The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex-SecYEG in the inner membrane-is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
- MeSH
- adenosintrifosfát metabolismus MeSH
- adenosintrifosfatasy genetika metabolismus MeSH
- bakteriální proteiny * metabolismus MeSH
- nukleotidy metabolismus MeSH
- proteiny SecA metabolismus MeSH
- proteiny z Escherichia coli * metabolismus MeSH
- translokační kanály SEC chemie MeSH
- transport proteinů MeSH
- Publikační typ
- časopisecké články MeSH
Obor medicinální chemie se často potýká s problémem suboptimálních vlastností aktivních látek. Za účelem zlepšení těchto vlastností byla vyvinuta řada důmyslných přístupů tvorby proléčiv. Proléčivo je inaktivovaná forma léčiva, která dočasně modifikuje jeho vlastnosti. V těle je pak proléčivo (nejčastěji enzymaticky) transformováno zpět na aktivní léčivo. Proléčiva mohou upravit řadu vlastností jako např. absorpci, rozpustnost, či cílené doručení do tkáně. Poměr proléčiv mezi schválenými léky v posledních letech stoupá, což podtrhuje význam této strategie pro medicinální chemii i klinické využití.
The field of medicinal chemistry is often struggling with suboptimal properties of active compounds. To address this issue, many sophisticated prodrug approaches have been developed. Prodrug is an inactive form of a drug which temporarily alters its properties. In the body, the prodrug is (most often enzymatically) transformed back to the parent active drug. Prodrugs can modify variety of properties such as absorption, solubility, or tissue targeted delivery. The number of prodrugs among approved drugs has been rising in the past years which underlines the importance of prodrugs for medicinal chemistry and clinical use.
Five 2'-deoxyribonucleoside triphosphates (dNTPs) derived from epigenetic pyrimidines (5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil, and 5-formyluracil) were prepared and systematically studied as substrates for nine DNA polymerases in competition with natural dNTPs by primer extension experiments. The incorporation of these substrates was evaluated by a restriction endonucleases cleavage-based assay and by a kinetic study of single nucleotide extension. All of the modified pyrimidine dNTPs were good substrates for the studied DNA polymerases that incorporated a significant percentage of the modified nucleotides into DNA even in the presence of natural nucleotides. 5-Methylcytosine dNTP was an even better substrate for most polymerases than natural dCTP. On the other hand, 5-hydroxymethyl-2'-deoxyuridine triphosphate was not the best substrate for SPO1 DNA polymerase, which naturally synthesizes 5hmU-rich genomes of the SPO1 bacteriophage. The results shed light onto the possibility of gene silencing through recycling and random incorporation of epigenetic nucleotides and into the replication of modified bacteriophage genomes.
- MeSH
- 5-methylcytosin * MeSH
- deoxyribonukleosidy MeSH
- DNA-dependentní DNA-polymerasy metabolismus MeSH
- DNA metabolismus MeSH
- epigeneze genetická MeSH
- nukleotidy metabolismus MeSH
- pyrimidinové nukleotidy * MeSH
- pyrimidiny MeSH
- restrikční enzymy metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Here, we define unappreciated mechanisms by which the RAD51 paralog complex RFS-1/RIP-1 limits the accumulation of RAD-51-ssDNA complexes with unfavorable nucleotide content. We find RAD51 paralogs promote the turnover of ADP-bound RAD-51 from ssDNA, in striking contrast to their ability to stabilize productive ATP-bound RAD-51 nucleoprotein filaments. In addition, RFS-1/RIP-1 inhibits binding of nucleotide-free RAD-51 to ssDNA. We propose that 'nucleotide proofreading' activities of RAD51 paralogs co-operate to ensure the enrichment of active, ATP-bound RAD-51 filaments on ssDNA to promote HR.
- MeSH
- adenosindifosfát farmakologie MeSH
- adenosintrifosfát farmakologie MeSH
- Caenorhabditis elegans metabolismus MeSH
- druhová specificita MeSH
- fluorescence MeSH
- interferometrie MeSH
- jednovláknová DNA metabolismus MeSH
- nukleotidy metabolismus MeSH
- proteiny Caenorhabditis elegans metabolismus MeSH
- rekombinasa Rad51 chemie metabolismus MeSH
- sekvenční homologie aminokyselin * MeSH
- stabilita proteinů účinky léků MeSH
- vazba proteinů účinky léků MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Parasites of the Plasmodium genus are unable to produce purine nucleotides de novo and depend completely on the salvage pathway. This fact makes plasmodial hypoxanthine-guanine-(xanthine) phosphoribosyltransferase [HG(X)PRT] a valuable target for development of antimalarial agents. A series of nucleotide analogues was designed, synthesized and evaluated as potential inhibitors of Plasmodium falciparum HGXPRT, P. vivax HGPRT and human HGPRT. These novel nucleoside phosphonates have a pyrrolidine, piperidine or piperazine ring incorporated into the linker connecting the purine base to a phosphonate group(s) and exhibited a broad range of Ki values between 0.15 and 72 μM. The corresponding phosphoramidate prodrugs, able to cross cell membranes, have been synthesized and evaluated in a P. falciparum infected human erythrocyte assay. Of the eight prodrugs evaluated seven exhibited in vitro antimalarial activity with IC50 values within the range of 2.5-12.1 μM. The bis-phosphoramidate prodrug 13a with a mean (SD) IC50 of 2.5 ± 0.7 μM against the chloroquine-resistant P. falciparum W2 strain exhibited low cytotoxicity in the human hepatocellular liver carcinoma (HepG2) and normal human dermal fibroblasts (NHDF) cell lines at a concentration of 100 μM suggesting good selectivity for further structure-activity relationship investigations.
- MeSH
- antimalarika chemická syntéza metabolismus farmakologie MeSH
- buněčné linie MeSH
- erytrocyty cytologie metabolismus parazitologie MeSH
- inhibitory enzymů chemie metabolismus MeSH
- léková rezistence účinky léků MeSH
- lidé MeSH
- nukleotidy chemie metabolismus MeSH
- pentosyltransferasy antagonisté a inhibitory metabolismus MeSH
- piperazin chemie MeSH
- piperidiny chemie MeSH
- Plasmodium falciparum účinky léků enzymologie MeSH
- Plasmodium vivax enzymologie MeSH
- preklinické hodnocení léčiv MeSH
- prekurzory léčiv chemická syntéza chemie metabolismus farmakologie MeSH
- protozoální proteiny antagonisté a inhibitory metabolismus MeSH
- pyrrolidiny chemie MeSH
- viabilita buněk účinky léků MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The nucleoside/nucleotide derived antiviral agents have been the most important components of antiviral therapy used in clinics. Recently, the focus of the medicinal chemists within this exciting research field has been affected mainly by the lack of effective therapies for the Hepatitis C virus (HCV) infection and several other "neglected" diseases caused by viruses such as Zika or Dengue. 2'-Methyl modified nucleosides and their monophosphate prodrugs (ProTides) have revolutionized the therapies for HCV in the last few years and, according to the latest research efforts, have also brought a promise for treatment of diseases caused by other members of Flaviviridae family. Here, we report on the design and synthesis of 5'-N and S modified ProTides derived from 2'-methyladenosine. We studied potential applicability of these derivatives as prodrugs of this archetypal antiviral compound.
- MeSH
- adenosin analogy a deriváty chemie MeSH
- antivirové látky chemická syntéza chemie farmakologie MeSH
- dusík chemie MeSH
- Hepacivirus účinky léků MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie MeSH
- nukleotidy chemie metabolismus farmakologie MeSH
- prekurzory léčiv chemická syntéza chemie farmakologie MeSH
- síra chemie MeSH
- virus dengue účinky léků MeSH
- virus zika účinky léků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Translesion synthesis (TLS) through DNA adducts of antitumor platinum complexes has been an interesting aspect of DNA synthesis in cells treated with these metal-based drugs because of its correlation to drug sensitivity. We utilized model systems employing a DNA lesion derived from a site-specific monofunctional adduct formed by antitumor [PtCl(en)(L)](NO3)2 (complex AMD, en = ethane-1,2-diamine, L = N-[2-(acridin-9-ylamino)ethyl]-N-methylpropionamidine) at a unique G residue. The catalytic efficiency of TLS DNA polymerases, which differ in their processivity and fidelity for the insertion of correct dCTP, with respect to the other incorrect nucleotides, opposite the adduct of AMD, was investigated. For a deeper understanding of the factors that control the bypass of the site-specific adducts of AMD catalyzed by DNA polymerases, we also used microscale thermophoresis (MST) to measure the thermodynamic changes associated with TLS across a single, site-specific adduct formed in DNA by AMD. The relative catalytic efficiency of the investigated DNA polymerases for the insertion of correct dCTP, with respect to the other incorrect nucleotides, opposite the AMD adduct, was reduced. Nevertheless, incorporation of the correct C opposite the G modified by AMD of the template strand was promoted by an increasing thermodynamic stability of the resulting duplex. The reduced relative efficiency of the investigated DNA polymerases may be a consequence of the DNA intercalation of the acridine moiety of AMD and the size of the adduct. The products of the bypass of this monofunctional lesion produced by AMD and DNA polymerases also resulted from the misincorporation of dNTPs opposite the platinated G residues. The MST analysis suggested that thermodynamic factors may contribute to the forces that governed enhanced incorporation of the incorrect dNTPs by DNA polymerases.
- MeSH
- adukty DNA chemie genetika metabolismus MeSH
- akridiny chemie farmakologie MeSH
- biokatalýza MeSH
- DNA-dependentní DNA-polymerasy metabolismus MeSH
- DNA biosyntéza MeSH
- guanin metabolismus MeSH
- katalýza MeSH
- nukleotidy genetika metabolismus MeSH
- oprava DNA MeSH
- replikace DNA MeSH
- sloučeniny platiny chemie farmakologie MeSH
- tepelná difuze MeSH
- termodynamika MeSH
- Publikační typ
- časopisecké články MeSH
RNA-binding proteins (RBPs) are critical to posttranscriptional gene regulation. Therefore, characterization of the RNA molecules bound by RBPs in vivo represent a key step in elucidating their function. The recently developed iCLIP technique allows single nucleotide resolution of the RNA binding footprints of RBPs. We present the iCLIP technique modified for its application to Trypanosoma brucei and most likely other kinetoplastid flagellates. By using the immuno- or affinity purification approach, it was successfully applied to the analysis of several RBPs. Furthermore, we also provide a detailed description of the iCLIP/iCLAP protocol that shall be particularly suitable for the studies of trypanosome RBPs.
- MeSH
- imunoprecipitace metody MeSH
- nukleotidy genetika metabolismus MeSH
- parazitologie metody MeSH
- proteiny vázající RNA analýza genetika metabolismus MeSH
- protozoální proteiny analýza genetika metabolismus MeSH
- RNA protozoální genetika metabolismus MeSH
- RNA genetika metabolismus MeSH
- Trypanosoma brucei brucei genetika MeSH
- ultrafialové záření MeSH
- vazba proteinů genetika účinky záření MeSH
- vazebná místa genetika MeSH
- zobrazení jednotlivé molekuly metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.
Squaramate-linked 2'-deoxycytidine 5'-O-triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate-linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys-containing peptides. Squaramate-linked DNA formed covalent cross-links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent.
- MeSH
- DNA metabolismus MeSH
- lidé MeSH
- lysin metabolismus MeSH
- nukleotidy metabolismus MeSH
- peptidy chemie MeSH
- proteiny chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
