neutral species and whether heteronuclear trihalides can lead to two different dihalides. The analysis is based on pronounced wavepacket dynamics induced by femtosecond UV pulses and associated both with the initial trihalide and the nascent dihalide species...
December 7, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27801588/conformational-heterogeneity-of-intracellular-loop-3-of-the-%C3%AE-opioid-g-protein-coupled-receptor
#16
Jing Huang, Sirish Kaushik Lakkaraju, Andrew Coop, Alexander D MacKerell
G-protein coupled receptors (GPCRs), including the μ-opioid receptor, interact with G-proteins and other proteins via their intracellular face as required for signal transduction. However, characterization of the structure of the intracellular face of GPCRs is complicated by the experimental methods used for structural characterization. In the present study we undertook a series of long-time molecular dynamics (MD) simulations, ranging from 1 to 5 μs, on the μ-opioid receptor in both the dimeric and monomeric states...
November 23, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/26964814/nested-reverse-transcriptase-polymerase-chain-reactions-targeting-the-messenger-rna-of-icl2-hspx-and-rrnap1-genes-to-detect-viable-mycobacterium-tuberculosis-directly-from-clinical-specimens
#17
Dhanurekha Lakshmipathy, Lily Therese Kulandai, Gayathri Ramasubban, Madhavan Hajib Narahari Rao, Sridhar Rathinam, Meenakshi Narasimhan
There is an urgent need for a rapid and reliable test to detect actively multiplying Mycobacterium tuberculosis directly from clinical specimens for an early initiation of the appropriate antituberculous treatment. This study was aimed at the optimization and application of nested reverse transcriptase-PCR (nRT-PCR) targeting the messenger RNA of the icl2, hspx, and rRNAP1 genes directly from sputum specimens, and their evaluation against the culture by the BACTEC MicroMGIT mycobacterial culture system. 203 Sputum samples from clinically suspected tuberculosis patients and 30 control specimens (clinically proven viral or bacterial infections other than tuberculosis) were included in this study...
December 2015: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/26717821/a-novel-vortex-assisted-liquid-liquid-microextraction-approach-using-auxiliary-solvent-determination-of-iodide-in-mineral-water-samples
#18
Serhii Zaruba, Andriy B Vishnikin, Vasil Andruch
A novel vortex-assisted liquid-liquid microextraction (VA-LLME) for determination of iodide was developed. The method includes the oxidation of iodide with iodate in the presence of hydrochloric acid followed by VA-LLME of the ion-pair formed between ICl2(-) and Astra Phloxine reagent (AP) and subsequent absorbance measurement at 555nm. The appropriate experimental conditions were investigated and found to be: 5mL of sample, 0.27molL(-)(1) HCl, 0.027mmolL(-1) KIO3 as the oxidation agent, 250μL of extraction mixture containing amyl acetate as the extraction solvent and carbon tetrachloride as the auxiliary solvent (1:1, v/v), 0...
2016: Talanta
https://www.readbyqxmd.com/read/26708364/electrochemistry-of-iodide-iodine-and-iodine-monochloride-in-chloride-containing-nonhaloaluminate-ionic-liquids
#19
Cameron L Bentley, Alan M Bond, Anthony F Hollenkamp, Peter J Mahon, Jie Zhang
The electrochemical behavior of iodine remains a contemporary research interest due to the integral role of the I(-)/I3(-) couple in dye-sensitized solar cell technology. The neutral (I2) and positive (I(+)) oxidation states of iodine are known to be strongly electrophilic, and thus the I(-)/I2/I(+) redox processes are sensitive to the presence of nucleophilic chloride or bromide, which are both commonly present as impurities in nonhaloaluminate room temperature ionic liquids (ILs). In this study, the electrochemistry of I(-), I2, and ICl has been investigated by cyclic voltammetry at a platinum macrodisk electrode in a binary IL mixture composed of 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) and 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C2mim][NTf2])...
February 2, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/26254469/the-ribosome-sec61-translocon-complex-forms-a-cytosolically-restricted-environment-for-early-polytopic-membrane-protein-folding
#20
Melissa A Patterson, Anannya Bandyopadhyay, Prasanna K Devaraneni, Josha Woodward, LeeAnn Rooney, Zhongying Yang, William R Skach
Transmembrane topology of polytopic membrane proteins (PMPs) is established in the endoplasmic reticulum (ER) by the ribosome Sec61-translocon complex (RTC) through iterative cycles of translocation initiation and termination. It remains unknown, however, whether tertiary folding of transmembrane domains begins after the nascent polypeptide integrates into the lipid bilayer or within a proteinaceous environment proximal to translocon components. To address this question, we used cysteine scanning mutagenesis to monitor aqueous accessibility of stalled translation intermediates to determine when, during biogenesis, hydrophilic peptide loops of the aquaporin-4 (AQP4) water channel are delivered to cytosolic and lumenal compartments...
November 27, 2015: Journal of Biological Chemistry
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