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https://www.readbyqxmd.com/read/28051765/exploring-conformational-equilibria-of-a-heterodimeric-abc-transporter
#1
M Hadi Timachi, Cedric Aj Hutter, Michael Hohl, Tufa Assafa, Simon Böhm, Anshumali Mittal, Markus A Seeger, Enrica Bordignon
ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift...
January 4, 2017: ELife
https://www.readbyqxmd.com/read/28028694/a-new-model-of-flavonoids-affinity-towards-p-glycoprotein-genetic-algorithm-support-vector-machine-with-features-selected-by-a-modified-particle-swarm-optimization-algorithm
#2
Ying Cui, Qinggang Chen, Yaxiao Li, Ling Tang
Flavonoids exhibit a high affinity for the purified cytosolic NBD (C-terminal nucleotide-binding domain) of P-glycoprotein (P-gp). To explore the affinity of flavonoids for P-gp, quantitative structure-activity relationship (QSAR) models were developed using support vector machines (SVMs). A novel method coupling a modified particle swarm optimization algorithm with random mutation strategy and a genetic algorithm coupled with SVM was proposed to simultaneously optimize the kernel parameters of SVM and determine the subset of optimized features for the first time...
December 27, 2016: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/28013220/potentiation-of-drug-induced-phospholipidosis-in-vitro-through-peglyated-graphene-oxide-as-the-nanocarrier
#3
Liecheng Yang, Xiaoyan Zhong, Qian Li, Xihui Zhang, Yangyun Wang, Kai Yang, Leshuai W Zhang
Cationic amphiphilic drugs (CADs) are small molecules that can induce phospholipidosis (PLD), causing the intracellular accumulation of phospholipid in the lamellar bodies. Nanotechnology based drug delivery systems have been used widely, while it is unknown if drug-induced PLD (DIP) can be potentiated through drug retention by indigestible nanocarriers. Due to the high drug loading capacity of graphene, we investigated if PEGylated graphene oxide (PEG-GO) loaded with CAD could potentiate DIP. Tamoxifen induced the accumulation of NBD-PE, a fluorescence labeled phospholipid in human hepatoma HepG2 cells, while PEG-GO loaded with tamoxifen (PEG-GO/tamoxifen) further potentiated PLD...
December 24, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28013030/interaction-of-e-coli-hsp90-with-dnak-involves-the-dnaj-binding-region-of-dnak
#4
Andrea N Kravats, Shannon M Doyle, Joel R Hoskins, Olivier Genest, Erin Doody, Sue Wickner
The 90-kDa heat shock protein (Hsp90) is a widely conserved and ubiquitous molecular chaperone that participates in ATP-dependent protein remodeling in both eukaryotes and prokaryotes. It functions in conjunction with Hsp70 and the Hsp70 cochaperones, an Hsp40 (J-protein) and a nucleotide exchange factor. In Escherichia coli, the functional collaboration between Hsp90Ec and Hsp70, DnaK, requires that the two chaperones directly interact. We used molecular docking to model the interaction of Hsp90Ec and DnaK...
December 21, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28011176/alkyl-substituted-phenylamino-derivatives-of-7-nitrobenz-2-oxa-1-3-diazole-as-uncouplers-of-oxidative-phosphorylation-and-antibacterial-agents-involvement-of-membrane-proteins-in-the-uncoupling-action
#5
Yuri N Antonenko, Stepan S Denisov, Ljudmila S Khailova, Pavel A Nazarov, Tatyana Rokitskaya, Vadim N Tashlitsky, Alexander M Firsov, Galina A Korshunova, Elena A Kotova
In search for new effective uncouplers of oxidative phosphorylation, we studied 4-aryl amino derivatives of a fluorescent group 7-nitrobenz-2-oxa-1,3-diazol (NBD). In our recent work (Denisov et al., Bioelectrochemistry, 2014), NBD-conjugated alkyl amines (NBD-Cn) were shown to exhibit uncoupling activity. It was concluded that despite a pKa value being about 10, the expected hindering of the uncoupling activity could be overcome by insertion of an alkyl chain. There is evidence in the literature that the introduction of an aryl substituent in the 4-amino NBD group shifts the pKa to neutral values...
December 21, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27994156/linking-parasite-populations-in-hosts-to-parasite-populations-in-space-through-taylor-s-law-and-the-negative-binomial-distribution
#6
Joel E Cohen, Robert Poulin, Clément Lagrue
The spatial distribution of individuals of any species is a basic concern of ecology. The spatial distribution of parasites matters to control and conservation of parasites that affect human and nonhuman populations. This paper develops a quantitative theory to predict the spatial distribution of parasites based on the distribution of parasites in hosts and the spatial distribution of hosts. Four models are tested against observations of metazoan hosts and their parasites in littoral zones of four lakes in Otago, New Zealand...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27956761/nemo-binding-domain-peptide-attenuates-lipopolysaccharide-induced-acute-lung-injury-by-inhibiting-the-nf-%C3%AE%C2%BAb-signaling-pathway
#7
Jianhua Huang, Li Li, Weifeng Yuan, Linxin Zheng, Zhenhui Guo, Wenjie Huang
The aim of the present study is to investigate the protective effects and relevant mechanisms exerted by NEMO-binding domain peptide (NBD) against lipopolysaccharide- (LPS-) induced acute lung injury (ALI) in mice. The ALI model was induced by intratracheally administered atomized LPS (5 mg/kg) to BABL/c mice. Half an hour before LPS administration, we treated the mice with increasing concentrations of intratracheally administered NBD or saline aerosol. Two hours after LPS administration, each group of mice was sacrificed...
2016: Mediators of Inflammation
https://www.readbyqxmd.com/read/27933796/structural-dynamics-of-the-heterodimeric-abc-transporter-tm287-288-induced-by-atp-and-substrate-binding
#8
Tadaomi Furuta, Yukiko Sato, Minoru Sakurai
TM287/288 is a heterodimeric ATP-binding cassette (ABC) transporter, which harnesses the energy of ATP binding and hydrolysis at the nucleotide-binding domains (NBDs) to transport a wide variety of molecules through the transmembrane domains (TMDs) by alternating inward- and outward-facing conformations. Here, we conducted multiple 100 ns molecular dynamics simulations of TM287/288 in different ATP- and substrate-bound states to elucidate the effects of ATP and substrate binding. As a result, the binding of two ATP molecules to the NBDs induced the formation of the consensus ATP-binding pocket (ABP2) or the NBD dimerization, whereas these processes did not occur in the presence of a single ATP molecule or when the protein was in its apo state...
December 6, 2016: Biochemistry
https://www.readbyqxmd.com/read/27917812/nasobiliary-drainage-for%C3%A2-benign-recurrent-intrahepatic-cholestasis%C3%A2-in-patients-refractory-to-standard-therapy
#9
Tolga Yakar, Mehmet Demir, Huseyin S Gokturk, Ayse G Unler Kanat, Alper Parlakgumus, Birol Ozer, Ender Serin
PURPOSE: Benign recurrent intrahepatic cholestasis (BRIC) is characterized by episodic cholestasis and pruritus without anatomical obstruction. The aim of this study was to evaluate the safety and efficacy of nasobiliary drainage (NBD) in patients with BRIC refractory to medical therapy and to determine whether the use of NBD prolongs the episode duration. METHODS: This was a multicenter retrospective study consisting of 33 patients suffering from BRIC. All patients were administrated medical treatment and 16 patients who were refractory to standard medical therapies improved on treatment with temporary endoscopic NBD...
1, 2016: Clinical and Investigative Medicine. Médecine Clinique et Experimentale
https://www.readbyqxmd.com/read/27914246/tract-based-analysis-of-white-matter-integrity-in-psychotic-and-nonpsychotic-bipolar-disorder
#10
Andrew Ji, Douglass Godwin, Jerrel Rutlin, Sridhar Kandala, Joshua S Shimony, Daniel Mamah
BACKGROUND: At least 50% of individuals with bipolar disorder (BD) present with psychosis during their lifetime. Psychotic symptoms have sometimes been linked to specific genetic and phenotypic markers. This study aims to explore potential differences between bipolar disorder subtypes by measuring white matter integrity of the brain and relationships with clinical measures. METHODS: Diffusion tensor imaging and clinical measures were acquired from 102 participants, grouped as psychotic bipolar disorder (PBD) (n=48), non-psychotic bipolar disorder (NBD) (n=24), and healthy controls (n=30)...
February 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/27912062/atomic-structure-of-the-cystic-fibrosis-transmembrane-conductance-regulator
#11
Zhe Zhang, Jue Chen
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27908240/new-fluorescent-macrolide-derivatives-for-studying-interactions-of-antibiotics-and-their-analogs-with-the-ribosomal-exit-tunnel
#12
A G Tereshchenkov, A V Shishkina, V V Karpenko, V A Chertkov, A L Konevega, P S Kasatsky, A A Bogdanov, N V Sumbatyan
Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27897331/a-convenient-and-validated-enantiomer-separation-of-chiral-aliphatic-amines-as-nitrobenzoxadiazole-derivatives-on-polysaccharide-derived-chiral-stationary-phases-under-simultaneous-ultraviolet-and-fluorescence-detection
#13
Suraj Adhikari, Jong Seong Kang, Wonjae Lee
A convenient method using a fluorogenic agent, 4-chloro-7-nitro-1,2,3-benzoxadiazole (NBD-Cl), was developed for enantiomer separation of chiral aliphatic amines including amino alcohols by normal high-performance liquid chromatography. The enantiomer separation of chiral aliphatic amines as NBD derivatives was performed on six covalently bonded and four coated-type polysaccharide-derived chiral stationary phases (CSPs) under simultaneous ultraviolet (UV) and fluorescence detection (FLD). Among the covalently bonded CSPs, Chiralpak IE showed the best enantiomer separation for most analytes...
December 2016: Chirality
https://www.readbyqxmd.com/read/27879637/temperature-triggered-switchable-helix-helix-inversion-of-poly-phenylacetylene-bearing-l-valine-ethyl-ester-pendants-and-its-chiral-recognition-ability
#14
Yanli Zhou, Chunhong Zhang, Yuan Qiu, Lijia Liu, Taotao Yang, Hongxing Dong, Toshifumi Satoh, Yoshio Okamoto
A phenylacetylene containing the l-valine ethyl ester pendant (PAA-Val) was synthesized and polymerized by an organorhodium catalyst (Rh(nbd)BPh₄) to produce the corresponding one-handed helical cis-poly(phenylacetylene) (PPAA-Val). PPAA-Val showed a unique temperature-triggered switchable helix-sense in chloroform, while it was not observed in highly polar solvents, such as N,N'-dimethylformamide (DMF). By heating the solution of PPAA-Val in chloroform, the sign of the CD absorption became reversed, but recovered after cooling the solution to room temperature...
November 21, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27872481/imaging-cellular-dynamics-with-spectral-relaxation-imaging-microscopy-distinct-spectral-dynamics-in-golgi-membranes-of-living-cells
#15
Alireza Lajevardipour, James W M Chon, Amitabha Chattopadhyay, Andrew H A Clayton
Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27870912/atp-hydrolysis-induced-conformational-changes-in-the-vitamin-b12-transporter-btucd-revealed-by-md-simulations
#16
Chao Pan, Jingwei Weng, Wenning Wang
ATP binding cassette (ABC) transporters utilize the energy of ATP hydrolysis to uni-directionally transport substrates across cell membrane. ATP hydrolysis occurs at the nucleotide-binding domain (NBD) dimer interface of ABC transporters, whereas substrate translocation takes place at the translocation pathway between the transmembrane domains (TMDs), which is more than 30 angstroms away from the NBD dimer interface. This raises the question of how the hydrolysis energy released at NBDs is "transmitted" to trigger the conformational changes at TMDs...
2016: PloS One
https://www.readbyqxmd.com/read/27870528/catalytically-triggered-energy-release-from-strained-organic-molecules-the-surface-chemistry-of-quadricyclane-and-norbornadiene-on-pt-111
#17
Udo Bauer, Susanne Mohr, Tibor Döpper, Philipp Bachmann, Florian Späth, Fabian Düll, Matthias Schwarz, Olaf Brummel, Lukas Fromm, Ute Pinkert, Andreas Görling, Andreas Hirsch, Julien Bachmann, Hans-Peter Steinrück, Jörg Libuda, Christian Papp
We have investigated the surface chemistry of the polycyclic valence-isomer pair norbornadiene (NBD) and quadricyclane (QC) on Pt(111). The NBD/QC system is considered to be a prototype for energy storage in strained organic compounds. By using a multimethod approach, including UV photoelectron, high-resolution X-ray photoelectron, and IR reflection-absorption spectroscopic analysis and DFT calculations, we could unambiguously identify and differentiate between the two molecules in the multilayer phase, which implies that the energy-loaded QC molecule is stable in this state...
November 21, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27859900/reactive-conjugated-polymers-synthesis-modification-and-electrochemical-properties-of-polypentafluorophenylacetylene-co-polymers
#18
Mathamsanqa N Bhebhe, Eva Alvarez De Eulate, Yiwen Pei, Damien W M Arrigan, Peter J Roth, Andrew B Lowe
(Co)Polymers containing pentafluorophenylacetylene (F5 PA) have been prepared for the first time mediated by [Rh(nbd)Cl]2 /NEt3 to give materials with properties typical of poly(phenylacetylene)s prepared with this catalyst/co-catalyst combination. It is demonstrated that the F5 PA repeat units in these new (co)polymers serve as convenient reactive species for post-polymerization modification with thiols via para-fluoro aromatic nucleophilic substitution reactions to give an entirely new family of novel thioether-functional polyene materials accompanied by absorption maxima shifts of up to 130 nm...
November 18, 2016: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/27853796/investigation-of-thiolysis-of-nbd-amines-for-the-development-of-h2s-probes-and-evaluating-the-stability-of-nbd-dyes
#19
Fanbo Song, Zhifei Li, Jiayuan Li, Shuai Wu, Xianbo Qiu, Zhen Xi, Long Yi
In order to evaluate the thiolysis of NBD (7-nitro-1,2,3-benzoxadiazole) amines for development of H2S probes, herein we investigated the reactivity and selectivity of a series of NBD amines for the first time. The piperazinyl- and piperidyl-based NBD probes could react efficiently with micromolar H2S in buffer (pH 7.4), while such NBD(S) (nitrobenzothiadiazole) derivatives showed much slow thiolysis even in the presence of millimolar H2S. Low reactivity was also observed for thiolysis of these ethylamino-, ethanolamino- and anilino-based NBD probes...
November 29, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27853462/ethylene-potentiates-sulfur-mediated-reversal-of-cadmium-inhibited-photosynthetic-responses-in-mustard
#20
Nafees A Khan, Mohd Asgher, Tasir S Per, Asim Masood, Mehar Fatma, M I R Khan
The potential of exogenous ethylene and sulfur (S) in reversal of cadmium (Cd)-inhibited photosynthetic and growth responses in mustard (Brassica juncea L. cv. Pusa Jai Kisan) were studied. Plants grown with 50 μM Cd showed increased superoxide and H2O2 accumulation and lipid peroxidation together with increased activity of 1-aminocyclopropane carboxylic acid synthase (ACS) and ethylene production and inhibition of photosynthesis and growth. Application of 1 mM SO4(2-) or 200 μL L(-1) ethephon (ethylene source) influenced photosynthetic and growth performance equally in presence or absence of Cd...
2016: Frontiers in Plant Science
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