Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.

• MeSH
• difuze MeSH
• fluorescenční barviva chemie   metabolismus   MeSH
• fosfatidylcholiny chemie   MeSH
• lipidové dvojvrstvy chemie   metabolismus   MeSH
• polyethylenglykoly chemie   MeSH
• simulace molekulární dynamiky MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R2 = 0.7 correlation between the computed ΔG'int_rel and experimental ΔTm's for the remaining ligands has been very encouraging.

• MeSH
• Bacillus thuringiensis enzymologie   ultrastruktura   MeSH
• cytokiny chemie   genetika   MeSH
• Escherichia coli enzymologie   ultrastruktura   MeSH
• krystalografie rentgenová MeSH
• kvantová teorie MeSH
• leukocyty mononukleární chemie   enzymologie   MeSH
• lidé MeSH
• membránové proteiny chemie   genetika   ultrastruktura   MeSH
• nukleotidy biosyntéza   chemie   genetika   MeSH
• přirozená imunita genetika   MeSH
• substrátová specifita MeSH
• Thermotoga maritima enzymologie   ultrastruktura   MeSH
• Vibrio cholerae enzymologie   ultrastruktura   MeSH
• vztahy mezi strukturou a aktivitou * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The effect of non-ionic detergents on baclofen (GABAB-R agonist)-stimulated G-protein activity was measured as a [(35)S]GTPgammaS binding assay in the plasma membranes (PM) isolated from the brain tissue. The effect was clearly biphasic--a decrease in the activity was followed by an activation maximum and finally, at high concentrations, drastic inhibition of the G-protein activity was noticed. Contrarily, specific radioligand binding to GABAB-receptor was inhibited in the whole range of detergent concentrations step by step, i.e. it was strictly monophasic. The magnitude of both detergent effects was decreased in the same order of potency: Brij58>Triton X-100>Digitonin. The identical order was found when comparing detergents ability to alter fluorescence anisotropy of the membrane probe 1,6-diphenyl-1,3,5-hexatriene (rDPH) incorporated into the hydrophobic PM interior. Decrease of rDPH, in the order of Brij58>Triton X-100>Digitonin, was reflected as decrease of the S-order parameter and rotation correlation time phi paralleled by an increase of diffusion wobbling constant Dw (analysis by time-resolved fluorescence according to "wobble-in-cone" model). The influence of the detergents on the membrane organization at the polar headgroup region was characterized by Laurdan generalized polarization (GP). As before, the effect of detergents on GP parameters proceeded in the order: Brij58>Triton X-100>Digitonin.

• MeSH
• 2-naftylamin analogy a deriváty   MeSH
• buněčná membrána metabolismus   účinky léků   MeSH
• cetomakrogol farmakologie   MeSH
• difenylhexatrien MeSH
• difuze MeSH
• financování organizované MeSH
• fluorescenční barviva MeSH
• fluorescenční spektrometrie MeSH
• krysa rodu rattus MeSH
• laurany MeSH
• mozek metabolismus   účinky léků   MeSH
• oktoxynol farmakologie   MeSH
• proteiny vázající GTP metabolismus   MeSH
• receptory GABA-B metabolismus   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH

Volume transmission in the brain is mediated by the diffusion of neurotransmitters, modulators and other neuroactive substances in the extracellular space. The effects of nitric oxide synthase inhibition on extracellular space diffusion properties were studied using two different approaches, the histological dextran method and the real-time iontophoretic tetramethylammonium method. The spread of biotinylated dextran (mol. wt 3000) in the extracellular space was measured morphometrically following microinjection into the neostriatum of male rats. Two parameters were used to describe the spread of biotinylated dextran in brain tissue, namely, total volume of spread and the mean grey value. The nonspecific nitric oxide synthase inhibitors NG-nitro-L-arginine methyl ester (10-100 mg/kg) and NG-monomethyl-L-arginine acetate (30-200 mg/kg) decreased the total volume of spread of dextran in a dose-dependent manner. 7-Nitroindazole monosodium salt (50-100 mg/kg), a specific neuronal nitric oxide synthase inhibitor, did not change the total volume of spread of dextran. Using the tetramethylammonium method, the extracellular space diffusion properties can be described by the volume fraction (alpha = extracellular space volume/total tissue volume), tortuosity lambda (lambda2 = free diffusion coefficient/apparent diffusion coefficient in tissue), and non-specific uptake kappa' [Nicholson C. and Sykova E. (1998) Trends Neurosci. 21, 207-215]. Nitric oxide synthase inhibition by NG-nitro-L-arginine methyl ester (50 mg/kg) had relatively little effect on volume fraction and tortuosity, and no changes were observed after NG-monomethyl-L-arginine acetate (20 mg/kg) or 7-nitroindazole monosodium salt (100 mg/kg) treatment. A substantial increase was found only in non-specific uptake, by 13% after NG-nitro-L-arginine methyl ester and by 16% after NG-monomethyl-L-arginine acetate, which correlates with the decreased total volume of spread of dextran observed with the dextran method. NG-Nitro-L-arginine methyl ester treatment (100 mg/kg) decreased striatal blood flow and increased mean arterial blood pressure. The changes in dextran spread and non-specific uptake can be explained by an increased capillary clearance following the inhibition of endothelial nitric oxide synthase, as neuronal nitric oxide synthase inhibition had no effect. The observed changes after non-specific nitric oxide synthase inhibition may affect the extracellular space concentration of neurotransmitters and modulators, and influence volume transmission pathways in the central nervous system by increased capillary and/or cellular clearance rather than by changes in extracellular space diffusion.

• MeSH
• biotin analogy a deriváty   aplikace a dávkování   farmakokinetika   MeSH
• časové faktory MeSH
• dextrany aplikace a dávkování   farmakokinetika   MeSH
• difuze MeSH
• extracelulární prostor enzymologie   metabolismus   účinky léků   MeSH
• fluorescenční barviva MeSH
• gangliová stimulancia diagnostické užití   MeSH
• hematoencefalická bariéra účinky léků   MeSH
• indazoly farmakologie   MeSH
• inhibitory enzymů * farmakologie   MeSH
• krysa rodu rattus MeSH
• kvartérní amoniové sloučeniny diagnostické užití   MeSH
• mozkový krevní oběh účinky léků   MeSH
• neostriatum * enzymologie   účinky léků   ultrastruktura   MeSH
• NG-nitroargininmethylester farmakologie   MeSH
• počítačové zpracování obrazu MeSH
• potkani Sprague-Dawley MeSH
• proteiny nervové tkáně metabolismus   MeSH
• synthasa oxidu dusnatého, typ I MeSH
• synthasa oxidu dusnatého * antagonisté a inhibitory   metabolismus   MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• práce podpořená grantem MeSH

Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.

• MeSH
• elektronová kryomikroskopie MeSH
• elongační faktory chemie   genetika   metabolismus   ultrastruktura   MeSH
• Escherichia coli genetika   metabolismus   MeSH
• iniciační faktory chemie   metabolismus   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• messenger RNA chemie   genetika   metabolismus   MeSH
• mutace MeSH
• peptidy chemie   metabolismus   MeSH
• proteiny vázající RNA chemie   metabolismus   MeSH
• proteiny z Escherichia coli chemie   genetika   metabolismus   ultrastruktura   MeSH
• proteosyntéza MeSH
• ribozomy chemie   metabolismus   ultrastruktura   MeSH
• RNA transferová chemie   genetika   metabolismus   MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH

A model for the complex between E. coli RNase HI and the DNA/RNA hybrid (previously refined by molecular dynamics simulations) was used to determine the impact of the internucleotide linkage modifications (either 3-O-CH2-P-O-5' or 3-O-P-CH2-O-5) on the ability of the modified-DNA/RNA hybrid to create a complex with the protein. Modified internucleotide linkages were incorporated systematically at different positions close to the 3-end of the DNA strand to interfere with the DNA binding site of RNase H. Altogether, six trajectories were produced (length 1.5ns). Mutual hydrogen bonds connecting both strands of the nucleic acids hybrid, DNA with RNase H, RNA with RNase H, and the scissile bond with the Mg++. 4H2O chelate complex (bound in the active site) were analyzed in detaiL Many residues were involved in binding of the DNA (Arg88, Asn84, Trp85, Trp104, Tyr73, Lys99, Asn100, Thr43, and Asn 16) and RNA (Gln76, Gln72, Tyr73, Lys122, Glu48, Asn44, and Cys13) strand to the substrate-binding site of the RNase H enzyme. The most remarkable disturbance of the hydrogen bonding net was observed for structures with modified internucleotide linkages positioned in a way to interact with the Trp104, Tyr73, Lys99, and Asn100 residues (situated in the middle of the DNA binding site, where a cluster of Trp residues forms a rigid core of the protein structure).

• MeSH
• bakteriální RNA chemie   MeSH
• chemické modely MeSH
• DNA chemie   MeSH
• Escherichia coli enzymologie   MeSH
• hořčík chemie   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• nukleotidy chemie   MeSH
• organofosfonáty chemie   MeSH
• počítačová simulace MeSH
• ribonukleasa H chemie   MeSH
• RNA chemie   MeSH
• tryptofan chemie   MeSH
• tyrosin chemie   MeSH
• vazebná místa MeSH
• vodíková vazba MeSH

• MeSH
• degenerace nervu MeSH
• regenerace nervu MeSH
• Schwannovy buňky patofyziologie   fyziologie   anatomie a histologie   MeSH

• Konspekt
• Lékařské vědy. Lékařství
• NLK Obory
• anatomie
• neurovědy

The patients with mantle cell lymphoma (MCL) have translocation t(11;14) associated with cyclin D1 overexpression. We observed that iron (an essential cofactor of dioxygenases including prolyl hydroxylases [PHDs]) depletion by deferoxamine blocked MCL cells' proliferation, increased expression of DNA damage marker γH2AX, induced cell cycle arrest and decreased cyclin D1 level. Treatment of MCL cell lines with dimethyloxalylglycine, which blocks dioxygenases involving PHDs by competing with their substrate 2-oxoglutarate, leads to their decreased proliferation and the decrease of cyclin D1 level. We then postulated that loss of EGLN2/PHD1 in MCL cells may lead to down-regulation of cyclin D1 by blocking the degradation of FOXO3A, a cyclin D1 suppressor. However, the CRISPR/Cas9-based loss-of-function of EGLN2/PHD1 did not affect cyclin D1 expression and the loss of FOXO3A did not restore cyclin D1 levels after iron chelation. These data suggest that expression of cyclin D1 in MCL is not controlled by ENGL2/PHD1-FOXO3A pathway and that chelation- and 2-oxoglutarate competition-mediated down-regulation of cyclin D1 in MCL cells is driven by yet unknown mechanism involving iron- and 2-oxoglutarate-dependent dioxygenases other than PHD1. These data support further exploration of the use of iron chelation and 2-oxoglutarate-dependent dioxygenase inhibitors as a novel therapy of MCL.

• MeSH
• aminokyseliny dikarboxylové farmakologie   MeSH
• chelátory železa farmakologie   MeSH
• cyklin D1 metabolismus   MeSH
• deferoxamin farmakologie   MeSH
• deficit železa MeSH
• dioxygenasy antagonisté a inhibitory   metabolismus   MeSH
• down regulace účinky léků   MeSH
• hydroxylace MeSH
• hypoxie buňky účinky léků   MeSH
• inhibitory enzymů farmakologie   MeSH
• kyseliny ketoglutarové farmakologie   MeSH
• lidé MeSH
• lymfom z plášťových buněk enzymologie   MeSH
• messenger RNA genetika   metabolismus   MeSH
• nádorové buněčné linie MeSH
• poškození DNA MeSH
• prolyl-4-hydroxylasy HIF metabolismus   MeSH
• protein FOXO3 genetika   metabolismus   MeSH
• železo MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Lysosomální onemocnění jsou vzácné, dědičně podmíněné nemoci způsobené nedostatečnou aktivitou některého z lysosomálních enzymů, event. transportních proteinů. První příznaky se mohou objevit kdykoli od novorozeneckého období až do pozdní dospělosti, časné formy mívají těžký průběh s rychlou progresí a infaustní prognózou. Postižení je multisystémové s trvalou progresí obtíží a postižením metabolicky aktivních orgánů či tkání – kostní dřeň, játra, kosti, kosterní svaly, myokard, CNS. Diagnózu definitivně potvrdíme průkazem snížené aktivity daného enzymu a mutační analýzou. Některé ze střádavých nemocí můžeme účinně léčit podáním rekombinantních enzymů intravenózně či omezením množství střádaného substrátu. U malého počtu lysosomálních onemocnění je úspěšná transplantace kostní dřeně. Je nutná mezioborová spolupráce včetně zajištění genetického poradenství a prenatální diagnostiky v rodinách pacientů. První část sdělení je věnována obecné charakteristice lysosomálních onemocnění a problematice nejčastějších onemocnění, které je možné v současné době v České republice léčit (Gaucherova nemoc, Pompeho nemoc, Fabryho nemoc, Niemann-Pickova nemoc, nemoc ze střádání esteru cholesterolu). Ve druhé části článku je věnována pozornost problematice mukopolysacharidóz, které představují další skupinu vzácných lysosomálních onemocnění.

Lysosomal storage diseases are rare genetic diseases caused by insufficient activity of some of the lysosomal enzymes and/or transport proteins. Initial symptoms may appear any time from the neonatal period to late adulthood; early forms tend to have a severe course with rapid progression and unfavorable prognosis. There is multisystem involvement with continuous progression of symptoms and involvement of metabolically active organs or tissues – the bone marrow, liver, bones, skeletal muscles, myocardium, or CNS. The diagnosis is definitively confirmed by demonstration of reduced activity of the particular enzyme and by mutation analysis. Some of the storage diseases can be effectively treated by intravenous administration of recombinant enzymes or by limiting the amount of the substrate stored. In a small number of lysosomal storage diseases, bone marrow transplantation is successful. Multidisciplinary collaboration, including genetic counseling and prenatal diagnosis in patient families, is required. The first part of the paper deals with general characteristics of lysosomal storage diseases and the most common diseases that are currently treatable in the Czech Republic (Gaucher’s disease, Pompe disease, Fabry disease, Niemann–Pick disease, cholesterol ester storage disease). The second part of the paper deals with mucopolysaccharidoses, another group of rare lysosomal storage diseases.

• Klíčová slova
• enzymová substituční léčba, substrát redukční terapie,
• MeSH
• 1-deoxynojirimycin analogy a deriváty   MeSH
• alfa-glukosidasy MeSH
• časná diagnóza MeSH
• dítě MeSH
• dospělí MeSH
• enzymová substituční terapie metody   využití   MeSH
• Fabryho nemoc diagnóza   farmakoterapie   patofyziologie   MeSH
• Gaucherova nemoc diagnóza   farmakoterapie   klasifikace   MeSH
• genetické nemoci vrozené * diagnóza   farmakoterapie   klasifikace   MeSH
• genistein MeSH
• glykogenóza typu II diagnóza   farmakoterapie   klasifikace   MeSH
• inhibitory enzymů farmakologie   MeSH
• inhibitory glykosidových hydrolas MeSH
• inhibitory proteinkinas MeSH
• kojenec MeSH
• lidé MeSH
• lyzozomální nemoci z ukládání * diagnóza   ekonomika   farmakoterapie   klasifikace   MeSH
• mladiství MeSH
• mukopolysacharidózy diagnóza   ekonomika   terapie   MeSH
• Niemannova-Pickova nemoc typu C diagnóza   farmakoterapie   patofyziologie   MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• příznaky a symptomy MeSH
• vzácné nemoci * diagnóza   farmakoterapie   klasifikace   MeSH
• Wolmanova nemoc MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH

The bacterium Pseudomonas putida KT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as lignocellulosic residues or plastics. However, P. putida on its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to address this limitation by adopting a recombinant cellulosome strategy for this host. In this work, we report an essential step in this endeavor-a display of designer enzyme-anchoring protein "scaffoldins", encompassing cohesin binding domains from divergent cellulolytic bacterial species on the P. putida surface. Two P. putida chassis strains, EM42 and EM371, with streamlined genomes and differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were optimally delivered to their surface with one of four tested autotransporter systems (Ag43 from Escherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results not only highlight the value of cell surface engineering for presentation of recombinant proteins on the envelope of Gram-negative bacteria but also pave the way toward designer cellulosome strategies tailored for P. putida.

• MeSH
• beta-glukosidasa metabolismus   MeSH
• celulosa metabolismus   MeSH
• celulozómy metabolismus   MeSH
• chromozomální proteiny, nehistonové chemie   MeSH
• Escherichia coli metabolismus   MeSH
• genom bakteriální * MeSH
• membránové proteiny metabolismus   MeSH
• metabolické inženýrství metody   MeSH
• proteinové domény MeSH
• proteiny buněčného cyklu chemie   MeSH
• proteiny z Escherichia coli metabolismus   MeSH
• Pseudomonas putida genetika   metabolismus   MeSH
• rekombinantní proteiny metabolismus   MeSH
• vnější bakteriální membrána metabolismus   MeSH
• zelené fluorescenční proteiny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH