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Glucose hypometabolism, mitochondrial dysfunction, and cholinergic deficits have been reported in early stages of Alzheimer’s disease (AD). Here, we examine these parameters in TgF344-AD rats, an Alzheimer model that carries amyloid precursor protein and presenilin-1 mutations, and of wild type F344 rats. In mitochondria isolated from rat hippocampi, we found reductions of complex I and oxidative phosphorylation in transgenic rats. Further impairments, also of complex II, were observed in aged (wild-type and transgenic) rats. Treatment with a “cocktail” containing magnesium orotate, benfotiamine, folic acid, cyanocobalamin, and cholecalciferol did not affect mitochondrial activities in wild-type rats but restored diminished activities in transgenic rats to wild-type levels. Glucose, lactate, and pyruvate levels were unchanged by age, genetic background, or treatment. Using microdialysis, we also investigated extracellular concentrations of acetylcholine that were strongly reduced in transgenic animals. Again, ACh levels in wild-type rats did not change upon treatment with nutrients, whereas the cocktail increased hippocampal acetylcholine levels under physiological stimulation. We conclude that TgF344-AD rats display a distinct mitochondrial and cholinergic dysfunction not unlike the findings in patients suffering from AD. This dysfunction can be partially corrected by the application of the “cocktail” which is particularly active in aged rats. We suggest that the TgF344-AD rat is a promising model to further investigate mitochondrial and cholinergic dysfunction and potential treatment approaches for AD.
Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane (“proton pumping”). The mechanism of proton pumping is still a matter of debate. Many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. Therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a temperature of 100 K. No ligand exchanges or other major structural changes upon reduction of the cytochrome coxidase from Paracoccus denitrificans were observed. The three histidine CuB ligands are well defined in the oxidized and in the reduced states. These results are hardly compatible with the “histidine cycle” mechanisms formulated previously.
The potential of a protein-engineered His tag to immobilize macromolecules in a predictable orientation at metal-chelating lipid interfaces was investigated using recombinant 20 S proteasomes His-tagged in various positions. Electron micrographs demonstrated that the orientation of proteasomes bound to chelating lipid films could be controlled via the location of their His tags: proteasomes His-tagged at their sides displayed exclusively side-on views, while proteasomes His-tagged at their ends displayed exclusively end-on views. The activity of proteasomes immobilized at chelating lipid interfaces was well preserved. In solution, His-tagged proteasomes hydrolyzed casein at rates comparable with wild-type proteasomes, unless the His tags were located in the vicinity of the N termini of α-subunits. The N termini of α-subunits might partly occlude the entrance channel in α-rings through which substrates enter the proteasome for subsequent degradation. A combination of electron micrographs and atomic force microscope topographs revealed a propensity of vertically oriented proteasomes to crystallize in two dimensions on fluid lipid films. The oriented immobilization of His-tagged proteins at biocompatible lipid interfaces will assist structural studies as well as the investigation of biomolecular interaction via a wide variety of surface-sensitive techniques including single-molecule analysis.
ATP-binding cassette (ABC) systems translocate a wide range of solutes across cellular membranes. The thermophilic Gram-negative eubacterium Thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 ABC proteins, which are largely uncharacterized. Here, we functionally analyzed the first two and only ABC half-transporters of the hyperthermophilic bacterium, TmrA and TmrB. The ABC system mediates uptake of the drug Hoechst 33342 in inside-out oriented vesicles that is inhibited by verapamil. TmrA and TmrB form a stable heterodimeric complex hydrolyzing ATP with a Km of 0.9 mm and kcat of 9 s−1 at 68 °C. Two nucleotides can be trapped in the heterodimeric ABC complex either by vanadate or by mutation inhibiting ATP hydrolysis. Nucleotide trapping requires permissive temperatures, at which a conformational ATP switch is possible. We further demonstrate that the canonic glutamate 523 of TmrA is essential for rapid conversion of the ATP/ATP-bound complex into its ADP/ATP state, whereas the corresponding aspartate in TmrB (Asp-500) has only a regulatory role. Notably, exchange of this single noncanonic residue into a catalytic glutamate cannot rescue the function of the E523Q/D500E complex, implicating a built-in asymmetry of the complex. However, slow ATP hydrolysis in the newly generated canonic site (D500E) strictly depends on the formation of a posthydrolysis state in the consensus site, indicating an allosteric coupling of both active sites.
The ATP-binding cassette half-transporter Mdl1 from Saccharomyces cerevisiae has been proposed to be involved in the quality control of misassembled respiratory chain complexes by exporting degradation products generated by the m-AAA proteases from the matrix. Direct functional or structural data of the transport complex are, however, not known so far. After screening expression in various hosts, Mdl1 was overexpressed 100-fold to 1% of total mitochondrial membrane protein in S. cerevisiae. Based on detergent screens, Mdl1 was solubilized and purified to homogeneity. Mdl1 showed a high binding affinity for MgATP (Kd = 0.26 μm) and an ATPase activity with a Km of 0.86 mm (Hill coefficient of 0.98) and a turnover rate of 2.6 ATP/s. Mutagenesis of the conserved glutamate downstream of the Walker B motif (E599Q) or the conserved histidine of the H-loop (H631A) abolished ATP hydrolysis, whereas ATP binding was not affected. Mdl1 reconstituted into liposomes showed an ATPase activity similar to the solubilized complex. By single particle electron microscopy, a first three-dimensional structure of the mitochondrial ATP-binding cassette transporter was derived at 2.3-nm resolution, revealing a homodimeric complex in an open conformation.
The ABC transporter Mdl1p, a structural and functional homologue of the transporter associated with antigen processing (TAP) plays an important role in intracellular peptide transport from the mitochondrial matrix of Saccharomyces cerevisiae. To characterize the ATP hydrolysis cycle of Mdl1p, the nucleotide-binding domain (NBD) was overexpressed in Escherichia coli and purified to homogeneity. The isolated NBD was active in ATP binding and hydrolysis with a turnover of 25 ATP per minute and a Km of 0.6 mm and did not show cooperativity in ATPase activity. However, the ATPase activity was non-linearly dependent on protein concentration (Hill coefficient of 1.7), indicating that the functional state is a dimer. Dimeric catalytic transition states could be trapped either by incubation with orthovanadate or beryllium fluoride, or by mutagenesis of the NBD. The nucleotide composition of trapped intermediate states was determined using [alpha-32P]ATP and [gamma-32P]ATP. Three different dimeric intermediate states were isolated, containing either two ATPs, one ATP and one ADP, or two ADPs. Based on these experiments, it was shown that: (i) ATP binding to two NBDs induces dimerization, (ii) in all isolated dimeric states, two nucleotides are present, (iii) phosphate can dissociate from the dimer, (iv) both nucleotides are hydrolyzed, and (v) hydrolysis occurs in a sequential mode. Based on these data, we propose a processive-clamp model for the catalytic cycle in which association and dissociation of the NBDs depends on the status of bound nucleotides.
The purification and functional reconstitution of a five-component oligopeptide ATP-binding cassette transporter with a remarkably wide substrate specificity are described. High-affinity peptide uptake was dependent on liganded substrate-binding protein OppA, which interacts with the translocator OppBCDF with higher affinity than unliganded OppA. Transport screening with combinatorial peptide libraries revealed that (i) the Opp transporter is not selective with respect to amino acid side chains of the transported peptides; (ii) any peptide that can bind to OppA is transported via Opp, including very long peptides up to 35 residues long; and (iii) the binding specificity of OppA largely determines the overall transport selectivity.
The transporter associated with antigen processing (TAP) plays a key role in the adaptive immune response by pumping antigenic peptides into the endoplasmic reticulum for subsequent loading of major histocompatibility complex class I molecules. TAP is a heterodimer consisting of TAP1 and TAP2. Each subunit is composed of a transmembrane domain and a nucleotide-binding domain, which energizes the peptide transport. To analyze ATP hydrolysis of each subunit we developed a method of trapping 8-azido-nucleotides to TAP in the presence of phosphate transition state analogs followed by photocross-linking, immunoprecipitation, and high resolution SDS-PAGE. Strikingly, trapping of both TAP subunits by beryllium fluoride is peptide-specific. The peptide concentration required for half-maximal trapping is identical for TAP1 and TAP2 and directly correlates with the peptide binding affinity. Only a background level of trapping was observed for low affinity peptides or in the presence of the herpes simplex viral protein ICP47, which specifically blocks peptide binding to TAP. Importantly, the peptide-induced trapped state is reached after ATP hydrolysis and not in a backward reaction of ADP binding and trapping. In the trapped state, TAP can neither bind nor exchange nucleotides, whereas peptide binding is not affected. In summary, these data support the model that peptide binding induces a conformation that triggers ATP hydrolysis in both subunits of the TAP complex within the catalytic cycle.
The lysosomal ABC transporter associated with antigen processing-like (TAPL, ABCB9) acts as an ATP-dependent polypeptide transporter with broad length selectivity. To characterize in detail its substrate specificity, a procedure for functional reconstitution of human TAPL was developed. By intensive screening of detergents, ideal solubilization conditions were evolved with respect to efficiency, long term stability, and functionality of TAPL. TAPL was isolated in a two-step procedure with high purity and, subsequently, reconstituted into proteoliposomes. The peptide transport activity of reconstituted TAPL strongly depends on the lipid composition. With the help of combinatorial peptide libraries, the key positions of the peptides were localized to the N- and C-terminal residues with respect to peptide transport. At both ends, TAPL favors positively charged, aromatic, or hydrophobic residues and disfavors negatively charged residues as well as asparagine and methionine. Besides specific interactions of both terminal residues, electrostatic interactions are important, since peptides with positive net charge are more efficiently transported than negatively charged ones.
The transporter associated with antigen processing (TAP) translocates antigenic peptides from the cytosol into the endoplasmic reticular lumen for subsequent loading onto major histocompatibility complex (MHC) class I molecules. These peptide-MHC complexes are inspected at the cell surface by cytotoxic T-lymphocytes. Assembly of the functional peptide transport and loading complex depends on intra- and intermolecular packing of transmembrane helices (TMs). Here, we have examined the membrane topology of human TAP1 within an assembled and functional transport complex by cysteine-scanning mutagenesis. The accessibility of single cysteine residues facing the cytosol or endoplasmic reticular lumen was probed by a minimally invasive approach using membrane-impermeable, thiol-specific fluorophores in semipermeabilized “living” cells. TAP1 contains ten transmembrane segments, which place the N and C termini in the cytosol. The transmembrane domain consists of a translocation core of six TMs, a building block conserved among most ATP-binding cassette transporters, and a unique additional N-terminal domain of four TMs, essential for tapasin binding and assembly of the peptide-loading complex. This study provides a first map of the structural organization of the TAP machinery within the macromolecular MHCI peptide-loading complex.
P2X1 receptor subunits assemble in the ER of Xenopus oocytes to homotrimers that appear as ATP-gated cation channels at the cell surface. Here we address the extent to which N-glycosylation contributes to assembly, surface appearance, and ligand recognition of P2X1receptors. SDS-polyacrylamide gel electrophoresis (PAGE) analysis of glycan minus mutants carrying Gln instead of Asn at five individual NXT/S sequons reveals that Asn284 remains unused because of a proline in the +4 position. The four other sites (Asn153, Asn184, Asn210, and Asn300) carryN-glycans, but solely Asn300 located only eight residues upstream of the predicted reentry loop of P2X1acquires complex-type carbohydrates. Like parent P2X1, glycan minus mutants migrate as homotrimers when resolved by blue native PAGE. Recording of ATP-gated currents reveals that elimination of Asn153 or Asn210 diminishes or increases functional expression levels, respectively. In addition, elimination of Asn210 causes a 3-fold reduction of the potency for ATP. If three or all four N-glycosylation sites are simultaneously eliminated, formation of P2X1 receptors is severely impaired or abolished, respectively. We conclude that at least oneN-glycan per subunit of either position is absolutely required for the formation of P2X1 receptors and that individual N-glycans possess marked positional effects on expression levels (Asn154, Asn210) and ATP potency (Asn210).
One current goal in native mass spectrometry is the assignment of binding affinities to noncovalent complexes. Here we introduce a novel implementation of the existing laser-induced liquid bead ion desorption (LILBID) mass spectrometry method: this new method, LILBID laser dissociation curves, assesses binding strengths quantitatively. In all LILBID applications, aqueous sample droplets are irradiated by 3 µm laser pulses. Variation of the laser energy transferred to the droplet during desorption affects the degree of complex dissociation. In LILBID laser dissociation curves, laser energy transfer is purposely varied, and a binding affinity is calculated from the resulting complex dissociation. A series of dsDNAs with different binding affinities was assessed using LILBID laser dissociation curves. The binding affinity results from the LILBID laser dissociation curves strongly correlated with the melting temperatures from UV melting curves and with dissociation constants from isothermal titration calorimetry, standard solution phase methods. LILBID laser dissociation curve data also showed good reproducibility and successfully predicted the melting temperatures and dissociation constants of three DNA sequences. LILBID laser dissociation curves are a promising native mass spectrometry binding affinity method, with reduced time and sample consumption compared to melting curves or titrations.
Gephyrin is an ubiquitously expressed protein that, in the nervous system, is essential for synaptic anchoring of glycine receptors (GlyRs) and major GABAA receptor subtypes. The binding of gephyrin to the GlyR depends on an amphipathic motif within the large intracellular loop of the GlyRβ subunit. The mouse gephyrin gene consists of 30 exons. Ten of these exons, encoding cassettes of 5–40 amino acids, are subject to alternative splicing (C1–C7, C4′–C6′). Since one of the cassettes, C5′, has recently been reported to exclude GlyRs from GABAergic synapses, we investigated which cassettes are found in gephyrin associated with the GlyR. Gephyrin variants were purified from rat spinal cord, brain, and liver by binding to the glutathione S-transferase-tagged GlyRβ loop or copurified with native GlyR from spinal cord by affinity chromatography and analyzed by mass spectrometry. In addition to C2 and C6′, already known to be prominent, C4 was found to be abundant in gephyrin from all tissues examined. The nonneuronal cassette C3 was easily detected in liver but not in GlyR-associated gephyrin from spinal cord. C5 was present in brain and spinal cord polypeptides, whereas C5′ was coisolated mainly from liver. Notably C5′-containing gephyrin bound to the GlyRβ loop, inconsistent with its proposed selectivity for GABAA receptors. Our data show that GlyR-associated gephyrin, lacking C3, but enriched in C4 without C5, differs from other neuronal and nonneuronal gephyrin isoforms.
Background: In the past, protease inhibitors (PIs) and the reverse transcriptase inhibitor abacavir were identified increasing the risk for thromboembolic complications and cardiovascular events (CVE) of HIV infected patients taking a combination antiretroviral therapy (cART). Results of the previous HIV-PLA I-study lead to the assumption that platelet activation could play a substantial role in increasing CVE risks.
Methods: The open label, monocentric HIV-PLA II-study investigated HIV-1-infected, therapy-naïve adults (n=45) starting with cART, consisting either of boosted PI (atazanavir, n= 6, darunavir, n=11), NNRTI (efavirenz, n=14) or integrase inhibitor (raltegravir, n=14), each plus tenofovir/emtricitabine co-medication. Main exclusion criteria were tobacco smoking, the intake of NSAIDs or abacavir or past CVE. Platelet adhesive molecule p-selectin (CD62P) and FITC anti-human Integrin α-IIb/Integrin β-3 (CD41/CD61) antibody (PAC-1) binding, monocyte CD11b/monocyte-associated CD41 expression and the endogenous thrombin potential (ETP) were assessed ex vivo-in vitro at baseline, weeks 4, 12 and 24. Therapy regimens were blinded to the investigators for laboratory and statistical analyses.
Results: CD11b and ETP showed no significant changes or differences between all study groups. In contrast, the mean + SD mean fluorescence units (MFI) of CD62P and PAC-1 increased significantly in patients taking PI, indicating an enhanced potential for thrombocyte activation and aggregation.
Conclusion: CD62P expression, detecting the ɑ-platelet degranulation of pro-inflammatory and pro-thrombotic factors and adhesive proteins, and PAC-1 expression, representing a marker for conformation changes of the GIIb/IIIa receptor, increased significantly in patients taking HIV protease inhibitors. The findings of this study revealed a yet unknown pathway of platelet activation, possibly contributing to the increased risk for CVE under HIV protease inhibitor containing cART.
Clinical Trial Registration No.: DRKS00000288.
Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.
Electronic circular dichroism unravels atropisomers of a broadly absorbing fulgide derivative
(2022)
We prepared and studied six atropisomers with different chiroptical properties emerging from a single, robust, broadly-absorbing fulgide photoswitch. After separation of the different atropisomers via HPLC on a chiral column, their isomerization processes at room temperature and the energy barriers of the different species were investigated in detail using spectroscopic and theoretical methods.
In the development of photolabile protecting groups, it is of high interest to selectively modify photochemical properties with structural changes as simple as possible. In this work, knowledge of fluorophore optimization was adopted and used to design new coumarin- based photocages. Photolysis efficiency was selectively modulated by inactivating competitive decay channels, such as twisted intramolecular charge transfer (TICT) or hydrogen-bonding, and the photolytic release of the neurotransmitter serotonin was demonstrated. Structural modifications inspired by the fluorophore ATTO 390 led to a significant increase in the uncaging cross section that can be further improved by the simple addition of a double bond. Ultrafast transient absorption spectroscopy gave insights into the underlying solvent-dependent photophysical dynamics. The chromophores presented here are excellently suited as new photocages in the visible wavelength range due to their simple synthesis and their superior photochemical properties.
We synthesized two green-light activatable 5’-caps for oligonucleotides based on the BODIPY and coumarin scaffold. Both bear an alkyne functionality allowing their use in numerous biological applications. They were successfully incorporated in oligonucleotides via solid-phase synthesis. Copper-catalyzed alkyne-azide cycloaddition (CuAAC) using a bisazide photo-tether gave cyclic oligonucleotides that could be relinearized by activation with green light and were shown to exhibit high stability against exonucleases. Chemical ligation as another example for bioconjugation yielded oligonucleotides with an internal strand break site. Irradiation at 530 nm or 565 nm resulted in complete photolysis of both caging groups.
Purpose: The quality testing and approval procedure for most pharmaceutical products is a streamlined process with standardized procedures for the determination of critical quality attributes. However, the evaluation of semisolid dosage forms for topical drug delivery remains a challenging task. The work presented here highlights confocal Raman microscopy (CRM) as a valuable tool for the characterization of such products.
Methods: CRM, a laser-based method, combining chemically-selective analysis and high resolution imaging, is used for the evaluation of different commercially available topical acyclovir creams.
Results: We show that CRM enables the spatially resolved analysis of microstructural features of semisolid products and provides insights into drug distribution and polymorphic state as well as the composition and arrangement of excipients. Further, we explore how CRM can be used to monitor phase separation and to study skin penetration and the interaction with fresh and cryopreserved excised human skin tissue.
Conclusion: This study presents a comprehensive overview and illustration of how CRM can facilitate several types of key analyses of semisolid topical formulations and of their interaction with their biological target site, illustrating that CRM is a useful tool for research, development as well as for quality testing in the pharmaceutical industry.
Non-alcoholic steatohepatitis (NASH) - a hepatic manifestation of the metabolic syndrome - is a multifactorial disease with alarming global prevalence. It involves steatosis, inflammation and fibrosis in the liver, thus demanding multiple modes of action for robust therapeutic efficacy. Aiming to fuse complementary validated anti-NASH strategies in a single molecule, we have designed and systematically optimized a scaffold for triple activation of farnesoid X receptor (FXR), peroxisome proliferator-activated receptor (PPAR) α and PPARδ. Pilot profiling of the resulting triple modulator demonstrated target engagement in native cellular settings and in mice, rendering it a suitable tool to probe the triple modulator concept in vivo. In DIO NASH in mice, the triple agonist counteracted hepatic inflammation and reversed hepatic fibrosis highlighting the potential of designed polypharmacology in NASH.
Antigen presentation via major histocompatibility complex class I (MHC I) molecules is essential to mount an adaptive immune response against pathogens and cancerous cells. To this end, the transporter associated with antigen processing (TAP) delivers snippets of the cellular proteome, resulting from proteasomal degradation, into the ER lumen. After peptide loading and editing by the peptide-loading complex (PLC), stable peptide-MHC I complexes are released for cell surface presentation. Since the process of MHC I trafficking is poorly defined, we established an approach to control antigen presentation by introduction of a photo-caged amino acid in the catalytic ATP-binding site of TAP. By optical control, we initiate TAP-dependent antigen translocation, thus providing new insights into TAP function within the PLC and MHC I trafficking in living cells. Moreover, this versatile approach has the potential to be applied in the study of other cellular pathways controlled by P-loop ATP/GTPases.
Despite all advances in drug delivery, the limitations of the analytical technologies involved in the characterization of next-generation nanomedicines are still impeding further progress of an emerging market. Discriminating between different formulations and batches, drug release is one of the most important quality criteria in development and quality control of pharmaceutics. Unfortunately, there are only few methods available to sensitively measure this important parameter for nanosized carriers. With the development of the dispersion releaser (DR) technology our group has set up a dialysis-based technique that was tested with a number of nanocarrier and nanocrystal formulations such as liposomes and polymeric nanoparticles. By supporting formulation development with a more reliable methodology to assess the drug release from nanosized carriers, a first step has been made to improve future products.
Quinone methide precursors protected with alkyldithiomethyl groups have been synthesized and converted into PNA conjugates. Stable in the absence of reducing agents, the electrophilic quinone methide is released by glutathione in concentrations typical for the cytosol. Self-alkylation then occurs or crosslinking of RNA when hybridized with complementary strands. Fastest reactions are seen for the sterically least hindered compound.
The Mycobacterium tuberculosis tyrosine-specific phosphatase MptpA and its cognate kinase PtkA are prospective targets for anti-tuberculosis drugs as they interact with the host defense response within the macrophages. Although both are structurally well-characterized, the functional mechanism regulating their activity remains poorly understood. Here, we investigate the effect of post-translational oxidation in regulating the function of MptpA. Treatment of MptpA with H2O2/NaHCO3, mimicking cellular oxidative stress conditions, leads to oxidation of the catalytic cysteine (C11) and to a conformational rearrangement of the phosphorylation loop (D-loop) by repositioning the conserved tyrosine 128 (Y128) and generating a temporarily inactive preclosed state of the phosphatase. Thus, the catalytic cysteine in the P-loop acts as a redox switch and regulates the phosphatase activity of MptpA.
The p53 protein family is the most studied protein family of all. Sequence analysis and structure determination have revealed a high
similarity of crucial domains between p53, p63 and p73. Functional studies, however, have shown a wide variety of different tasks in
tumor suppression, quality control and development. Here we review the structure and organization of the individual domains of
p63 and p73, the interaction of these domains in the context of full-length proteins and discuss the evolutionary origin of this
protein family.
FACTS:
● Distinct physiological roles/functions are performed by specific isoforms.
● The non-divided transactivation domain of p63 has a constitutively high activity while the transactivation domains of p53/p73
are divided into two subdomains that are regulated by phosphorylation.
● Mdm2 binds to all three family members but ubiquitinates only p53.
● TAp63α forms an autoinhibited dimeric state while all other vertebrate p53 family isoforms are constitutively tetrameric.
● The oligomerization domain of p63 and p73 contain an additional helix that is necessary for stabilizing the tetrameric states.
During evolution this helix got lost independently in different phylogenetic branches, while the DNA binding domain became
destabilized and the transactivation domain split into two subdomains.
OPEN QUESTIONS:
● Is the autoinhibitory mechanism of mammalian TAp63α conserved in p53 proteins of invertebrates that have the same function
of genomic quality control in germ cells?
● What is the physiological function of the p63/p73 SAM domains?
● Do the short isoforms of p63 and p73 have physiological functions?
● What are the roles of the N-terminal elongated TAp63 isoforms, TA* and GTA?
tRNAs are L-shaped RNA molecules of ~ 80 nucleotides that are responsible for decoding the mRNA and for the incorporation of the correct amino acid into the growing peptidyl-chain at the ribosome. They occur in all kingdoms of life and both their functions, and their structure are highly conserved. The L-shaped tertiary structure is based on a cloverleaf-like secondary structure that consists of four base paired stems connected by three to four loops. The anticodon base triplet, which is complementary to the sequence of the mRNA, resides in the anticodon loop whereas the amino acid is attached to the sequence CCA at the 3′-terminus of the molecule. tRNAs exhibit very stable secondary and tertiary structures and contain up to 10% modified nucleotides. However, their structure and function can also be maintained in the absence of nucleotide modifications. Here, we present the assignments of nucleobase resonances of the non-modified 77 nt tRNAIle from the gram-negative bacterium Escherichia coli. We obtained assignments for all imino resonances visible in the spectra of the tRNA as well as for additional exchangeable and non-exchangeable protons and for heteronuclei of the nucleobases. Based on these assignments we could determine the chemical shift differences between modified and non-modified tRNAIle as a first step towards the analysis of the effect of nucleotide modifications on tRNA’s structure and dynamics.
Cytochrome P450 enzymes are a large superfamily of membrane-bound heme-containing monooxygenases. They are essential for the oxidative metabolism of endogenous substrates such as steroids and fatty acids, and biotransformation of xenobiotic substrates such as pollutants and drugs. Although the highest expression of CYPs is found in the liver, their cardiovascular expression is not negligible with CYP450 subfamilies being responsible for the production of vasoactive lipids. Of importance, the enzymatic activity of all microsomal CYP450 isoenzymes is dependent on the cytochrome P450 reductase (POR), an electron donor.
In the first part of this work, the role of cytochrome P450 monooxygenases on the biotransformation of organic nitrates was investigated. Recombinant SupersomesTM were selected and incubated with NTG and PETN, where nitrite release was measured as a nitric oxide (NO) footprint. The capacity of the recombinant POR/CYP450 system to release nitrite from NO prodrugs was shown to be CYP-specific and dose-dependent. To study the involvement of CYP450 enzymes in the vascular biotransformation of organic nitrates in vivo, a smooth muscle-cell specific, inducible knockout model of POR (smcPOR-/-) was generated. Organ chamber experiments revealed that the vascular POR/CYP450 system had no impact on the dilator response of NTG and PETN. In line with previous publications, inhibition of ALDH2, known as the main enzyme responsible for the activation of NTG and PETN, and/or abolishment of the endogenous NO production did not reveal a contribution of the POR/CYP450 system to the dilator response of NTG and PETN. To better understand these results, we looked at the expression of the hepatic and vascular expression of the POR/CYP450 system where the hepatic was increased by 10- to 40-fold as shown by Western blot analysis. We concluded that due to insufficient vascular expression of CYP450 enzymes their contribution to the bioactivation of NTG and PETN is only minor.
The second part of this work focused on the cardiac relevance of endothelial isoenzymes. For that purpose, an endothelial cell-specific, tamoxifen-inducible knockout model of POR was generated and characterized in the present study. RNA-sequencing of the heart of healthy mice revealed that the CYP450 expression is cell-specific with cardiac endothelial cells (ECs) exhibiting an enrichment in the expression of the Cyp4 family (ω-oxidation of fatty acids) and of the Cyp2 family (production of EETs). Under non-stredded conditions (i.e. 30 days after inducing the knockout by tamoxifen feeding), endothelial deletion of POR was associated with cardiac remodelling as observed by an increase in the ratio of heart weight to body weight and an increase in the cardiomyocyte area. RNA-sequencing of cardiac ECs suggested that loss of POR might alter ribosomal biogenesis and protein synthesis, which could potentially affect the cardiac contractility in ecPOR-/- mice. Metabolomics from cardiac tissue of CTL and ecPOR-/- mice were not indicative for an important metabolic function of the endothelial POR/CYP450 system in the heart. The combination of transverse aortic constriction (TAC) with endothelial deletion of POR accelerates the development of heart failure in mice as detected by a reduction in cardiac output and stroke volume. These effects were mediated most likely by a reduction in vascular EETs production, which increases vascular stiffness, resulting in cardiac remodeling.
Several lines of evidence suggest the ligand-sensing transcription factor Nurr1 as a promising target to treat neurodegenerative diseases. Nurr1 modulators to validate and exploit this therapeutic potential are rare, however. To identify novel Nurr1 agonist chemotypes, we have employed the Nurr1 activator amodiaquine as template for microscale analogue library synthesis. The first set of analogues was based on the 7-chloroquiolin-4-amine core fragment of amodiaquine and revealed superior N-substituents compared to diethylaminomethylphenol contained in the template. A second library of analogues was subsequently prepared to replace the chloroquinolineamine scaffold. The two sets of analogues enabled a full scaffold hop from amodiaquine to a novel Nurr1 agonist sharing no structural features with the lead but comprising superior potency on Nurr1. Additionally, pharmacophore modeling based on the entire set of active and inactive analogues suggested key features for Nurr1 agonists.
Candida boidinii NAD+-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential applications in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of the wild-type CbFDH at cryogenic and ambient temperatures as well as Val120Thr mutant at cryogenic temperature determined at the Turkish Light Source "Turkish DeLight". The structures reveal new hydrogen bonds between Thr120 and water molecules in the mutant CbFDH's active site, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, our findings provide invaluable insights into future protein engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.
Candida boidinii NAD+-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential applications in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of the wild-type CbFDH at cryogenic and ambient temperatures as well as Val120Thr mutant at cryogenic temperature determined at the Turkish Light Source "Turkish DeLight". The structures reveal new hydrogen bonds between Thr120 and water molecules in the mutant CbFDH's active site, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, our findings provide invaluable insights into future protein engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.
BH3 mimetics are promising novel anticancer therapeutics. By selectively inhibiting BCL-2, BCL-xL, or MCL-1 (i.e. ABT-199, A-1331852, S63845) they shift the balance of pro- and anti-apoptotic proteins in favor of apoptosis. As Bromodomain and Extra Terminal (BET) protein inhibitors promote pro-apoptotic rebalancing, we evaluated the potential of the BET inhibitor JQ1 in combination with ABT-199, A-1331852 or S63845 in rhabdomyosarcoma (RMS) cells. The strongest synergistic interaction was identified for JQ1/A-1331852 and JQ1/S63845 co-treatment, which reduced cell viability and long-term clonogenic survival. Mechanistic studies revealed that JQ1 upregulated BIM and NOXA accompanied by downregulation of BCL-xL, promoting pro-apoptotic rebalancing of BCL-2 proteins. JQ1/A-1331852 and JQ1/S63845 co-treatment enhanced this pro-apoptotic rebalancing and triggered BAK- and BAX-dependent apoptosis since a) genetic silencing of BIM, BAK or BAX, b) inhibition of caspase activity with zVAD.fmk and c) overexpression of BCL-2 all rescued JQ1/A-1331852- and JQ1/S63845-induced cell death. Interestingly, NOXA played a different role in both treatments, as genetic silencing of NOXA significantly rescued from JQ1/A-1331852-mediated apoptosis but not from JQ1/S63845-mediated apoptosis. In summary, JQ1/A-1331852 and JQ1/S63845 co-treatment represent new promising therapeutic strategies to synergistically trigger mitochondrial apoptosis in RMS.
Currently, a wide variety of complex non-oral dosage forms are entering the global healthcare market. Although many assays have been described in recent research, harmonized procedures and standards for testing their in vitro performance remain widely unexplored. Among others, dialysis-based techniques such as the Pharma Test Dispersion Releaser are developed for testing the release of drugs from nanoparticles, liposomes, or extracellular vesicle preparations. Here, we provide advanced strategies and practical advice for the development and validation of dialysis-based techniques, including documentation, analysis, and interpretation of the raw data. For this purpose, key parameters of the release assay, including the hydrodynamics in the device at different stirring rates, the selectivity for particles and molecules, as well as the effect of excipients on drug permeation were investigated. At the highest stirring rate, a more than twofold increase in the membrane permeation rate (from 0.99 × 10−3 to 2.17 × 10−3 cm2/h) was observed. Additionally, we designed a novel computer model to identify important quality parameters of the dialysis experiment and to calculate error-corrected release profiles. Two hydrophilic creams of diclofenac, Voltaren® Emulgel, and Olfen® gel, were tested and provide first-hand evidence of the robustness of the assay in the presence of semisolid dosage forms.
During evolution of an RNA world, the development of enzymatic function was essential. Such enzymatic function was linked to RNA sequences capable of adopting specific RNA folds that possess catalytic pockets to promote catalysis. Within this primordial RNA world, initially evolved self-replicating ribozymes presumably mutated to ribozymes with new functions. Schultes and Bartel (Science 2000, 289, 448–452) investigated such conversion from one ribozyme to a new ribozyme with distinctly different catalytic functions. Within a neutral network that linked these two prototype ribozymes, a single RNA chain could be identified that exhibited both enzymatic functions. As commented by Schultes and Bartel, this system possessing one sequence with two enzymatic functions serves as a paradigm for an evolutionary system that allows neutral drifts by stepwise mutation from one ribozyme into a different ribozyme without loss of intermittent function. Here, we investigated this complex functional diversification of ancestral ribozymes by analyzing several RNA sequences within this neutral network between two ribozymes with class III ligase activity and with self-cleavage reactivity. We utilized rapid RNA sample preparation for NMR spectroscopic studies together with SHAPE analysis and in-line probing to characterize secondary structure changes within the neutral network. Our investigations allowed delineation of the secondary structure space and by comparison with the previously determined catalytic function allowed correlation of the structure-function relation of ribozyme function in this neutral network.
Polo-like kinase 1 (PLK1) is a crucial regulator of cell cycle progression. It is established that the activation of PLK1 depends on the coordinated action of Aurora-A and Bora. Nevertheless, very little is known about the spatiotemporal regulation of PLK1 during G2, specifically, the mechanisms that keep cytoplasmic PLK1 inactive until shortly before mitosis onset. Here, we describe PLK1 dimerization as a new mechanism that controls PLK1 activation. During the early G2 phase, Bora supports transient PLK1 dimerization, thus fine-tuning the timely regulated activation of PLK1 and modulating its nuclear entry. At late G2, the phosphorylation of T210 by Aurora-A triggers dimer dissociation and generates active PLK1 monomers that support entry into mitosis. Interfering with this critical PLK1 dimer/monomer switch prevents the association of PLK1 with importins, limiting its nuclear shuttling, and causes nuclear PLK1 mislocalization during the G2-M transition. Our results suggest a novel conformational space for the design of a new generation of PLK1 inhibitors.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ∼70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade
(2020)
Stroke is a leading cause of death and disability. Recovery depends on a delicate balance between inflammatory responses and immune suppression, tipping the scale between brain protection and susceptibility to infection. Peripheral cholinergic blockade of immune reactions fine-tunes this immune response, but its molecular regulators are unknown. Here, we report a regulatory shift in small RNA types in patient blood sequenced two days after ischemic stroke, comprising massive decreases of microRNA levels and concomitant increases of transfer RNA fragments (tRFs) targeting cholinergic transcripts. Electrophoresis-based size-selection followed by RT-qPCR validated the top 6 upregulated tRFs in a separate cohort of stroke patients, and independent datasets of small and long RNA sequencing pinpointed immune cell subsets pivotal to these responses, implicating CD14+ monocytes in the cholinergic inflammatory reflex. In-depth small RNA targeting analyses revealed the most-perturbed pathways following stroke and implied a structural dichotomy between microRNA and tRF target sets. Furthermore, lipopolysaccharide stimulation of murine RAW 264.7 cells and human CD14+ monocytes upregulated the top 6 stroke-perturbed tRFs, and overexpression of stroke-inducible tRF-22-WE8SPOX52 using an ssRNA mimic induced downregulation of immune regulator Z-DNA binding protein 1 (Zbp1). In summary, we identified a “changing of the guards” between RNA types that may systemically affect homeostasis in post-stroke immune responses, and pinpointed multiple affected pathways, which opens new venues for establishing therapeutics and biomarkers at the protein- and RNA-level.
Significance Statement Ischemic stroke triggers peripheral immunosuppression, increasing the susceptibility to post-stroke pneumonia that is linked with poor survival. The post-stroke brain initiates intensive communication with the immune system, and acetylcholine contributes to these messages; but the responsible molecules are yet unknown. We discovered a “changing of the guards,” where microRNA levels decreased but small transfer RNA fragments (tRFs) increased in post-stroke blood. This molecular switch may re-balance acetylcholine signaling in CD14+ monocytes by regulating their gene expression and modulating post-stroke immunity. Our observations point out to tRFs as molecular regulators of post-stroke immune responses that may be potential therapeutic targets.
Transfer RNA fragments replace microRNA regulators of the cholinergic post-stroke immune blockade
(2020)
Stroke is a leading cause of death and disability. Recovery depends on balance between inflammatory response and immune suppression, which can be CNS-protective but may worsen prognosis by increasing patients’ susceptibility to infections. Peripheral cholinergic blockade of immune reactions fine-tunes this immune response, but its molecular regulators are unknown. Therefore, we sought small RNA balancers of the cholinergic anti-inflammatory pathway in peripheral blood from ischemic stroke patients. Using RNA-sequencing and RT-qPCR, we discovered in patients’ blood on day 2 after stroke a “change of guards” reflected in massive decreases in microRNAs (miRs) and increases in transfer RNA fragments (tRFs) targeting cholinergic transcripts. Electrophoresis-based size-selection followed by RT-qPCR validated the top 6 upregulated tRFs in a separate cohort of stroke patients, and independent small RNA-sequencing datasets presented post-stroke enriched tRFs as originating from lymphocytes and monocytes. In these immune compartments, we found CD14+ monocytes to express the highest amounts of cholinergic transcripts. In-depth analysis of CD14+ regulatory circuits revealed minimally overlapping subsets of transcription factors carrying complementary motifs to miRs or tRFs, indicating different roles for the stroke-perturbed members of these small RNA species. Furthermore, LPS-stimulated murine RAW264.7 cells presented dexamethasone-suppressible upregulation of the top 6 tRFs identified in human patients, indicating an evolutionarily conserved and pharmaceutically treatable tRF response to inflammatory cues. Our findings identify tRF/miR subgroups which may co-modulate the homeostatic response to stroke in patients’ blood and open novel venues for establishing RNA-targeted concepts for post-stroke diagnosis and therapeutics.
Transfer RNA fragments replace microRNA regulators of the cholinergic poststroke immune blockade
(2020)
Stroke is a leading cause of death and disability. Recovery depends on a delicate balance between inflammatory responses and immune suppression, tipping the scale between brain protection and susceptibility to infection. Peripheral cholinergic blockade of immune reactions fine-tunes this immune response, but its molecular regulators are unknown. Here, we report a regulatory shift in small RNA types in patient blood sequenced 2 d after ischemic stroke, comprising massive decreases of microRNA levels and concomitant increases of transfer RNA fragments (tRFs) targeting cholinergic transcripts. Electrophoresis-based size-selection followed by qRT-PCR validated the top six up-regulated tRFs in a separate cohort of stroke patients, and independent datasets of small and long RNA sequencing pinpointed immune cell subsets pivotal to these responses, implicating CD14+ monocytes in the cholinergic inflammatory reflex. In-depth small RNA targeting analyses revealed the most-perturbed pathways following stroke and implied a structural dichotomy between microRNA and tRF target sets. Furthermore, lipopolysaccharide stimulation of murine RAW 264.7 cells and human CD14+ monocytes up-regulated the top six stroke-perturbed tRFs, and overexpression of stroke-inducible tRF-22-WE8SPOX52 using a single-stranded RNA mimic induced down-regulation of immune regulator Z-DNA binding protein 1. In summary, we identified a “changing of the guards” between small RNA types that may systemically affect homeostasis in poststroke immune responses, and pinpointed multiple affected pathways, which opens new venues for establishing therapeutics and biomarkers at the protein and RNA level.
Nanoarzneimittel haben in den letzten Jahren in der Therapie verschiedener Erkrankungen immer mehr an Bedeutung gewonnen. Dadurch hat auch die Anzahl zugelassener Arzneimittel mit an Arzneistoffträgern wie Liposomen gebundenen Wirkstoffen zugenommen. Weil für die Zulassung, neben der Wirksamkeit und Unbedenklichkeit, auch die Qualität der neuen Arzneimittel gewährleistet sein muss, spielen die verschiedenen Eigenschaften der Arzneistoffträger eine wichtige Rolle in der Qualitätskontrolle. Neben der Partikelgröße, der Partikelgrößenverteilung und der Oberflächenladung spielt die (Rest-)Kristallinität des Wirkstoffs und die Wirkstofffreisetzung eine wesentliche Rolle für die erfolgreiche in vivo-Performance von Nanoarzneimitteln. Zur Bestimmung der Wirkstofffreisetzung aus kolloidalen Arzneistoffträgern wie Liposomen, Nanopartikeln oder Mizellen gibt es bis heute keine Standardmethoden. In der Forschung und der pharmazeutischen Industrie werden folglich verschiedene Methoden wie Filtration, Zentrifugation oder Dialyse verwendet, um den freigesetzten Wirkstoff zu bestimmen. Dabei ist die Wahl der Separationsmethode auf die Eigenschaften der Arzneistoffträger abzustimmen.
In der vorliegenden Arbeit wurde eine dialysebasierte Apparatur, der Dispersion Releaser (DR), zur Untersuchung der in vitro Wirkstofffreisetzung aus kolloidalen Trägersystemen eingesetzt. Diese kann direkt mit den Apparaturen I/II der Arzneibücher der Europäischen Union (Ph. Eur.) und der Vereinigten Staaten (USP) gekoppelt werden. Zur Untersuchung der Wirkstofffreisetzung wird die Formulierung in das Donorkompartiment gegeben, sodass der freigesetzte Wirkstoff infolge über die Dialysemembran in das Akzeptorkompartiment permeiert. Dort kann dieser mittels HPLC analysiert werden. Besonders hervorzuheben ist das synchrone Rühren in beiden Kompartimenten des DR, worüber andere dialysebasierte Apparaturen nicht verfügen.
Die Entwicklung und Patentierung eines funktionsfähigen Prototyps des DR erfolgte an der Goethe Universität, Frankfurt am Main und wurde im Rahmen dieser Arbeit gemeinsam mit der Pharma Test Apparatebau AG (Hainburg, Deutschland) zu einer kommerziell erwerbbaren Apparatur (Pharma Test Dispersion Releaser, PTDR) weiterentwickelt. Innerhalb dieser Kollaboration wurde der Prototyp des DR unter Einbezug der Anforderungen der pharmazeutischen Industrie rekonstruiert. Eine erleichterte Anwendung für den Nutzer wurde dabei mitberücksichtigt.
Die finale Apparatur wurde zuletzt einer ausgiebigen Validierung unterzogen, bei der Diclofenac und Hydrocortison als Modellarzneistoffe dienten. Neben Untersuchungen zur Hydrodynamik und dem Einfluss der Umdrehungszahl auf die Membranpermeationsrate kM wurde eine Methode mit Gold-Nanopartikeln zur Bestimmung der Dichtigkeit des Systems entwickelt. Hierbei wurden Messungen mit einer UV/Vis-Methode und mit dynamischer Lichtstreuung durchgeführt, um die Abwesenheit der Goldpartikel im Akzeptorkompartiment nachzuweisen. Der Einfluss von Proteinen im Freisetzungsmedium auf die Membran-permeation wurde ebenfalls untersucht.
Der DR wurde ursprünglich zur Untersuchung von parenteralen Nanoformulierungen entwickelt. Aufgrund der bisher noch nicht erfolgten Untersuchung von halbfesten Zubereitungen im DR, wurde die Apparatur im Rahmen dieser Forschungsarbeit für zwei verschiedene Diclofenac-Gele (Voltaren® Emulgel, Olfen® Gel) unter verschiedenen Bedingungen evaluiert. Dabei konnte unter non-sink-Bedingungen der Einfluss der lipophilen Phase des Voltaren® Emulgels (GlaxoSmithKline Consumer Healthcare GmbH & Co. KG, München, Deutschland) gezeigt werden. Im Vergleich zum fettfreien Olfen® Gel (Mepha Pharma AG, Basel, Schweiz) zeigte Voltaren® Emulgel eine vollständige Freisetzung unter den erschwerten Löslichkeitsbedingungen.
Mit Hydrocortison als Modellsubstanz wurden vier verschiedene Proliposomen zur vaginalen An¬wendung formuliert. Neben der Charakterisierung der Partikelgröße und der Verkapselungs¬effizienz wurden Messungen mit dynamischer Differenzkalorimetrie durch-geführt und Aufnahmen zur morphologischen Charakterisierung mittels Transmissions-elektronen¬mikroskopie der Liposomen erstellt. Die Wirkstofffreisetzung des Hydrocortisons aus dem rekonstituierten liposomalen Gel sowie die Permeabilität über eine Zellmonoschicht wurde vergleichend untersucht. Dabei wurden Zelllinien aus humanem Cervixkarzinom beziehungsweise Endometriumkarzinom eingesetzt. Die Unterschiede der Formulierungen konnten vom DR sensitiver erfasst werden und die Verkapselungseffizienz als relevanter Faktor für die in vivo-Performance festgelegt werden.
Weil die tatsächliche Wirkstofffreisetzung durch die Permeation über die Dialysemembran überlagert werden kann, wurde neben der Standardisierung der Konstruktion die Auswertung mit Hilfe eines neuen mathematischen Modells, das auf dem Fick’schen Diffusionsgesetz basiert, verbessert. Das Normalisieren des Freisetzungsprofils mit Hilfe des mathematischen Modells dient dazu, die tatsächliche Wirkstofffreisetzung zu berechnen und den Vergleich verschiedener Freisetzungen ohne den Einfluss der Membranpermeation zu ermöglichen. Im Zuge der Validierung des DR wurde das mathematische Modell ebenfalls erfolgreich validiert.
In der vorliegenden Forschungsarbeit wurde eine neue Konstruktion des DR für die kommerzielle Anwendung entwickelt und validiert. Nebenbei wurde der Auswerteprozess zur Berechnung der diffusionsbereinigten Wirkstofffreisetzung vereinheitlicht und validiert. Zuletzt wurde das Anwendungsgebiet des DR von parenteralen Nanoformulierungen auf halbfeste Arzneiformen erweitert.
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease causing dementia and poses significant health risks to middle-aged and elderly people. Brain magnetic resonance imaging (MRI) is the most widely used diagnostic method for AD. However, it is challenging to collect sufficient brain imaging data with high-quality annotations. Weakly supervised learning (WSL) is a machine learning technique aimed at learning effective feature representation from limited or low-quality annotations. In this paper, we propose a WSL-based deep learning (DL) framework (ADGNET) consisting of a backbone network with an attention mechanism and a task network for simultaneous image classification and image reconstruction to identify and classify AD using limited annotations. The ADGNET achieves excellent performance based on six evaluation metrics (Kappa, sensitivity, specificity, precision, accuracy, F1-score) on two brain MRI datasets (2D MRI and 3D MRI data) using fine-tuning with only 20% of the labels from both datasets. The ADGNET has an F1-score of 99.61% and sensitivity is 99.69%, outperforming two state-of-the-art models (ResNext WSL and SimCLR). The proposed method represents a potential WSL-based computer-aided diagnosis method for AD in clinical practice.
The prevention of tau protein aggregations is a therapeutic goal for the treatment of Alzheimer's disease (AD), and hydromethylthionine (HMT) (also known as leucomethylthioninium-mesylate [LMTM]), is a potent inhibitor of tau aggregation in vitro and in vivo. In two Phase 3 clinical trials in AD, HMT had greater pharmacological activity on clinical endpoints in patients not receiving approved symptomatic treatments for AD (acetylcholinesterase (AChE) inhibitors and/or memantine) despite different mechanisms of action. To investigate this drug interaction in an animal model, we used tau-transgenic L1 and wild-type NMRI mice treated with rivastigmine or memantine prior to adding HMT, and measured changes in hippocampal acetylcholine (ACh) by microdialysis. HMT given alone doubled hippocampal ACh levels in both mouse lines and increased stimulated ACh release induced by exploration of the open field or by infusion of scopolamine. Rivastigmine increased ACh release in both mouse lines, whereas memantine was more active in tau-transgenic L1 mice. Importantly, our study revealed a negative interaction between HMT and symptomatic AD drugs: the HMT effect was completely eliminated in mice that had been pre-treated with either rivastigmine or memantine. Rivastigmine was found to inhibit AChE, whereas HMT and memantine had no effects on AChE or on choline acetyltransferase (ChAT). The interactions observed in this study demonstrate that HMT enhances cholinergic activity in mouse brain by a mechanism of action unrelated to AChE inhibition. Our findings establish that the drug interaction that was first observed clinically has a neuropharmacological basis and is not restricted to animals with tau aggregation pathology. Given the importance of the cholinergic system for memory function, the potential for commonly used AD drugs to interfere with the treatment effects of disease-modifying drugs needs to be taken into account in the design of clinical trials.
Riboswitches are regulatory RNA elements that undergo functionally important allosteric conformational switching upon binding of specific ligands. The here investigated guanidine-II riboswitch binds the small cation, guanidinium, and forms a kissing loop-loop interaction between its P1 and P2 hairpins. We investigated the structural changes to support previous studies regarding the binding mechanism. Using NMR spectroscopy, we confirmed the structure as observed in crystal structures and we characterized the kissing loop interaction upon addition of Mg2+ and ligand for the riboswitch aptamer from Escherichia coli. We further investigated closely related mutant constructs providing further insight into functional differences between the two (different) hairpins P1 and P2. Formation of intermolecular interactions were probed by small-angle X-ray scattering (SAXS) and NMR DOSY data. All data are consistent and show the formation of oligomeric states of the riboswitch induced by Mg2+ and ligand binding.
Im Rahmen dieser Arbeit wurde die schnelle Energietransfer- (EET) und Elektronentransfer (ET)-Dynamik unterschiedlichster Quantenpunkte (QD) spektroskopisch untersucht. Die untersuchten Systeme bestanden in den meisten Fällen aus Donor-Akzeptor-Paaren, bei denen die Halbleiternanokristalle als Donor fungierten. Der Fokus lag dabei auf der gezielten Anpassung des Donors, um die optimale Funktionalität zu erreichen. Die Untersuchung der Nanokristalle erstreckte sich daher von einfachen Kernen über verschiedene Kern-Schale-Partikel bis hin zu völlig anderen Strukturen wie Nanoplatelets (NPL). Als Akzeptor wurden eine Vielzahl von Molekülen verwendet, die sich als Elektronen- und/oder Energieakzeptoren für die verschiedenen QDs eignen.
1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5′-UTR of SARS-CoV-2
(2022)
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5′- and 3′-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5′-untranslated region (5′-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5′-UUUCGU-3′ hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
The formation of amyloid-β oligomers plays a key role in the onset of Alzheimer’s disease. We investigated the aggregation of amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing those structural properties, which lead to the formation of mature fibrils. We can show that the arrangement of the first oligomers is crucial for the topology of the resulting species, leading to the formation of non-toxic aggregates or fibrils.
Herein, we present a multi-cycle chemoenzymatic synthesis of modified RNA with simplified solid-phase handling to overcome size limitations of RNA synthesis. It combines the advantages of classical chemical solid-phase synthesis and enzymatic synthesis using magnetic streptavidin beads and biotinylated RNA. Successful introduction of light-controllable RNA nucleotides into the tRNAMet sequence was confirmed by gel electrophoresis and mass spectrometry. The methods tolerate modifications in the RNA phosphodiester backbone and allow introductions of photocaged and photoswitchable nucleotides as well as photocleavable strand breaks and fluorophores.
The heterotetrameric human transfer RNA (tRNA) splicing endonuclease (TSEN) catalyzes the excision of intronic sequences from precursor tRNAs (pre-tRNAs)1. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH)2–8. The three-dimensional (3D) assembly of TSEN/CLP1, the mechanism of substrate recognition, and the molecular details of PCH-associated mutations are not fully understood. Here, we present cryo-electron microscopy structures of human TSEN with intron-containing pre-tRNATyrgta and pre-tRNAArgtct. TSEN exhibits broad structural homology to archaeal endonucleases9 but has evolved additional regulatory elements that are involved in handling and positioning substrate RNA. Essential catalytic residues of subunit TSEN34 are organized for the 3’ splice site which emerges from a bulge-helix configuration. The triple-nucleotide bulge at the intron/3’-exon boundary is stabilized by an arginine tweezer motif of TSEN2 and an interaction with the proximal minor groove of the helix. TSEN34 and TSEN54 define the 3’ splice site by holding the tRNA body in place. TSEN54 adapts a bipartite fold with a flexible central region required for CLP1 binding. PCH-associated mutations are located far from pre-tRNA binding interfaces explaining their negative impact on structural integrity of TSEN without abrogating its catalytic activity in vitro10. Our work defines the molecular framework of pre-tRNA recognition and cleavage by TSEN and provides a structural basis to better understand PCH in the future.
Structure-function relationships in substrate binding protein dependent secondary transporters
(2023)
This work provides new insights into the relevance of SBP dependent secondary transport systems, especially in the thus far under-researched subgroup of TAXI transporters. Importantly, we identified and characterized the TAXI transport system TAXIPm-PQM from Proteus mirabilis. We demonstrated that, in contrast to previously characterized SBP dependent secondary transport systems, TAXIPm-PQM is a proton coupled system and transports the C5-dicarboxylate α- ketoglutarate. Since initially the transport of α-ketoglutarate could only be demonstrated in vivo but not in vitro using established protocols (Mulligan et al. 2009), we investigated in detail the differences between the in vivo and in vitro assay. This resulted in a bioinformatic analysis of TRAP and TAXI signal peptides, which strongly implied that TAXIPm-P requires a transmembrane anchor to allow for transport. We then provided TAXIPm-P surface tethered to the membrane in in vitro transport assays and confirmed the prediction of our bioinformatic analysis that TAXIPm-PQM deploys a membrane-anchored instead of a soluble SBP. Furthermore, the TAXI transport system TAXIMh-PQM from Marinobacter hydrocarbonoclasticus transports fumarate only if both membrane domains Q and M are present. For further characterization, Michaelis-Menten kinetics and affinities were determined for both TAXI transport systems TAXIPm-PQM from Proteus mirabilis and TAXIMh-PQM from Marinobacter hydrocarbonoclasticus. In addition, nanobodies were selected for the membrane domain TAXIPm-QM from Proteus mirabilis to stabilize different conformations which can serve in subsequent structural elucidation studies. Furthermore, the TRAP SBP TRAPHi-SiaP from Haemophilus influenzae was shown to interact not only with its corresponding membrane domain TRAPHi-SiaQM but with at least one additional transporter. It was thereby excluded that TRAPHi- SiaP transfers N-acetylneuraminic acid to the only native E. coli TRAP transporter TRAPEc-YiaMNO and suggested to rather interact with a SBP dependent ABC transport system as this protein family represents the largest SBP dependent protein group in E. coli (Moussatova et al. 2008).
Salt-inducible kinases (SIKs) are key metabolic regulators. Imbalance of SIK function is associated with the development of diverse cancers, including breast, gastric and ovarian cancer. Chemical tools to clarify the roles of SIK in different diseases are, however, sparse and are generally characterized by poor kinome-wide selectivity. Here, we have adapted the pyrido[2,3-d]pyrimidin-7-one-based PAK inhibitor G-5555 for the targeting of SIK, by exploiting differences in the back-pocket region of these kinases. Optimization was supported by high-resolution crystal structures of G-5555 bound to the known off-targets MST3 and MST4, leading to a chemical probe, MRIA9, with dual SIK/PAK activity and excellent selectivity over other kinases. Furthermore, we show that MRIA9 sensitizes ovarian cancer cells to treatment with the mitotic agent paclitaxel, confirming earlier data from genetic knockdown studies and suggesting a combination therapy with SIK inhibitors and paclitaxel for the treatment of paclitaxel-resistant ovarian cancer.
Unc-51-like kinase 4 (ULK4) is a pseudokinase that has been linked to the development of several diseases. Even though sequence motifs required for ATP binding in kinases are lacking, ULK4 still tightly binds ATP and the presence of the cofactor is required for structural stability of ULK4. Here we present a high-resolution structure of a ULK4-ATPγS complex revealing a highly unusual ATP binding mode in which the lack of the canonical VAIK motif lysine is compensated by K39, located N-terminal to αC. Evolutionary analysis suggests that degradation of active site motifs in metazoan ULK4 has co-occurred with an ULK4 specific activation loop, which stabilizes the C-helix. In addition, cellular interaction studies using BioID and biochemical validation data revealed high confidence interactors of the pseudokinase and armadillo repeat domains. Many of the identified ULK4 interaction partners were centrosomal and tubulin associated proteins and several active kinases suggesting new roles for ULK4.
Highlights: Structure of the ULK4 ATP complex reveals a unique ATP binding mode.
Disease associated mutations modulate ATP binding and ULK4 stability
Degradation of active site motifs co-occurred in evolution with an ULK4 specific activation loop
BioID suggests a role of ULK4 regulating centrosomal and cytoskeletal functions,
MKK7 (MEK7) is a key regulator of the JNK stress signaling pathway and targeting MKK7 has been proposed as a chemotherapeutic strategy. Detailed understanding of the MKK7 structure and factors that impact its activity is therefore of critical importance. Here, we present a comprehensive set of MKK7 crystal structures revealing insights into catalytic domain plasticity and the role of the N-terminal regulatory helix, conserved in all MAP2Ks, mediating kinase activation. Crystal structures harboring this regulatory helix revealed typical structural features of active kinase, providing exclusively a first model of the MAP2K active state. A small molecule screening campaign yielded multiple scaffolds, including type-II irreversible inhibitors a binding mode that has not been reported previously. We also observed an unprecedented allosteric pocket located in the N-terminal lobe for the approved drug ibrutinib. Collectively, our structural and functional data expand and provide alternative targeting strategies for this important MAP2K kinase.
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, noncanonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK, and CLK. By use of the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a noncanonical binding mode in CLK1, providing a rationale for selectivity over the closely related CLK3 which harbors a smaller DFG-1 alanine. Our data suggest that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
The nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus, targeting this protein domain may offer a therapeutic strategy to combat the current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally-occurring nucleotides, small molecules as well as nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and it provides chemical starting points for future inhibitor development.
DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a super-resolution technique with relatively easy-to-implement multi-target imaging. However, image acquisition is slow as sufficient statistical data has to be generated from spatio-temporally isolated single emitters. Here, we train the neural network (NN) DeepSTORM to predict fluorophore positions from high emitter density DNA-PAINT data. This achieves image acquisition in one minute. We demonstrate multi-colour super-resolution imaging of structure-conserved semi-thin neuronal tissue and imaging of large samples. This improvement can be integrated into any single-molecule imaging modality to enable fast single-molecule super-resolution microscopy.
N6-methyladenosine (m6A) is the most abundant and well understood modification in eukaryotic mRNA and was first identified in polyadenylated parts of the mRNA.The distinct distribution of m6A in the transcriptome with special enrichment in long internal exons, 39UTRs and around stop codons was uncovered by early biochemical work and later on antibody based sequencing techniques. The so called m6A writer, reader and eraser machinery is responsible for the dynamic and with that regulatory nature of the m6A modification. As m6A writer, the human N6-methyltransferase complex (MTC) cotranscriptionally methylates the central adenine within a RRACH (preferably GGACU) sequence context to form m6A in the nascent RNA chain.9–15 The catalytic core of the complex is formed by the two proteins METTL3 and METTL14, with the active site located in the methyltransferase domain (MTD) of METTL3.16–18 The DPPW motif near the methyl donor S-adenosylmethionine (SAM) binding site in this MTD was postulated to bind the target adenine during catalysis. Moreover, a positively charged groove in the METTL3-METTL14 interface, the C-terminal RGG domain in METTL14 and the zinc finger motifs in METTL3 were identified as important domains for RNA binding. However, to date there are no full-length or substrate-RNA-bound structures of the catalytic METTL3-METTL14 complex.
In addition, a set of accessory proteins assembles to the METTL3-METTL14 heterodimer to form the full MTC, mediated by WTAP that firmly binds to the N-terminal leader helix in METTL3.20 WTAP was shown to locate the whole complex to the nuclear speckles and can modulate m6A deposition to specific sites in the RNA. Moreover, WTAP acts as binding platform for other accessory proteins including VIRMA, RBM15, ZC3H13 and HAKAI that are mostly identified to mediate position specific methylation. For example, RBM15 was shown to mediates region-selective methylation in a WTAP dependent manner, directing specificity towards U-rich sequences.
The observed specificity of the methyltransferase complex to methylate only site specific DRACH sequenced is still poorly understood. Some possible modulators like the role of the accessory proteins are under investigation, however, the structural context of the RNA methylation sites or a structural preference of the complex have been mainly neglected so far. Moreover, the structural dynamics of this methylation process still remain elusive. This thesis contributes to the afore-mentioned aspects by analysis of the methylation process regarding RNA structure sensitivity with enzymatic activity assays and its dynamic nature by implementing a smFRET approach.
We hypothesized the target RNA secondary structure to be an additional important modulator of methylation efficiency, based on the RNA binding elements of the complex (positively charged binding groove, zinc finger domain, RGG domain) and the supposed target adenine binding in the active site. Here, we postulated the possibility for a flipped-out adenine to be of special relevance, which is closely related to the local stability of the target adenine containing structure. Moreover, efficient binding of the protein complex to the RNA should require the ability to anchor the RNA on both sides of the target sequence.
Large international airports were identified as sources of ultrafine particles (UFPs) (Hu et al., 2009; Yu et al., 2012; Hsu et al., 2013; Keuken et al., 2015; Hudda and Fruin, 2016). Since September 2017 UFP emissions originating from the Frankfurt International Airport, Germany are monitored by the Hessian Agency for Nature Conservation, Environment and Geology (HLNUG) showing elevated UFP concentrations during airport operating hours (05:00–23:00 CET) (Ditas et al., 2022). Referring to that, the organic chemical composition of aviation-related UFPs emerging from the Frankfurt Airport was analysed by performing a comprehensive non-target screening of UFP filter samples.
Aluminium-filter samples were collected at an air quality monitoring station 4 km north of the Frankfurt Airport, using a 13-stage impactor system (Nano-MOUDI). The chemical
characterization of UFPs in the size range of 10-18 nm, 18-32 nm and 32-56 nm was accomplished by ultra-high-performance liquid chromatography, heated electrospray ionisation and mass analysis using an Orbitrap high-resolution mass spectrometer. Non-target screening revealed that the majority of detected compounds belong to homologous series of two different types of organic esters, which are base stocks of aircraft lubrication oils.
In reference to five different jet engine lubrication oils of various manufacturers, the corresponding lubricant base stocks and their additives, two amines and one organophosphate, were identified in the UFPs by the use of matching retention time, exact mass and MS/MS fragmentation pattern of single organic molecules. The quantitative analysis of the jet engine oil constituents in the aviation-related UFPs with diameters < 56 nm was accomplished by standard addition. By characterizing the Nano-MOUDI, loss factors for each size stage were determined and used for correction accordingly. Particle-number size distribution measurements, conducted parallel to the filter sampling, enabled the determination of the jet engine oil contribution to the UFP mass.
Furthermore, the nucleation and particle formation potential of a commonly used synthetic jet engine lubrication oil was investigated in the laboratory. Thermodenuder experiments at 20 °C and 300 °C were carried out to monitor the gas-to-particle partitioning behaviour of jet engine oils. At 300 °C a significantly higher number of particles with a mean diameter of ~10 nm are formed, leading to a more than fivefold increase in total particle numbers compared to 20 °C. Particle diameters of the newly formed oil particles in the laboratory experiment appeared in the same size region as UFPs emerging from Frankfurt Airport. Particles originating from the Frankfurt city centre direction showed larger diameters.
Results indicate that aircraft emissions strongly influence the total mass of 10-18 nm particles. The jet oil fraction decreases for bigger particles (e.g., 18-56 nm), implying that these oils form new particles in the cooling exhaust gases of aircraft engines. In addition, non-target screening and in vitro bioassays on aviation-related PM2.5 filter samples were combined to provide indications for potential toxicologically relevant compounds in dependence of different wind directions and airport operations. Most recently, the applied non-target screening method was also used to identify seasonal variations in the organic aerosol composition in Beijing.
F-type ATP synthases are multiprotein complexes composed of two separate coupled motors (F1 and FO) generating adenosine triphosphate (ATP) as the universal major energy source in a variety of relevant biological processes in mitochondria, bacteria and chloroplasts. While the structure of many ATPases is solved today, the precise assembly pathway of F1FO-ATP synthases is still largely unclear. Here, we probe the assembly of the F1 complex from Acetobacterium woodii. Using laser induced liquid bead ion desorption (LILBID) mass spectrometry, we study the self-assembly of purified F1 subunits in different environments under non-denaturing conditions. We report assembly requirements and identify important assembly intermediates in vitro and in cellula. Our data provide evidence that nucleotide binding is crucial for in vitro F1 assembly, whereas ATP hydrolysis appears to be less critical. We correlate our results with activity measurements and propose a model for the assembly pathway of a functional F1 complex.
Die vorliegende Dissertation mit dem Titel “Structural dynamics of eukaryotic H/ACA RNPs from Saccharomyces cerevisiae & Structural dynamics of the Guanidine-II riboswitch from Escherichia coli” besteht aus zwei Projekten. Das erste Projekt befasst sich mit den eukaryotischen H/ACA Ribonukleoproteinen (RNP) aus der Hefe. Diese können sequenzspezifisch in der RNA ein Uridin Nukleotid in das Rotationsisomer Pseudouridin (Ψ) umwandeln. Die H/ACA RNPs bestehen aus einer Leit-RNA und vier Proteinen, der katalytisch aktiven Pseudouridylase Cbf5, Nhp2, Gar1 und Nop10. Die Leit-RNA besteht in Eukaryoten konserviert aus zwei Haarnadelstrukturen, die von einem H-Box oder ACA-Box Sequenzmotiv gefolgt sind. In jeder dieser Haarnadeln befindet sich ein ungepaarter Bereich, die sogenannte Pseudouridylierungstasche, wo durch komplementäre Basenpaarung die Ziel-RNA gebunden wird. Fehlerhafte H/ACA RNPs können beim Menschen zu schweren Krankheiten wie verschiedenen Krebsarten oder dem Knochenmarksversagen Dyskeratosis congenita führen, aber sie bieten auch Möglichkeiten zum Einsatz als Therapiemethode. In dieser Arbeit wurde hauptsächlich der zweiteilige Aufbau der H/ACA RNPs untersucht.
Dafür wurden zunächst die einzelnen Komponenten hergestellt werden. Cbf5, Nop10 und Gar1 wurden zusammen heterolog in E. coli exprimiert und gereinigt. Außerdem wurden mehrere Deletionsvarianten von Gar1 hergestellt. Zusätzlich wurde die Leit-RNA unmarkiert über T7 Transkription synthetisiert, sowie sechs verschiedene FRET-Konstrukte mit verschiedenen Markierungschemas der Fluorophore Cy3 und Cy5 über DNA-geschiente Ligation. Anschließend wurde über Größenausschlusschromatographie und radioaktiven Aktivitätsassays geprüft, dass sich die aktiven H/ACA RNPs in vitro aus den einzelnen Komponenten rekonstituieren lassen.
In smFRET Experimenten wurden einzelne Haarnadelstrukturen mit dem zweiteiligen Komplexen verglichen. Dabei konnte gezeigt werden, dass die H3 Haarnadel durch die Anwesenheit von H5 dynamischer und heterogener wurde, während H5 überwiegend unbeeinflusst war. Außerdem konnte die dreidimensionale Orientierung der Haarnadelstrukturen in verschiedenen Assemblierungsschritten mittels smFRET untersucht werden. Hier deutete sich an, dass in Abwesenheit von Proteinen beide Haarnadeln eher entgegengesetzt stehen als in einer parallelen Konformation. Cbf5 scheint den Linker zwischen den Beiden auszustrecken bzw. zu orientieren und die Haarnadelstrukturen etwas gegeneinander zu neigen. Ein Zusammenspiel von Nhp2 und Gar1 war nötig um die oberen Bereiche der Haarnadeln zusammenzuziehen. Es konnte auch ein Modell für den vollen H/ACA RNP vorgeschlagen werden. Im kompletten Komplex könnte das Zusammenziehen der Haarnadelstrukturen durch Nhp2 und Gar1 mit dem Effekt von Cbf5 konkurrieren und könnte hauptsächlich den oberen Bereich von H3 betreffen. Zum Schluss wurde das Zusammenspiel von Gar1 und Nhp2 auf eine Abhängigkeit von den RGG Domänen von Gar1 hin untersucht. Hier besteht möglicherweise eine Hierarchie, die eine Kooperativität von den N- und C-terminalen Domänen benötigt.
Das zweite Projekt befasst sich mit dem Guanidin-II Riboschalter aus E. coli. Der Riboschalter kann das toxische Molekül Guanidinium (Gdm+) spezifisch in seiner Aptamerdomäne binden und dadurch die Genexpression von Proteinen zur Detoxifizierung von Gdm+ aktivieren. Der Riboschalter besteht aus zwei Haarnadelstrukturen, mit einer Schleife, die aus der Sequenz ACGR besteht, wobei R ein Purin ist. In einem vorgeschlagenen Modell soll die Ribosomenbindestelle (Shine-Dalgarno Sequenz) in Abwesenheit von Ligand mit dem Linker komplementär Basenpaaren und so die Translation verhindern. Mit Ligand würde sich dann eine Schleifen-Schleifen Interaktion mit den beiden CG Basen ausbilden, wodurch die Anti-Shine-Dalgarno Sequenz nicht mehr zugänglich wäre. Bisherige Studien arbeiteten zumeist nur mit der Aptamerdomäne, den einzelnen Haarnadeln oder noch kleineren Elementen. In dieser Arbeit wurden die Strukturdynamiken von verschiedenen Längen, auch mit der Expressionsplatform, untersucht. Außerdem wurden verschiedene Mutationen analysiert und die Effekte auf den Riboschalter in seiner natürlichen Umgebung in E. coli.
Zunächst mussten insgesamt 24 FRET-Konstrukte hergestellt werden, die sich in Länge, Markierungsschema und Mutationen unterschieden. Hierfür wurde DNA-geschiente Ligation verwendet. Dank der verschiedenen Fluorophorpositionen konnte ein konformationelles Modell für die Aptamerdomäne vorgeschlagen werden. In diesem Modell könnte in Abwesenheit von Ionen das Aptamer offen vorliegen. Durch Mg2+ würde sich bereits eine lockere Schleifen-Schleifen Interaktion ausbilden. Zusätzlich deuten die Ergebnisse auf eine neue Konformation hin, der stabilisierten Schleifen-Schleifen Interaktion, bei der der Linker zusätzlich mit den Haarnadelstrukturen interagiert, beispielswese mit den Purinen an der vierten Schleifenposition...
Bleaching-independent, whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores
(2018)
We demonstrate bleaching-independent STED microscopy using fluorogenic labels that reversibly bind to their target structure. A constant exchange of labels guarantees the removal of photobleached fluorophores and their replacement by intact fluorophores, thereby circumventing bleaching-related limitations of STED super-resolution imaging in fixed and living cells. Foremost, we achieve a constant labeling density and demonstrate a fluorescence signal for long and theoretically unlimited acquisition times. Using this concept, we demonstrate whole-cell, 3D, multi-color and live cell STED microscopy with up to 100 min acquisition time.
Alzheimer’s Disease (AD) is a progressive and irreversible neurodegenerative disorder, characterized by the accumulation of abeta-amyloid aggregates, which triggers tau hyperphosphorylation and neuronal loss. While the precise mechanisms underlying neurodegeneration in AD are not entirely understood, it is known that loss of proteostasis is implicated in this process. Maintaining neuronal proteostasis requires proper transfer RNA (tRNA) modifications, which are crucial for optimal translation. However, research into tRNA epitranscriptome in AD is limited, and it is not yet clear how alterations in tRNA modifying enzymes and tRNA modifications might contribute to disease progression. Here, we report that expression of the tRNA modifying enzyme ELP3 is reduced in the brain of AD patients and amyloid AD mouse models, suggesting ELP3 is implicated in proteostasis dysregulation observed in AD. To investigate the role of ELP3 specifically in neuronal proteostasis impairments in the context of amyloid pathology, we analyzed SH-SY5Y neuronal cells carrying the amyloidogenic Swedish familial AD mutation in the APP gene (SH-SWE) or the wild-type gene (SH-WT). Similarly to the amyloid mouse models, SH-SWE exhibited reduced levels of ELP3 which was associated with tRNA hypomodifications and reduced abundance, as well as proteostasis impairments. Furthermore, the knock-down of ELP3 in SH-WT recapitulated the proteostasis impairments observed in SH-SWE cells. Importantly, the correction of tRNA deficits due to ELP3 reduction rescued and reverted proteostasis impairments of SH-SWE and SH-WT knock-down for ELP3, respectively. Additionally, SH-WT exposed to the secretome of SH-SWE or synthetic amyloid aggregates recapitulate the SH-SWE phenotype, characterized by reduced ELP3 expression, tRNA hypomodification and increased protein aggregation. Taken together, our data suggest that amyloid pathology dysregulates neuronal proteostasis through the reduction of ELP3 and tRNA modifications. This study highlights the modulation of tRNA modifications as a potential therapeutic avenue to restore neuronal proteostasis in AD and preserve neuronal function.
Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs
(2022)
As essential components of the cellular protein synthesis machineries, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of a large number of posttranscriptional chemical modifications. Maturation defaults resulting in lack of modifications in the tRNA core may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. Although modifications are typically introduced in tRNAs independently of each other, several modification circuits have been identified in which one or more modifications stimulate or repress the incorporation of others. We previously identified m1A58 as a late modification introduced after more initial modifications, such as Ѱ55 and T54 in yeast elongator tRNAPhe. However, previous reports suggested that m1A58 is introduced early along the tRNA modification process, with m1A58 being introduced on initial transcripts of initiator tRNAiMet, and hence preventing its degradation by the nuclear surveillance and RTD pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m1A58 incorporation, we examined the m1A58 modification pathways in yeast elongator and initiator tRNAs. For that, we first implemented a generic approach enabling the preparation of tRNAs containing specific modifications. We then used these specifically modified tRNAs to demonstrate that the incorporation of T54 in tRNAPhe is directly stimulated by Ѱ55, and that the incorporation of m1A58 is directly and individually stimulated by Ѱ55 and T54, thereby reporting on the molecular aspects controlling the Ѱ55 → T54 → m1A58 modification circuit in yeast elongator tRNAs. We also show that m1A58 is efficiently introduced on unmodified tRNAiMet, and does not depend on prior modifications. Finally, we show that the m1A58 single modification has tremendous effects on the structural properties of yeast tRNAiMet, with the tRNA elbow structure being properly assembled only when this modification is present. This rationalizes on structural grounds the degradation of hypomodified tRNAiMet lacking m1A58 by the nuclear surveillance and RTD pathways.
Cyclophilins, or immunophilins, are proteins found in many organisms including bacteria, plants and humans. Most of them display peptidyl-prolyl cis-trans isomerase activity, and play roles as chaperones or in signal transduction. Here, we show that cyclophilin anaCyp40 from the cyanobacterium Anabaena sp. PCC 7120 is enzymatically active, and seems to be involved in general stress responses and in assembly of photosynthetic complexes. The protein is associated with the thylakoid membrane and interacts with phycobilisome and photosystem components. Knockdown of anacyp40 leads to growth defects under high-salt and high-light conditions, and reduced energy transfer from phycobilisomes to photosystems. Elucidation of the anaCyp40 crystal structure at 1.2-Å resolution reveals an N-terminal helical domain with similarity to PsbQ components of plant photosystem II, and a C-terminal cyclophilin domain with a substrate-binding site. The anaCyp40 structure is distinct from that of other multi-domain cyclophilins (such as Arabidopsis thaliana Cyp38), and presents features that are absent in single-domain cyclophilins.
Locomotion, the way animals independently move through space by active muscle contractions, is one of the most apparent animal behaviors. However, in many situations it is more beneficial for animals to actively prevent locomotion, for instance to briefly stop before reorienting with the aim of avoiding predators, or to save energy and recuperate from stress during sleep. The molecular and cellular mechanisms underlying such locomotion inhibition still remain elusive. So, the aim of this study was to utilize the practical genetic model organism Caenorhabditis elegans to efficiently tackle relevant questions on how animals are capable of suppressing locomotion.
Nerve cells, mostly called neurons, are known to control locomotion patterns by activating some and inhibiting other muscle groups in a spatiotemporal manner via local secretion of molecules known as neurotransmitters. This study particularly focuses on whether neuropeptides modulate such neurotransmission to prevent locomotion. Neuropeptides are small protein-like molecules that are secreted by specific neurons and that act in the brain by activating G protein-coupled receptors (GPCRs) expressed in other target neurons. They can act as hormones, neuromodulators or neurotransmitters. DNA sequences coding for neuropeptides and their cognate receptors are similar across diverse species and thus indicate evolutionary conservation of their molecular signaling pathways. This could potentially also imply that regulatory functions of specific neuropeptides are also similar across species and are thus meaningful to unravel more general mechanisms for instance underlying locomotion inhibition.
Specifically, we find that the modulatory interneuron RIS constitutes a dedicated stop neuron of which the activity is sufficient to initiate rapid locomotion arrest in C. elegans while maintaining its body posture. Similar to its known function in larval sleep, RIS requires RFamide neuropeptides encoded by the flp 11 gene for this activity, in addition to GABA. Furthermore, we find that spontaneous calcium activity transients in RIS are compartmentalized and correlated with locomotion stop. These findings illustrate that a single neuron can regulate both stopping and sleeping phenotypes.
Secondly, we show that C. elegans RPamide neuropeptides encoded by nlp-22 and nlp-2 regulate sleep and wakefulness, respectively. We unexpectedly find that these peptides activate gonadotropin-releasing hormone (GnRH)-like receptors dose dependently and we highlight their sequence resemblance to other bilaterian GnRH-like neuropeptides. In addition, we show that these receptors are expressed in distinct subsets of neurons that are associated with motor behavior. Finally, we show that nlp 22 encoded peptides signal through GNNR 6 receptors to regulate larval sleep and that nlp 2 encoded peptides require both GNRR 3 and GNRR 6 receptors to promote wakefulness.
In sum, we find that locomotion inhibition in C. elegans is regulated by multiple, but evolutionary conserved RFamide and GnRH-like RPamide neuropeptidergic signaling pathways.
Caspase-2 is the evolutionary most conserved member of the caspase family and was shown to be involved in genotoxic stress induced apoptosis, control of aneuploidy, and ageing related metabolic changes. However, its role in apoptosis seems redundant due to the observation, that knockout does not inhibit apoptotic signalling exclusively. Instead, knockout of caspase-2 leads to tumor susceptibility in vivo, which led to the assumption, that caspase-2 has non-apoptotic functions and can act as a tumor suppressor. The underlying mechanism of the tumor suppressor activity of caspase-2 has not been clarified so far. Furthermore, caspase-2, has a prominent, and as pro-enzyme exclusive localisation in the nucleus and other subcellular compartments, implicating a distinct and location specific role.
In this study, a novel caspase-2 specific substrate, termed p54nrb, was identified. P54nrb is harbouring a caspase-2 specific cleavage site at the aspartate residue D422, and cleavage of p54nrb leads apparently to disruption of its putative DNA binding domain at the C-terminus.
P54nrb is a nuclear multifunctional RNA and DNA binding protein, known for roles in transcriptional regulation, DNA unwinding and repair, RNA splicing, and retention of defective RNA. Overexpression of p54nrb has been observed in several human cancers, such as cervix carcinoma, melanoma, and colon carcinoma.
Data from this study revealed, that depletion of p54nrb in tumor cell lines results in a loss of resistance to drug induced cell death and to reduced capability of anchorage independent growth, which is functionally equivalent to a reduced tumorigenic potential. Meanwhile, p54nrb depletion alone is not cytotoxic.
The investigation of p54nrb dependent gene regulations by high resolution quantitative proteomics uncovered an altering expression of multiple tumorigenic genes. For two of these candidates, the tumorigenic protease cathepsin-Z and the anti-apoptotic gelsolin, p54nrb dependent expression was detected universally in all three investigated tumor cell lines, cervix carcinoma, melanoma, and colon carcinoma. Additionally, a direct interaction of p54nrb with the cathepsin Z and gelsolin encoding DNA, but not with their corresponding mRNA, could be demonstrated.
Conjointly, this study unveils a novel mechanistic feature of caspase-2 as a tumor suppressor. The caspase-2—p54nrb axis can orchestrate the levels of several tumorigenic proteins and thereby determine the cell death susceptibility and long-term tumor survival. These findings might be of great value for future therapeutic interventions and for overcoming drug resistance of tumors.
The photodynamic inactivation of nucleic acids with pyronin, methylene blue, thiopyronin and furocoumarines has been studied. The template efficiency of DNA in RNA-Polymerase reaction was found to be decreased after the treatment of DNA with these compounds. However, the magnitude of their inhibiting capacity varied from one compound to the other. Psoralen and thiopyronin were found to be the most active inhibitors followed by xanthotoxin and methylene blue respectively. At a lower temperature the inhibiting capacity of thiopyronin was considerably decreased but that of psoralen remained nearly unaffected. We have also tried to show evidence for a complimentary code in t-RNA through a specific destruction of guanine with thiopyronin.
The peptide loading complex (PLC) is a central machinery in adaptive immunity ensuring antigen presentation by major histocompatibility complex class I (MHC I) molecules to immune cells. If nucleated cells present foreign antigenic peptides from various origins (e.g., viral infected or cancer cells) on their cell surface they are targeted and eliminated by effector cells of the immune system to protect the organism against the hazard. The antigen presentation process starts with proteasomal degradation. Peptide loading and quality control of most, if not all, MHC I is performed by the PLC. Despite the main components, architecture, and general functions of this labile and multi-subunit assembly have been described, knowledge about the inner mechanics of MHC I loading and quality control in the PLC is limited. Detailed structural insights into the interactions and functions of key elements are lacking. In this PhD thesis, structural and functional aspects of the PLC in peptide loading and quality control of MHC I are unraveled, and the PLC was analyzed from an evolutionary perspective.
First, composition and architecture of native PLC isolated from different mammalian species was analyzed. Comparison of detergent-solubilized PLC from cow and sheep spleens with PLC isolated from human source showed a compositional conservation in mammals, with the central components TAP, ERp57, tapasin, calreticulin, and the MHC I heterodimer were conserved in these species. Negative-stain electron microscopy (EM) analyses revealed an identical overall architecture of PLCs from human, sheep, and cow with two major densities at opposing sides of the plane of the detergent micelle corresponding to endoplasmic reticulum (ER) luminal and cytosolic domains. Interestingly, the glucose-regulated protein 78 (GRP78) was associated only with the PLC from sheep and cow as revealed by mass spectrometry. This ER chaperone is involved in initial folding steps of MHC I but was not co-purified with human PLC, rendering it an interesting target for future functional and in-depth structural studies.
The human PLC was stabilized by reconstitution in membrane mimicking systems that replace the detergent, which is necessary to solubilize the complex. This stabilization allowed detailed structural analysis by single-particle cryogenic electron microscopy (cryo-EM). The structure of the MHC I editing module in the PLC, composed of tapasin, ERp57, calreticulin, MHC I, and β-2-microglobulin (β2m), was solved at an overall resolution of 3.7 Å. Within the structure, two important features were visualized: (i) the editing loop of tapasin, which is directly involved in peptide proofreading of MHC I; (ii) the A-branch of the Asn86 tethered N-linked glycan on MHC I. Both features are crucial elements in the quality control and peptide editing process on MHC I. The editing loop interacts with the peptide binding groove in MHC I. It disturbs the interaction between a cargo peptide C terminus and the F-pocket in the binding groove by displacing Tyr84 and the helices α1 and α2. The helix displacement widens the F-pocket which allows a faster peptide exchange on MHC I. The glycan is bound in its monoglucosylated form (Glc1Man9GlcNAc2) by the lectin domain of calreticulin. The A-branch of this glycan is stretched between MHC I Asn86 and the lectin domain, leading to the hypothesis that the glycan will be released from calreticulin once MHC I is loaded with a favored peptide (pMHC I).
For investigation of the glycan status of MHC I, intact protein liquid chromatography coupled mass spectrometry (LC-MS) was performed under denaturating conditions. An allosteric coupling between peptide loading and removal of the terminal glucose by α-Glucosidase II (GluII) was discovered. In addition, the PLC remained fully intact after peptide loading, which demonstrated GluII action on the PLC once MHC I is loaded.
With establishing GluII as transient interaction partner, this work deepens the knowledge of the molecular sociology of the PLC and how the PLC is involved in the endoplasmic reticulum quality control (ERQC). Further investigation of the ER aminopeptidases ERAP1 and ERAP2 showed that these enzymes neither alone nor together stably interact with the PLC. In contrast, both work independent from the PLC on free peptides in the ER.
LC-MS analysis of the PLC components revealed a very unusual glycosylation pattern of tapasin. Tapasin was observed with N-linked glycans ranging from the full glycan (Man9GlcNAc2) to heavily trimmed glycans, where only a single GlcNAc remained attached to Asn233. In the PLC, tapasin is probably shielded from degradation by ERQC and can remain functional and intact without a full N-linked glycan.
Bei der UV-Bestrahlung von Uracil-[5.6-3H] bilden sich je nach eingestrahlter Energie dimeres Uracil und Uracil-Wasseranlagerungsprodukt [5.6-Dihydro-6-hydroxyuracil] als radioaktive Photoprodukte. Während bei der Synthese des Wasseranlagerungsproduktes ein beträchtlicher sekundärer Isotopeneffekt wirksam wird, verändert sich die Radioaktivität des dimeren Uracils gegenüber der des Ausgangsuracils kaum.
Wird das Wasseranlagerungsprodukt durch Erwärmen zu Uracil zurückgewandelt, so dehydratisiert das Molekül ebenfalls unter Mitwirkung eines Isotopeneffektes. Wird das Uracildimere zu Uracil rückgewandelt, so beobachtet man keinen Isotopeneffekt.
Bei der Bestrahlung von Uracil in Tritium-haltigem Wasser werden nur sehr geringe Radioaktivitäten in die Photoprodukte eingebaut. Der Isotopeneffekt beträgt ca. 8. — Durch Synthese der Photoprodukte aus spezifisch an C-5 oder C-6 Tritium-markiertem Uracil bzw. durch Bromierung von 5.6-Tritium-markiertem Uracil bzw. dessen Photoprodukten zu den 5-Brom-Derivaten erhält man Hinweise, daß der Geschwindigkeits-bestimmende Schritt der Wasseraddition an C-6 des Uracils verläuft. Die inversen sekundären Isotopeneffekte betragen für Tritium an C-6 etwa 0,65, für Tritium an C-5 dagegen nur 0,95.
The transient receptor potential (TRP) ankyrin type 1 (TRPA1) channel is highly expressed in a subset of sensory neurons where it acts as an essential detector of painful stimuli. However, the mechanisms that control the activity of sensory neurons upon TRPA1 activation remain poorly understood. Here, using in situ hybridization and immunostaining, we found TRPA1 to be extensively co-localized with the potassium channel Slack (KNa1.1, Slo2.2, or Kcnt1) in sensory neurons. Mice lacking Slack globally (Slack−/−) or conditionally in sensory neurons (SNS-Slack−/−) demonstrated increased pain behavior after intraplantar injection of the TRPA1 activator allyl isothiocyanate. By contrast, pain behavior induced by the TRP vanilloid 1 (TRPV1) activator capsaicin was normal in Slack-deficient mice. Patch-clamp recordings in sensory neurons and in a HEK cell line transfected with TRPA1 and Slack revealed that Slack-dependent potassium currents (IKS) are modulated in a TRPA1-dependent manner. Taken together, our findings highlight Slack as a modulator of TRPA1-mediated, but not TRPV1-mediated, activation of sensory neurons.
Keywords: TRPA1; slack; dorsal root ganglia; pain; mice
Bei saurer Hydrolyse wird aus den 5-Halogenuracildesoxyribosiden die DR ** etwa 3 -4-mal rascher abgespalten als aus TdR oder UdR. CdR wird unter den gleichen Bedingungen 16-fach schneller hydrolysiert. Im Gegensatz dazu ist die Ribose im Cytidin um ein Mehrfaches fester gebunden als im Uridin. Im TdR-Dimeren wird durch die Absättigung der 5.6-Doppelbindung die Stabilität der N-glykosidischen Bindung stark erniedrigt. Aus diesen Befunden ergibt sich ein Hinweis auf die Elektronendichte-Verteilung im Pyrimidinring und damit eine chemische Basis für das mutagene Verhalten verschiedener unnatürlicher Desoxyriboside.
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
Specialized surveillance mechanisms are essential to maintain the genetic integrity of germ cells, which are not only the source of all somatic cells but also of the germ cells of the next generation. DNA damage and chromosomal aberrations are, therefore, not only detrimental for the individual but affect the entire species. In oocytes, the surveillance of the structural integrity of the DNA is maintained by the p53 family member TAp63α. The TAp63α protein is highly expressed in a closed and inactive state and gets activated to the open conformation upon the detection of DNA damage, in particular DNA double-strand breaks. To understand the cellular response to DNA damage that leads to the TAp63α triggered oocyte death we have investigated the RNA transcriptome of oocytes following irradiation at different time points. The analysis shows enhanced expression of pro-apoptotic and typical p53 target genes such as CDKn1a or Mdm2, concomitant with the activation of TAp63α. While DNA repair genes are not upregulated, inflammation-related genes become transcribed when apoptosis is initiated by activation of STAT transcription factors. Furthermore, comparison with the transcriptional profile of the ΔNp63α isoform from other studies shows only a minimal overlap, suggesting distinct regulatory programs of different p63 isoforms.
Age-related multifactorial diseases, such as the neurodegenerative Alzheimer’s disease (AD), still remain a challenge to today’s society. One mechanism associated with AD and aging in general is mitochondrial dysfunction (MD). Increasing MD is suggested to trigger other pathological processes commonly associated with neurodegenerative diseases. Silibinin A (SIL) is the main bioactive compound of the Silymarin extract from the Mediterranean plant Silybum marianum (L.) (GAERTN/Compositae). It is readily available as a herbal drug and well established in the treatment of liver diseases as a potent radical scavenger reducing lipid peroxidation and stabilize membrane properties. Recent data suggest that SIL might also act on neurological changes related to MD. PC12APPsw cells produce low levels of human Aβ and thus act as a cellular model of early AD showing changed mitochondrial function. We investigated whether SIL could affect mitochondrial function by measuring ATP, MMP, as well as respiration, mitochondrial mass, cellular ROS and lactate/pyruvate concentrations. Furthermore, we investigated its effects on the mitochondrial membrane parameters of swelling and fluidity in mitochondria isolated from the brains of mice. In PC12APPsw cells, SIL exhibits strong protective effects by rescuing MMP and ATP levels from SNP-induced mitochondrial damage and improving basal ATP levels. However, SIL did not affect mitochondrial respiration and mitochondrial content. SIL significantly reduced cellular ROS and pyruvate concentrations. Incubation of murine brain mitochondria with SIL significantly reduces Ca2+ induced swelling and improves membrane fluidity. Although OXPHOS activity was unaffected at this early stage of a developing mitochondrial dysfunction, SIL showed protective effects on MMP, ATP- after SNP-insult and ROS-levels in APPsw-transfected PC12 cells. Results from experiments with isolated mitochondria imply that positive effects possibly result from an interaction of SIL with mitochondrial membranes and/or its antioxidant activity. Thus, SIL might be a promising compound to improve cellular health when changes to mitochondrial function occur.
Es wird das Mikrowellenspektrum von Fluorwasserstoffassoziaten im X-und K-Band bei -70 °C und 0,01 Torr gemessen und analysiert. Dazu wird ein erstelltes Frequenzprogramm für den asymmetrischen Kreisel verwendet, sowie ein Extrapolationsprogramm, das eine in der Literatur angegebene druck-und temperaturabhängige Verteilung der Fluorwasserstoffassoziate auf für Mikrowellenspektroskopie geeignete Drücke und Temperaturen umzurechnen erlaubt. Es zeigt sich, daß planare hexamere und heptamere Fluorwasserstoffassoziate vorliegen mit F-F-F-Winkeln von etwa 104° und H-F-Bindungslängen von 0,9997 Å bzw. 0,9640 Å. Die Längen der Wasserstoff brücken sind 1,4998 Å bzw. 1,6105 Å. Ein Vergleich der Bindungslängen zeigt, daß bei Anlagerung von H-F an (HF)6 eine Kontraktion der Fluorwasserstoffbindung um 3,5% und eine Dilatation der Wasserstoffbrückenbindung um 1% stattfindet. Dieses Ergebnis steht im Einklang mit der oben erwähnten Assoziatverteilung, die eine Minderung der Kettenstabilität beim Übergang von hexamerer zu heptamerer Kette erwarten läßt.
The extremophile Alvinella pompejana, an annelid worm living on the edge of hydrothermal vents in the Pacific Ocean, is an excellent model system for studying factors that govern protein stability. Low intrinsic stability is a crucial factor for the susceptibility of the transcription factor p53 to inactivating mutations in human cancer. Understanding its molecular basis may facilitate the design of novel therapeutic strategies targeting mutant p53. By analyzing expressed sequence tag (EST) data, we discovered a p53 family gene in A. pompejana. Protein crystallography and biophysical studies showed that it has a p53/p63-like DNA-binding domain (DBD) that is more thermostable than all vertebrate p53 DBDs tested so far, but not as stable as that of human p63. We also identified features associated with its increased thermostability. In addition, the A. pompejana homolog shares DNA-binding properties with human p53 family DBDs, despite its evolutionary distance, consistent with a potential role in maintaining genome integrity. Through extensive structural and phylogenetic analyses, we could further trace key evolutionary events that shaped the structure, stability, and function of the p53 family DBD over time, leading to a potent but vulnerable tumor suppressor in humans.
RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. The dynamics study of RNA modifications has become an important part of epitranscriptomics field, as they are reversible and dynamically regulated far more than originally thought. Several evidences portrait a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. Therefore, a deeper investigation of RNA modifications dynamics including their specific profile, biosynthesis, maturation and degradation is required for pioneering disease diagnostics and potential therapeutics development.
Mammalian tissues reveal diverse physiology and functions, despite sharing identical genomes and overlapping transcription profiles. So far, most research on this diversity were referred to variable transcriptomic processing among tissues and differential post-translational modifications that tune the activity of ubiquitous proteins to each tissue’s needs. However, study of epitranscriptome dynamics relevance to tissues’ functions is not yet revealed. There are a few reports on mouse RNA modification profiles, which are focused on only one type of RNA and limited types of modifications. The first part of my dissertation aims to generate a comprehensive tissue-specific as well as RNA species-specific investigation of all existing RNA modifications, as well as investigating potential codon as an effector of translation diversity among tissues. Using isotope dilution mass spectrometry, I created a library including absolute quantification of 24 tRNA modifications, and up to 22 rRNA modifications. I find an almost identical pattern of modifications in 28S- and 18S-rRNA subunits, but different levels of most modifications in 5.8S-rRNA or tRNA among highly metabolic active organs to e.g. heart or spleen. The findings suggest a high degree of similarity between quantities of modifications between presented data to all previous literature, confirming that it is a suitable model to study the tissue-based RNA modification patterns.
The most noticeable difference exhibited was tRNA modifications, which suggests a discerning tRNA engagement in translation between different organs. This can be a good start for investigation of codon bias in enriched genes of specific tRNA modifications among different tissues that may cause differential translation pattern, causing organs diversity. Moreover, 5.8S rRNA data showed an organ-specific pattern, which proposes functional diversity of this rRNA subunit among different organs. Future studies must investigate the possible implications of organ-specific 5.8S rRNA modifications functions, to elucidate the core of the observed variations.
Abundance of RNA modifications is carefully regulated in cells. Part of this regulation is achieved by activity of enzymes removing RNA modifications, named RNA erasers. Literature has provided proof of demethylation activity of AlkBH family on different types of RNA. For instance, AlkBH5 is known to remove m6A in mRNA, and both AlkBH3 and AlkBH1 are reported to demethylate m1A and m3C in tRNA. So far, RNA erasers are mainly studied in vitro and direct in vivo studies are missing.
Mass spectrometry is a promising approach in the identification and quantification of many RNA modifications. However, mass spectrometric analysis by nature, offers only a static view of nucleic acid modifications, and fails to account for their cellular dynamics. Nucleic Acid Isotope Labeling coupled Mass Spectrometry (NAIL-MS) was developed as a powerful technique which differentiates among remaining, co-transcriptional and post-transcriptional incorporation of a target RNA modification. This temporal resolution captures the dynamic nature of RNA modifications, and offers absolute and relative quantification of all existing nucleosides in any given RNA sequence, including different isotopologues and isotopomers.
The objective of this study was to uncover the first “direct” iv vivo data on AlkBH1, 3 and 5 activities in demethylating each of their specific substrates. I investigated the RNA modification changes through pulse-chase experiments in collaboration with my colleagues Dr. Kayla Borland and Dr. Felix Hagelskamp. A remarkable observation was that AlkBH3 protein -but not AlkBH1- was overexpressed under methylating reagent treatment in vivo. These findings suggest that AlkBH3 -but not AlkBH1- is a methylation damage induced enzyme, that potentially triggers ASCC-AlkBH3 alkylation repair complex after aberrant methylation damage by MMS treatment. However, using NAIL-MS method, we could not detect any significant effect on demethylation activity of the enzymes in tRNA, rRNA or mRNA towards the possible substrates m6A, m1A, m3C, m5C and m7G in vivo. These distinct outcomes can be partially explained by probable existence of other unidentified demethylases that compensate for AlkBHs demethylation activity; or more probably, demethylation may still arise by remaining active AlkBHs to restore the original levels of the observed RNA modifications, since a stronger KD or a complete knockout of AlkBHs genes was not possible. Further research on fully knocked out AlkBHs genes can provide stronger evidence on unidentified demethylation activities in HEK cells.
YEATS-domain-containing MLLT1 is an acetyl/acyl-lysine reader domain, which is structurally distinct from well-studied bromodomains and has been strongly associated in development of cancer. Here, we characterized piperazine-urea derivatives as an acetyl/acyl-lysine mimetic moiety for MLLT1. Crystal structures revealed distinct interaction mechanisms of this chemotype compared to the recently described benzimidazole-amide based inhibitors, exploiting different binding pockets within the protein. Thus, the piperazine-urea scaffold offers an alternative strategy for targeting the YEATS domain family.
Dysfunction of YEATS-domain-containing MLLT1, an acetyl/acyl-lysine dependent epigenetic reader domain, has been implicated in the development of aggressive cancers. Mutations in the YEATS domain have been recently reported as a cause of MLLT1 aberrant reader function. However, structural basis for the reported alterations in affinity for acetyled/acylated histone has remained elusive. Here, we report the crystal structures of both insertion and substitution present in cancer, revealing significant conformational changes of the YEATS-domain loop 8. Structural comparison demonstrates that such alteration not only altered the binding interface for acetylated/acylated histones, but the sequence alterations in the T1 loop may enable dimeric assembly consistent inducing self-association behavior. Nevertheless, we show that also the MLLT1 mutants can be targeted by developed acetyllysine mimetic inhibitors with affinities similarly to wild type. Our report provides a structural basis for the altered behaviors and potential strategy for targeting oncogenic MLLT1 mutants.
G-protein-coupled receptors (GPCRs) from the largest family of receptors in the human body. They contain seven transmembrane helices. There are roughly 800-900 GPCR genes expressed in humans encoded by 4-5% of the human genome. These receptors are the most important signal transducers and play a crucial role in cell physiology and pathology, by using various extracellular stimuli to start complex intracellular signaling. GPCRs interact with a wide variety of stimuli from small molecules (photons, ions, amines) to large molecules (peptides, small proteins), and trigger downstream cascade effects by interacting with G-proteins, GPCR kinases, and ß-arrestin. Because of their crucial roles in many cellular functions, GPCRs are the most important drug targets for the pharmaceutical industry. Approximately 30% of the clinically approved drugs available in the market are against GPCRs. In this work achieved successful expression and purification of GPCRs from class-C and class-A families. Combined with biochemical experiments, DNP-ssNMR, and molecular simulation helped to decipher the mechanism of crosstalk between the allosteric modulator, and the orthosteric binding sites of the peptide receptor. The main findings and major highlights of this dissertation are outlined in the following paragraphs.
The calcium-sensing receptor (CaSR) belongs to the GPCR class-C family and contains a large extracellular domain. This receptor regulates Ca2+ homeostasis in blood and its absorption in the kidney and bone. To understand the molecular and structural mechanisms of these receptors their cDNAs were cloned into the pPICZ and pOET1 vectors to express them in Pichia pastoris and in Sf9 insect cells respectively. The CaSR was successfully expressed heterologously in Pichia pastoris and in the insect cell with high yield. The purified receptor purified in LMNG shows no aggregation in a monomeric state. Further optimization was performed to use it for cryo-EM sample preparation and structure determination. In 2nd part of the thesis, different mini G (mini Gs, mini Gi, mini Gqs, and mini Gsi) DNA constructs were made and expressed in E. coli. It's challenging to obtain active GPCR structures due to the instability of G-protein or G-protein-bound receptors. In this work, all mini-G proteins and chimera mini-G-protein-maltose binding protein (MBP) were cloned and expressed in E. coli and purified with a His-trap column with high purity.
In the last part of the thesis, to decipher the mechanism of allosteric modulation of orthosteric binding sites in the bradykinin receptor was produced and characterized in insect cells. Angiotensin I converting enzyme inhibitors (ACEIs), are very important drugs and are widely used for the treatment of hypertension, congestive heart failure, and diabetic neuropathy. These drugs target primarily the catalytic zinc center of the ACE. It has been shown that enalaprilat, a well-known ACEI, binds to a proposed zinc-binding site on hB1R and even directly activates the receptor. To obtain information on the influence of ACEIs on the receptor-peptide complex, and to have a better understanding of the molecular mechanism and structural plasticity of the bradykinin receptor and PAM, we used the three commercially available ACEIs captopril, enalaprilat, and lisinopril for our studies. An important result of this thesis is that though enalaprilat, captopril, and lisinopril all have similar functional properties in humans, each one regulates the orthosteric binding site of hB1R in a unique way. These findings provide atomic insights into the allosteric modulation of the bradykinin receptor. This study along with the effects of ACEI on the binding sites of receptors also deciphers the effects of the Zn2+ as well as the crosstalk between zinc binding sites and ACEI compounds. The binding of allosteric modulators induces distinct endogenous binding, which might aid in creating new possibilities in the pharmaceutical field.
Chromosomal translocations (CTs) are a genetic hallmark of cancer. They could be identified as recurrent genetic aberrations in hemato-malignancies and solid tumors. More than 40% of all "cancer genes" were identified in recurrent CTs. Most of these CTs result in the production of oncofusion proteins of which many have been studied over the past decades. They influence signaling pathways and/or alter gene expression. However, a precise mechanism for how these CTs arise and occur in a nearly identical fashion in individuals remains to be elucidated. Here, we performed experiments that explain the onset of CTs: proximity of genes able to produce prematurely terminated transcripts, which leads to the production of transspliced fusion RNAs, and finally, the induction of DNA double-strand breaks which are subsequently repaired via EJ repair pathways. Under these conditions, balanced chromosomal translocations could be specifically induced.
The lung tumor microenvironment plays a critical role in the tumorigenesis and metastasis of lung cancer, resulting from the crosstalk between cancer cells and microenvironmental cells. Therefore, comprehensive identification and characterization of cell populations in the complex lung structure is crucial for development of novel targeted anti-cancer therapies. Here, a hierarchical clustering approach with multispectral flow cytometry was established to delineate the cellular landscape of murine lungs under steady-state and cancer conditions. Fluorochromes were used multiple times to be able to measure 24 cell surface markers with only 13 detectors, yielding a broad picture for whole-lung phenotyping. Primary and metastatic murine lung tumor models were included to detect major cell populations in the lung, and to identify alterations to the distribution patterns in these models. In the primary tumor models, major altered populations included CD324+ epithelial cells, alveolar macrophages, dendritic cells, and blood and lymph endothelial cells. The number of fibroblasts, vascular smooth muscle cells, monocytes (Ly6C+ and Ly6C–) and neutrophils were elevated in metastatic models of lung cancer. Thus, the proposed clustering approach is a promising method to resolve cell populations from complex organs in detail even with basic flow cytometers.
Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and electron paramagnetic resonance experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interaction in cis in a ligand and Mg2+ dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+ dependent state for the guanidine-II riboswitch from E. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.
RNA research is very important since RNA molecules are involved in various gene regulatory mechanisms as well as pathways of cell physiology and disease development.1 RNAs have evolved from being considered as carriers of genetic information from DNA to proteins, with the three major types of RNA involved in protein synthesis, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).2 In addition to the RNAs involved in protein synthesis numerous regulatory non-coding RNAs (ncRNAs) have been discovered in the transcriptome. The regulatory ncRNAs are classified into small ncRNAs (sncRNAs) with transcripts less than 200 nucleotides (nt) and long non-coding RNAs (lncRNAs) with more than 200 nt.3
LncRNAs represent the most diverse and versatile class of ncRNAs that can regulate cellular functions of chromatin modification, transcription, and post-transcription through multiple mechanisms.4 They are involved in the formation of RNA:protein, RNA:RNA and RNA:DNA complexes as part of their gene regulatory mechanism.4,5 The RNA:DNA interactions can be divided into RNA:DNA heteroduplex formation, also called R-loops, and RNA:DNA:DNA triplex formation. In triplex formation, RNA binds to the major groove of double-stranded DNA through Hoogsteen or reverse Hoogsteen hydrogen bonding, resulting in parallel or anti-parallel triplexes, respectively. In vitro studies have confirmed the formation of RNA:DNA:DNA triplexes.6 However, the extent to which these interactions occur in cells and their effects on cellular function are still not understood, which is why these structures are so exciting to study (Chapter I RNA:DNA:DNA Triplexes).
This cumulative thesis investigates several functional and regulatory important RNAs. The first project involves the improved biochemical and biophysical characterization of RNA:DNA:DNA triplex formation between lncRNAs of interest and their target genes. Triplex formation was confirmed by a series of experiments including electromobility shift assays (EMSA), thermal melting assays, circular dichroism (CD), and liquid state nuclear magnetic resonance (NMR) spectroscopy. The following is a summary of the main findings of these publications.
In research article 5.1, the oxygen-sensitive HIF1α-AS1 was identified as a functionally important triplex-forming lncRNA in human endothelial cells using a combination of bioinformatics techniques, RNA/DNA pulldown, and biophysical experiments. Through RNA:DNA:DNA triplex formation, endogenous HIF1α-AS1 decreases the expression of several genes, including EPH receptor A2 (EPHA2) and adrenomedullin (ADM), by acting as an adaptor for the repressive human silencing hub (HUSH) complex, which has been studied by our collaborators in the groups of Leisegang and Brandes.
2) Triplex formation between HIF1α-AS1 and the target genes EPHA2 and ADM was investigated in biochemical and biophysical studies. The EMSA results indicated that HIF1α-AS1 forms a low mobility RNA:DNA:DNA triplex complex with the EPHA2 DNA target sequence. The CD spectrum of the triplex showed distinct features compared to the EPHA2 DNA duplex and the RNA:DNA heteroduplex. Melting curve analysis revealed a biphasic melting transition for triplexes, with a first melting point corresponding to the dissociation of the RNA strand with melting of the Hoogsteen hydrogen bonds. The second, higher melting temperature corresponds to the melting of stronger Watson-Crick base pairing. Stabilized triplexes were formed using an intramolecular EPHA2 DNA duplex hairpin construct in which both DNA strands were attached to a 5 nucleotide (nt) thymidine linker. This approach allowed improved triplex formation with lower RNA equivalents and higher melting temperatures. By NMR spectroscopy, the triplex characteristic signals were observed in the 1H NMR spectrum, the imino signals in a spectral region between 9 and 12 ppm resulting from the Hoogsteen base pairing. To elucidate the structural and sequence specific Hoogsteen base pairs 2D 1H,1H-NOESY measurements of the EPHA2 DNA duplex and the HIF1α-AS1:EPHA2 triplex were performed. The 1H,1H-NOESY spectrum of the HIF1α-AS1:EPHA2 triplex with a 10-fold excess of RNA was semi-quantitatively analyzed for changes in the DNA duplex spectrum. We discovered, strong and moderate attenuation of cross peak intensities in the imino region of the NOESY spectrum. This attenuation was proposed to result from weakening of Watson-Crick base pairing by Hoogsteen hydrogen bonding induced by RNA binding. The Hoogsteen interactions can be mapped based on the analysis of the cross peak attenuation in the NOESY spectra, which we used to generate a structural model of the RNA:DNA:DNA triplex. These biophysical results support the physiological function of HIF1α as a triplex-forming lncRNA that recruits the HUSH-epigenetic silencing complex to specific target genes such as EPHA2 and ADM, thereby silencing their gene expression through RNA:DNA:DNA triplex formation.
A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS). The insertion of the AH into the membrane core renders Opi1 sensitive to the lipid acyl chain composition and provides a means to adjust membrane biogenesis. By rational design of the AH, we tune the membrane-binding properties of Opi1 and control its responsiveness in vivo. Using extensive molecular dynamics simulations, we identify two PA-selective three-finger grips that tightly bind the PA phosphate headgroup while interacting less intimately with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.
A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important lipid intermediate and signaling lipid at the branch point of these pathways and constantly monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. Here, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for the selective binding to membranes containing PA over phosphatidylserine (PS). The insertion of the AH into the hydrophobic core of the membrane renders Opi1 sensitive to the lipid acyl chain composition as an important factor contributing to the regulation of membrane biogenesis. Based on these findings, we rationally designed the membrane binding properties of Opi1 to control its responsiveness in the physiological context. Using extensive molecular dynamics (MD) simulations, we identified two PA-selective three-finger grips that tightly bind the phosphate headgroup, while interacting less intimately and more transiently with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.
RNA sequencing analyses are often limited to identifying lowest p value transcripts, which does not address polygenic phenomena. To overcome this limitation, we developed an integrative approach that combines large-scale transcriptomic meta-analysis of patient brain tissues with single-cell sequencing data of CNS neurons, short RNA sequencing of human male- and female-originating cell lines, and connectomics of transcription factor and microRNA interactions with perturbed transcripts. We used this pipeline to analyze cortical transcripts of schizophrenia and bipolar disorder patients. Although these pathologies show massive transcriptional parallels, their clinically well-known sexual dimorphisms remain unexplained. Our method reveals the differences between afflicted men and women and identifies disease-affected pathways of cholinergic transmission and gp130-family neurokine controllers of immune function interlinked by microRNAs. This approach may open additional perspectives for seeking biomarkers and therapeutic targets in other transmitter systems and diseases.
RNA-sequencing analyses are often limited to identifying lowest p-value transcripts, which does not address polygenic phenomena. To overcome this limitation, we developed an integrative approach that combines large scale transcriptomic meta-analysis of patient brain tissues with single-cell sequencing data of CNS neurons, short RNA-sequencing of human male- and female-originated cell lines, and connectomics of transcription factor- and microRNA-interactions with perturbed transcripts. We used this pipeline to analyze cortical transcripts of schizophrenia and bipolar disorder patients. While these pathologies show massive transcriptional parallels, their clinically well-known sexual dimorphisms remain unexplained. Our method explicates the differences between afflicted men and women, and identifies disease-affected pathways of cholinergic transmission and gp130-family neurokine controllers of immune function, interlinked by microRNAs. This approach may open new perspectives for seeking biomarkers and therapeutic targets, also in other transmitter systems and diseases.
The SLC26 family of transporters maintains anion equilibria in all kingdoms of life. The family shares a 7 + 7 transmembrane segments inverted repeat architecture with the SLC4 and SLC23 families, but holds a regulatory STAS domain in addition. While the only experimental SLC26 structure is monomeric, SLC26 proteins form structural and functional dimers in the lipid membrane. Here we resolve the structure of an SLC26 dimer embedded in a lipid membrane and characterize its functional relevance by combining PELDOR/DEER distance measurements and biochemical studies with MD simulations and spin-label ensemble refinement. Our structural model reveals a unique interface different from the SLC4 and SLC23 families. The functionally relevant STAS domain is no prerequisite for dimerization. Characterization of heterodimers indicates that protomers in the dimer functionally interact. The combined structural and functional data define the framework for a mechanistic understanding of functional cooperativity in SLC26 dimers.
Membrane receptor clustering is fundamental to cell–cell communication; however, the physiological function of receptor clustering in cell signaling remains enigmatic. Here, we developed a dynamic platform to induce cluster formation of neuropeptide Y2 hormone receptors (Y2R) in situ by a chelator nanotool. The multivalent interaction enabled a dynamic exchange of histidine-tagged Y2R within the clusters. Fast Y2R enrichment in clustered areas triggered ligand-independent signaling as determined by an increase in cytosolic calcium and cell migration. Notably, the calcium and motility response to ligand-induced activation was amplified in preclustered cells, suggesting a key role of receptor clustering in sensitizing the dose response to lower ligand concentrations. Ligand-independent versus ligand-induced signaling differed in the binding of arrestin-3 as a downstream effector, which was recruited to the clusters only in the presence of the ligand. This approach allows in situ receptor clustering, raising the possibility to explore different receptor activation modalities.
Membrane receptors are central to cell-cell communication. Receptor clustering at the plasma membrane modulates physiological responses, and mesoscale receptor organization is critical for downstream signaling. Spatially restricted cluster formation of the neuropeptide Y2 hormone receptor (Y2R) was observed in vivo; however, the relevance of this confinement is not fully understood. Here, we controlled Y2R clustering in situ by a chelator nanotool. Due to the multivalent interaction, we observed a dynamic exchange in the microscale confined regions. Fast Y2R enrichment in clustered areas triggered a ligand-independent downstream signaling determined by an increase in cytosolic calcium, cell spreading, and migration. We revealed that the cell response to ligand-induced activation was amplified when cells were pre-clustered by the nanotool. Ligand-independent signaling by clustering differed from ligand-induced activation in the binding of arrestin-3 as downstream effector, which was recruited to the confined regions only in the presence of the ligand. This approach enables in situ clustering of membrane receptors and raises the possibility to explore different modalities of receptor activation.
The introduction of a trigonal boron atom into a polyaromatic hydrocarbon (PAH) core is an extremely powerful tool to provide organic scaffolds with optoelectronic properties as well as optimal packing in the solid state. However, boron-doped PAHs (B-PAHs) often display low processability due to their poor solubility. The distortion of the molecular scaffold provides a suitable strategy to enhance the solubility properties of B-PAHs while maintaining good stacking properties and sufficient electronic conjugation.
Extreme distortion of the molecular structure can be achieved in helical-shaped PAHs, namely helicenes which are screw-shaped inherently chiral polycycles, formed by ortho-fused aromatic or heteroaromatic rings. The presence of a helical structure in B-PAHs is expected to strongly influence their physico-chemical properties leading to compounds characterized by peculiar features promising for applications in next generation functional materials. Despite the great potential of this class of compounds, only few examples of borahelicenes have been reported in the literature and those mainly consist of carbohelicene-based structures. However, the considerable structural diversity achievable by introducing different boraheterocycles (oxaborine, borole, borepin) and other heteroaromatic rings (thiophene, furan, pyrrole) into the same helical scaffold, suggests that a large variety of compounds with intriguing features could be accessible via currently unexplored synthetic routes. The design, synthesis, and properties investigation of new boraheterohelicenes (BHHs) is therefore a relevant research topic and is the object of this PhD project, aimed to obtain several BHHs with structural diversity, as well as to study their reactivity, electrochemical and photophysical features for better understanding their potential as building blocks for material science.
The thesis work was carried out in part at the University of Milan in the laboratories of Prof. Emanuela Licandro and in part at the Goethe Universität Frankfurt am Main under the supervision of Prof. Dr. Matthias Wagner, within a co-tutelle programme. Owing to the long-standing expertise of Prof. Licandro group in the synthesis of tetrathia helicenes and that of Prof. Dr. Wagner group in the synthesis of boron-doped PAHs (e.g. boron helicene 4BH; Figure 1), I conceived this PhD project designing a series of thiahelicenes containing one or more B-O bond into the helical scaffold.Tetrathia helicenes, consisting of thiophene and benzene rings fused in an alternating fashion, are configurationally stable heterohelicenes which exist as pair of enantiomers.
This class of molecules is particularly interesting since it merges the properties of oligothiophenes with those of helicenes, giving rise to systems with peculiar electronic and chiroptical properties which make them appealing building blocks for applications in manifold fields of science, including optoelectronics, catalysis and biology.
The introduction of trigonal boron atom into a thiahelicene scaffold gives rise to a novel class of unexplored boron π-conjugated molecules with potentially interesting features.
The present Ph.D. thesis was therefore intended to provide a meaningful contribution in the development of innovative and versatile syntheses of BO-doped tetrathia helicenes as well as the study of their stereochemical and optoelectronic properties to identify potential applications of these systems in material science. The first selected structures containing one or two oxaborine rings in the helical scaffold are shown in figure 2. The presence of the bulky mesityl group at the boron atom is necessary to ensure stability to the molecule.
It is noteworthy that compound 2 is the skeletal isomer of 1, as the direction of the B-O bond is opposite in the two molecules. In the course of the research work, after the evaluation of the photophysical properties of 1, helicene 2 was designed to get information on the structure-property relationship and evaluate how the position of the BO-bond into the helical scaffold can influence the electronic properties of BO-doped thiahelicenes.
5-Lipoxygenase (5-LO) is the key enzyme in the formation of pro-inflammatory leukotrienes (LT) which play an important role in a number of inflammatory diseases. Accordingly, 5-LO inhibitors are frequently used to study the role of 5-LO and LT in models of inflammation and cancer. Interestingly, the therapeutic efficacy of these inhibitors is highly variable. Here we show that the frequently used 5-LO inhibitors AA-861, BWA4C, C06, CJ-13,610 and the FDA approved compound zileuton as well as the pan-LO inhibitor nordihydroguaiaretic acid interfere with prostaglandin E2 (PGE2) release into the supernatants of cytokine-stimulated (TNFα/IL-1β) HeLa cervix carcinoma, A549 lung cancer as well as HCA-7 colon carcinoma cells with similar potencies compared to their LT inhibitory activities (IC50 values ranging from 0.1–9.1 µM). In addition, AA-861, BWA4C, CJ-13,610 and zileuton concentration-dependently inhibited bacterial lipopolysaccharide triggered prostaglandin (PG) release into human whole blood. Western Blot analysis revealed that inhibition of expression of enzymes involved in PG synthesis was not part of the underlying mechanism. Also, liberation of arachidonic acid which is the substrate for PG synthesis as well as PGH2 and PGE2 formation were not impaired by the compounds. However, accumulation of intracellular PGE2 was found in the inhibitor treated HeLa cells suggesting inhibition of PG export as major mechanism. Further, experiments showed that the PG exporter ATP-binding cassette transporter multidrug resistance protein 4 (MRP-4) is targeted by the inhibitors and may be involved in the 5-LO inhibitor-mediated PGE2 inhibition. In conclusion, the pharmacological effects of a number of 5-LO inhibitors are compound-specific and involve the potent inhibition of PGE2 export. Results from experimental models on the role of 5-LO in inflammation and pain using 5-LO inhibitors may be misleading and their use as pharmacological tools in experimental models has to be revisited. In addition, 5-LO inhibitors may serve as new scaffolds for the development of potent prostaglandin export inhibitors.