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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
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
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
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
Jesús M Planesas, Violeta I Pérez-Nueno, José I Borrell, Jordi Teixidó
Several examples of allosteric modulators of GPCRs have been reported recently in the literature, but understanding their molecular mechanism presents a new challenge for medicinal chemistry. For the specific case of the cellular receptor CXCR4, it is known that pepducins (lipidated fragments of intracellular GPCR loops) such as ATI-2341 modulate CXCR4 activity agonistically via an allosteric mechanism. Moreover, there are also examples of small organic molecules such as AMD11070 and GSK812397 which may also act as allosteric antagonists...
July 2015: Journal of Molecular Graphics & Modelling
Tip W Loo, David M Clarke
P-glycoprotein (P-gp; ABCB1) is an ABC drug pump that protects us from toxic compounds. It is clinically important because it confers multidrug resistance. The homologous halves of P-gp each contain a transmembrane (TM) domain (TMD) with 6 TM segments followed by a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the interface between the TMDs and NBDs, respectively. Each NBD is connected to the TMDs by a transmission interface involving a pair of intracellular loops (ICLs) that form ball-and-socket joints...
July 3, 2015: Journal of Biological Chemistry
Alexander T Eprintsev, Dmitry N Fedorin, Alexei V Salnikov, Abir U Igamberdiev
Isocitrate lyase (EC catalyzes the reversible conversion of d-isocitrate to succinate and glyoxylate. It is usually associated with the glyoxylate cycle in glyoxysomes, although the non-glyoxysomal form has been reported and its relation to interconversion of organic acids outside the glyoxylate cycle suggested. We investigated the expression of two isocitrate lyase genes and activities of the glyoxysomal (ICL1) and cytosolic (ICL2) forms of isocitrate lyase in amaranth (Amaranthus caudatus L.) seedlings...
June 1, 2015: Journal of Plant Physiology
Luca Belmonte, Oscar Moran
The Cystic Fibrosis Transmembrane Regulator (CFTR) is a membrane protein whose mutations cause cystic fibrosis, a lethal genetic disease. We performed a molecular dynamic (MD) study of the properties of the nucleotide binding domains (NBD) whose conformational changes, upon ATP binding, are the direct responsible of the gating mechanisms of CFTR. This study was done for the wild type (WT) CFTR and for the two most common mutations, ΔF508, that produces a traffic defect of the protein, and the mutation G551D, that causes a gating defect on CFTR...
April 2015: Biochimie
Xiuchan Xiao, Xiaojun Zeng, Yuan Yuan, Nan Gao, Yanzhi Guo, Xuemei Pu, Menglong Li
G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for β2 adrenergic receptor (β2AR)...
January 28, 2015: Physical Chemistry Chemical Physics: PCCP
Andrew J M Shaw, Robert Corbo, David J D Wilson, Jason L Dutton
The formation of a new class of I(III) compound is reported; an N,N' chelated iodine cation ([bpy-ICl2](+); bpy = 2,2'-bipyridine). The complex is obtained as an [ICl4](-) salt and is formed via simple reaction of bpy with ICl3. The compound is relatively unstable, but may be stored as a solid and is shown to be competent in the oxidative chlorination of Au(I)-NHC complexes.
September 14, 2015: Dalton Transactions: An International Journal of Inorganic Chemistry
Jose Manuel Perez-Aguilar, Jufang Shan, Michael V LeVine, George Khelashvili, Harel Weinstein
With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT(2A)R) in the absence of ligand and bound to four distinct serotonergic agonists...
November 12, 2014: Journal of the American Chemical Society
Hui Huang, Ya-Xiong Tao
The melanocortin 3 receptor (MC3R) regulates several physiological functions, including feed efficiency, nutrient partitioning, fasting response, natriuresis, and immune reactions. Naturally occurring mutations in the MC3R gene have been shown to be associated with increased adiposity and lung diseases such as tuberculosis and cystic fibrosis. The DRY motif at the cytoplasmic end of transmembrane domain 3 (TM3) and the second intracellular loop 2 (ICL2) are known to be important for receptor function in several G protein-coupled receptors (GPCRs)...
December 2014: Journal of Molecular Endocrinology
Wei Wang, Bryan C Roessler, Kevin L Kirk
The CFTR channel is an essential mediator of electrolyte transport across epithelial tissues. CFTR opening is promoted by ATP binding and dimerization of its two nucleotide binding domains (NBDs). Phosphorylation of its R domain (e.g. by PKA) is also required for channel activity. The CFTR structure is unsolved but homology models of the CFTR closed and open states have been produced based on the crystal structures of evolutionarily related ABC transporters. These models predict the formation of a tetrahelix bundle of intracellular loops (ICLs) during channel opening...
October 31, 2014: Journal of Biological Chemistry
Douglas J Swartz, Leo Mok, Sri K Botta, Anukriti Singh, Guillermo A Altenberg, Ina L Urbatsch
Pgp (P-glycoprotein) is a prototype ABC (ATP-binding-cassette) transporter involved in multidrug resistance of cancer. We used directed evolution to replace six cytoplasmic Cys (cysteine) residues in Pgp with all 20 standard amino acids and selected for active mutants. From a pool of 75000 transformants for each block of three Cys, we identified multiple mutants that preserved drug resistance and yeast mating activity. The most frequent substitutions were glycine and serine for Cys427 (24 and 20%, respectively) and Cys1070 (37 and 25%) of the Walker A motifs in the NBDs (nucleotide-binding domains), Cys1223 in NBD2 (25 and 8%) and Cys638 in the linker region (24 and 16%), whereas close-by Cys669 tolerated glycine (16%) and alanine (14%), but not serine (absent)...
2014: Bioscience Reports
Nejla Stambouli, Mehdi Dridi, Ning-Ning Wei, Asma Jlizi, Abderahmen Bouraoui, Amel Ben Ammar Elgaaied
The chemokine receptor 5 (CCR5) belongs to the superfamily of serpentine G protein-coupled receptors (GPCRs). The DRY motif (Asp, Arg, Tyr) of the intracellular loop 2 (ICL2), which is highly conserved in the GPCRs has been shown to be essential for the stability of folding of CCR5 and the interaction with β-arrestin. But the molecular mechanism by which it recognizes and interacts with β-arrestin has not been elucidated. In the present study, we described the active state of the β-arrestin structure using normal mode analysis and characterized the binding cleft of CCR5-ICL2 with β-arrestin using SABRE© docking tool and molecular dynamics simulation...
2014: Journal of Biomolecular Structure & Dynamics
Massoud Kaykhaii, Mona Sargazi
Two new, rapid methodologies have been developed and applied successfully for the determination of trace levels of iodide in real water samples. Both techniques are based on a combination of in-syringe dispersive liquid-liquid microextraction (IS-DLLME) and micro-volume UV-Vis spectrophotometry. In the first technique, iodide is oxidized with nitrous acid to the colorless anion of ICl2(-) at high concentration of hydrochloric acid. Rhodamine B is added and by means of one step IS-DLLME, the ion-pair formed was extracted into toluene and measured spectrophotometrically...
2014: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Nejla Stambouli, Ning-Ning Wei, Asma Jlizi, Samah Aissa, Rim Abdelmalek, Baderredine Kilani, Amine Slim, Ben Aissa Hanen Tiouiri, Mahdi Dridi, Adel Hamza, Amel Ben Ammar Elgaied
We report the identification of a novel CC chemokine receptor 5 (CCR5) variant that seems associated with resistance to HIV-1 infection. The V130I mutation of the CCR5 receptor is located in the intracellular loop ICL2 known as DRY box and described in the literature as a nonsynonymous mutation present in nonhuman primates group. Extensive molecular modeling and dynamics simulations were performed to elucidate the mechanism by which the V130I mutation may induce conformational change of the CCR5 folding protein and prevent the interaction with the β-arrestin protein...
2014: Journal of Biomolecular Structure & Dynamics
Karina Martinez-Mayorga, Kendall G Byler, Austin B Yongye, Marc A Giulianotti, Colette T Dooley, Richard A Houghten
During the past five years, the three-dimensional structures of 14 different G-protein coupled receptors (GPCRs) have been resolved by X-ray crystallography. The most recently published structures, those of the opioid receptors (ORs), are remarkably important in pain modulation, drug addiction, and mood disorders. These structures, confirmed previously proposed key interactions conferring potency and antagonistic properties, including the well-known interaction with Asp138, conserved in all aminergic GPCRs...
August 2013: European Journal of Medicinal Chemistry
Carolin L Piechowski, Anne Rediger, Christina Lagemann, Jessica Mühlhaus, Anne Müller, Juliane Pratzka, Patrick Tarnow, Annette Grüters, Heiko Krude, Gunnar Kleinau, Heike Biebermann
Obesity is one of the most challenging global health problems. One key player in energy homeostasis is the melanocortin-4 receptor (MC4R), which is a family A G-protein-coupled receptor (GPCR). It has recently been shown that MC4R has the capacity to form homo- or heterodimers. Dimerization of GPCRs is of great importance for signaling regulation, with major pharmacological implications. Unfortunately, not enough is yet known about the detailed structural properties of MC4R dimers or the functional consequences of receptor dimerization...
August 2013: Journal of Molecular Endocrinology
Congxia Zheng, Linjie Chen, Xiaopan Chen, Xiaobai He, Jingwen Yang, Ying Shi, Naiming Zhou
The major effects of cannabinoids and endocannabinoids are mediated via two G protein-coupled receptors, CB1 and CB2, elucidation of the mechanism and structural determinants of the CB2 receptor coupling with G proteins will have a significant impact on drug discovery. In the present study, we systematically investigated the role of the intracellular loops in the interaction of the CB2 receptor with G proteins using chimeric receptors alongside the characterization of cAMP accumulation and ERK1/2 phosphorylation...
2013: PloS One
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