Refine
Year of publication
Document Type
- Article (87)
- Contribution to a Periodical (4)
- Preprint (2)
- Part of a Book (1)
Has Fulltext
- yes (94)
Is part of the Bibliography
- no (94)
Keywords
- NMR spectroscopy (14)
- SARS-CoV-2 (11)
- RNA (10)
- COVID19-NMR (5)
- G-quadruplexes (4)
- NMR (4)
- Solution NMR spectroscopy (4)
- Solution NMR-spectroscopy (4)
- rna (4)
- structural biology (4)
- 5′-UTR (3)
- Covid19-NMR (3)
- Mycobacterium tuberculosis (3)
- Non-structural protein (3)
- Protein drugability (2)
- RNA structures (2)
- aptamers (2)
- base pairing (2)
- biophysics (2)
- heteronuclear detection (2)
- kinetics (2)
- nuclear magnetic resonance spectroscopy (2)
- proteins (2)
- proteomics (2)
- reactive oxygen species (2)
- real-time NMR spectroscopy (2)
- small protein (2)
- small proteins (2)
- structure elucidation (2)
- 19F (1)
- 19F MR spectroscopy (1)
- 1H MR spectroscopy (1)
- 2'-deoxyguanosine riboswitch (1)
- 2-hydroxyglutarate (1)
- 2D NMR spectroscopy (1)
- 5'-UTR (1)
- 5_SL4 (1)
- ATG3 (1)
- B. subtilis (1)
- Bacterial Protein Kinases (1)
- Bacterial Protein Phosphatases (1)
- Biochemie (1)
- Biotin (1)
- Bradyrhizobium (1)
- C-mannosylation (1)
- CEST (1)
- COVID-19 (1)
- Covid19-nmr (1)
- DNA (1)
- DNA-PAINT (1)
- DNA-ligand complexes (1)
- Dimerization domain (1)
- Direct carbon (1)
- Drug Resistance (1)
- Drug discovery (1)
- Dynamische Kernpolarisation (1)
- E. coli (1)
- Echtzeit-NMR-Spektroskopie (1)
- Empfindlichkeitsverstärkung (1)
- Eph receptors (1)
- Ephrin ligand (1)
- Esters (1)
- Eukaryota (1)
- FBDD (1)
- FBS (1)
- FGFR (1)
- Fragment (1)
- G-protein-coupled receptors (1)
- G-quadruplex binders (1)
- Haloferax volcanii (1)
- HeLa cells (1)
- High-throughput screening (1)
- Hohes Magnetfeld (1)
- IDH mutation (1)
- IDH1 inhibitor (1)
- Internal ribosome entry site (1)
- Ligands (1)
- Low Molecular Weight PTP (1)
- Luciferase (1)
- Macrodomain (1)
- Methanosarcina mazei (1)
- Molecular modelling (1)
- MptpA (1)
- NMR Spectroscopy (1)
- NMR solution structure (1)
- NMR-Spektroskopie (1)
- NOESY (1)
- Nuclear magnetic resonance (1)
- Nucleic acid-binding domain (1)
- Nucleocapsid (1)
- Personalisierte Medizin (1)
- Phosphorylation (1)
- Primary metabolites (1)
- Protein druggability (1)
- Protein translation (1)
- PtkA (1)
- Quality control (1)
- RNA genome (1)
- RNA sequencing (RNA-Seq) (1)
- RNA stability (1)
- RNA synthesis (1)
- RNA therapy (1)
- RNASolution-state NMR (1)
- SHAPE analysis (1)
- SL1 (1)
- SL5a (1)
- SL5b (1)
- SL5b + c (1)
- SL5c (1)
- SSR128129E (1)
- Secondary metabolites (1)
- Shine-Dalgarno (1)
- Sinorhizobium fredii (1)
- Solubility (1)
- Solution-state NMR (1)
- Soybean (1)
- Stoffwechsel (1)
- Structural protein (1)
- TERRA RNA (1)
- Target validation (1)
- Translation initiation (1)
- UV/Vis spectroscopy (1)
- X-ray diffraction (1)
- Zellstudien (1)
- a-proteobacteria (1)
- accessory proteins (1)
- acute myeloid leukemia (1)
- adenine (1)
- alkylation (1)
- allostery (1)
- amino acids (1)
- analysis (1)
- analytical chemistry (1)
- antibiotics (1)
- autophagy (1)
- autophagy inhibition (1)
- barstar (1)
- biochemistry (1)
- biological chemistry (1)
- biological models (1)
- biophysical investigation (1)
- c-Myc (1)
- carbazole ligands (1)
- carbon direct detection (1)
- cell death (1)
- cell studies (1)
- cell-free protein synthesis (1)
- chemoenzymatic synthesis (1)
- chronic myeloid leukemia (1)
- circular dichroism (1)
- click chemistry (1)
- colorectal cancer (1)
- computational chemistry (1)
- conformation analysis (1)
- cysteine reactivity (1)
- cysteine-redox regulation (1)
- cytochromes (1)
- detection (1)
- diagnostic radiologic examination (1)
- drug design (1)
- entropy (1)
- eph receptor tyrosin kinase family (1)
- ephrins (1)
- fluorescence (1)
- fluorine (1)
- folding (1)
- folding landscapes (1)
- fragment screening (1)
- fragment-based screening (1)
- genetic code expansion (1)
- glioma (1)
- glutamine synthetase regulation (1)
- glutathione (1)
- glutathionylation (1)
- glycoproteins (1)
- guanidine riboswitch (1)
- hydroxynaphthoquinone (1)
- inhibitor (1)
- inhibitor design (1)
- intrinsically disordered protein (1)
- intrinsically disordered region (1)
- ions (1)
- isotope labeling (1)
- large functional RNAs (1)
- ligand design (1)
- ligands (1)
- ligases (1)
- light control (1)
- meta-stable structures (1)
- metabolic reprogramming (1)
- metabolic rewiring (1)
- metabolism (1)
- metals (1)
- molecular conformation (1)
- murine model (1)
- nitrogen direct detection (1)
- nitrogen regulation (1)
- nitroindoles (1)
- nitrosylation (1)
- non-canonical amino acid (1)
- non-natural nucleotide (1)
- nonstructural proteins (1)
- nucleobases (1)
- oligonucleotides (1)
- oncogene promoters (1)
- oxidases (1)
- oxidative folding (1)
- personalized medicine (1)
- photochemistry (1)
- plant symbioses (1)
- plasmid copy number (1)
- precision (1)
- proline isomerization (1)
- protein denaturation (1)
- protein folding (1)
- protein oxidation (1)
- protein phosphorylation (1)
- protein tyrosine kinase (1)
- protein tyrosine phosphatase (1)
- protons (1)
- quorum sensing (QS) (1)
- reductases (1)
- regioisomers (1)
- retinal (1)
- rhodopsin (1)
- ribosomal binding site (1)
- ribosomal exit tunnel (1)
- ribosome (1)
- riboswitches (1)
- ribozymes (1)
- roentgen rays (1)
- sORF (1)
- salmonella (1)
- selective isotopic labeling (1)
- site-specific labeling (1)
- small ORFs (1)
- small gene (1)
- small molecule inhibitor (1)
- solid-phase synthesis (1)
- spectrum (1)
- spectrum analysis (1)
- structural proteins (1)
- structure-activity relationships (1)
- structure–activity relationships (1)
- targeted therapy (1)
- temperature (1)
- temperature jump (1)
- thermometers (1)
- thiostrepton (1)
- transcription (1)
- transient complex (1)
- translation initiation region (1)
- tumor angiogenesis (1)
- tumor hypoxia (1)
- tumor perfusion (1)
- tyrosine kinase inhibitors (1)
- tyrosine kinase inhibitors. (1)
- tyrosine kinase signaling (1)
- zinc finger (1)
- µ-protein (1)
Institute
- Biochemie und Chemie (47)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (44)
- Biochemie, Chemie und Pharmazie (35)
- Exzellenzcluster Makromolekulare Komplexe (23)
- Sonderforschungsbereiche / Forschungskollegs (23)
- Biowissenschaften (19)
- Medizin (7)
- Präsidium (4)
- Georg-Speyer-Haus (3)
- Frankfurt Institute for Advanced Studies (FIAS) (1)
Long-range tertiary interactions determine the three-dimensional structure of a number of metabolite-binding riboswitch RNA elements and were found to be important for their regulatory function. For the guanine-sensing riboswitch of the Bacillus subtilis xpt-pbuX operon, our previous NMR-spectroscopic studies indicated pre-formation of long-range tertiary contacts in the ligand-free state of its aptamer domain. Loss of the structural pre-organization in a mutant of this RNA (G37A/C61U) resulted in the requirement of Mg2+ for ligand binding. Here, we investigate structural and stability aspects of the wild-type aptamer domain (Gsw) and the G37A/C61U-mutant (Gswloop) of the guanine-sensing riboswitch and their Mg2+-induced folding characteristics to dissect the role of long-range tertiary interactions, the link between pre-formation of structural elements and ligand-binding properties and the functional stability. Destabilization of the long-range interactions as a result of the introduced mutations for Gswloop or the increase in temperature for both Gsw and Gswloop involves pronounced alterations of the conformational ensemble characteristics of the ligand-free state of the riboswitch. The increased flexibility of the conformational ensemble can, however, be compensated by Mg2+. We propose that reduction of conformational dynamics in remote regions of the riboswitch aptamer domain is the minimal pre-requisite to pre-organize the core region for specific ligand binding.
In prokaryotes, RNA thermometers regulate a number of heat shock and virulence genes. These temperature sensitive RNA elements are usually located in the 5'-untranslated regions of the regulated genes. They repress translation initiation by base pairing to the Shine–Dalgarno sequence at low temperatures. We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence of the imino proton exchange rates via NMR spectroscopy. Exchange rates were analyzed for the wild-type (wt) RNA and the A8C mutant. The wt RNA was found to be stabilized by the extraordinarily stable G14–C25 base pair. The mismatch base pair in the wt RNA thermometer (A8–G31) is responsible for the smaller cooperativity of the unfolding transition in the wt RNA. Enthalpy and entropy values for the base-pair opening events exhibit linear correlation for both RNAs. The slopes of these correlations coincide with the melting points of the RNAs determined by CD spectroscopy. RNA unfolding occurs at a temperature where all nucleobases have equal thermodynamic stabilities. Our results are in agreement with a consecutive zipper-type unfolding mechanism in which the stacking interaction is responsible for the observed cooperativity. Furthermore, remote effects of the A8C mutation affecting the stability of nucleobase G14 could be identified. According to our analysis we deduce that this effect is most probably transduced via the hydration shell of the RNA.
Structured RNA regions are important gene control elements in prokaryotes and eukaryotes. Here, we show that the mRNA of a cyanobacterial heat shock gene contains a built-in thermosensor critical for photosynthetic activity under stress conditions. The exceptionally short 5´-untranslated region is comprised of a single hairpin with an internal asymmetric loop. It inhibits translation of the Synechocystis hsp17 transcript at normal growth conditions, permits translation initiation under stress conditions and shuts down Hsp17 production in the recovery phase. Point mutations that stabilized or destabilized the RNA structure deregulated reporter gene expression in vivo and ribosome binding in vitro. Introduction of such point mutations into the Synechocystis genome produced severe phenotypic defects. Reversible formation of the open and closed structure was beneficial for viability, integrity of the photosystem and oxygen evolution. Continuous production of Hsp17 was detrimental when the stress declined indicating that shutting-off heat shock protein production is an important, previously unrecognized function of RNA thermometers. We discovered a simple biosensor that strictly adjusts the cellular level of a molecular chaperone to the physiological need.
We present here a set of 13C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose 13C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C40 nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C10,H10 ribose signals. The experiments were applied to two RNA hairpin structures. The current set of 13C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, 13C-direct detected NMR methods constitute useful complements to the conventional 1H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs. Keywords: NMR spectroscopy , Direct carbon , detection , RNA
High-resolution NMR structure of an RNA model system : the 14-mer cUUCGg tetraloop hairpin RNA
(2009)
We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 Å) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.
Both the genomes of the epsilonproteobacteria Wolinella succinogenes and Campylobacter jejuni contain operons (sdhABE) that encode for so far uncharacterized enzyme complexes annotated as ‘non-classical’ succinate:quinone reductases (SQRs). However, the role of such an enzyme ostensibly involved in aerobic respiration in an anaerobic organism such as W. succinogenes has hitherto been unknown. We have established the first genetic system for the manipulation and production of a member of the non-classical succinate:quinone oxidoreductase family. Biochemical characterization of the W. succinogenes enzyme reveals that the putative SQR is in fact a novel methylmenaquinol:fumarate reductase (MFR) with no detectable succinate oxidation activity, clearly indicative of its involvement in anaerobic metabolism. We demonstrate that the hydrophilic subunits of the MFR complex are, in contrast to all other previously characterized members of the superfamily, exported into the periplasm via the twin-arginine translocation (tat)-pathway. Furthermore we show that a single amino acid exchange (Ala86→His) in the flavoprotein of that enzyme complex is the only additional requirement for the covalent binding of the otherwise non-covalently bound FAD. Our results provide an explanation for the previously published puzzling observation that the C. jejuni sdhABE operon is upregulated in an oxygen-limited environment as compared with microaerophilic laboratory conditions.
The cell division cycle protein 37 (Cdc37) and the 90-kDa heat shock protein (Hsp90) are molecular chaperones, which are crucial elements in the protein signaling pathway. The largest class of client proteins for Cdc37 and Hsp90 are protein kinases. The catalytic domains of these kinases are stabilized by Cdc37, and their proper folding and functioning is dependent on Hsp90. Here, we present the x-ray crystal structure of the 16-kDa middle domain of human Cdc37 at 1.88 angstroms resolution and the structure of this domain in complex with the 23-kDa N-terminal domain of human Hsp90 based on heteronuclear solution state NMR data and docking. Our results demonstrate that the middle domain of Cdc37 exists as a monomer. NMR and mutagenesis experiments reveal Leu-205 in Cdc37 as a key residue enabling complex formation. These findings can be very useful in the development of small molecule inhibitors against cancer.
In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.
Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain
(2007)
Divalent cations are important in the folding and stabilization of complex RNA structures. The adenine-sensing riboswitch controls the expression of mRNAs for proteins involved in purine metabolism by directly sensing intracellular adenine levels. Adenine binds with high affinity and specificity to the ligand binding or aptamer domain of the adenine-sensing riboswitch. The X-ray structure of this domain in complex with adenine revealed an intricate RNA-fold consisting of a three-helix junction stabilized by long-range base-pairing interactions and identified five binding sites for hexahydrated Mg2+-ions. Furthermore, a role for Mg2+-ions in the ligand-induced folding of this RNA was suggested. Here, we describe the interaction of divalent cations with the RNA–adenine complex in solution as studied by high-resolution NMR spectroscopy. Paramagnetic line broadening, chemical shift mapping and intermolecular nuclear Overhauser effects (NOEs) indicate the presence of at least three binding sites for divalent cations. Two of them are similar to those in the X-ray structure. The third site, which is important for the folding of this RNA, has not been observed previously. The ligand-free state of the RNA is conformationally heterogeneous and contains base-pairing patterns detrimental to ligand binding in the absence of Mg2+, but becomes partially pre-organized for ligand binding in the presence of Mg2+. Compared to the highly similar guanine-sensing riboswitch, the folding pathway for the adenine-sensing riboswitch aptamer domain is more complex and the influence of Mg2+ is more pronounced.
The outer segment of vertebrate photoreceptors is a specialized compartment that hosts all the signaling components required for visual transduction. Specific to rod photoreceptors is an unusual set of three glutamic acid-rich proteins (GARPs) as follows: two soluble forms, GARP1 and GARP2, and the N-terminal cytoplasmic domain (GARP′ part) of the B1 subunit of the cyclic GMP-gated channel. GARPs have been shown to interact with proteins at the rim of the disc membrane. Here we characterized native GARP1 and GARP2 purified from bovine rod photoreceptors. Amino acid sequence analysis of GARPs revealed structural features typical of “natively unfolded” proteins. By using biophysical techniques, including size-exclusion chromatography, dynamic light scattering, NMR spectroscopy, and circular dichroism, we showed that GARPs indeed exhibit a large degree of intrinsic disorder. Analytical ultracentrifugation and chemical cross-linking showed that GARPs exist in a monomer/multimer equilibrium. The results suggested that the function of GARP proteins is linked to their structural disorder. They may provide flexible spacers or linkers tethering the cyclic GMP-gated channel in the plasma membrane to peripherin at the disc rim to produce a stack of rings of these protein complexes along the long axis of the outer segment. GARP proteins could then provide the environment needed for protein interactions in the rim region of discs.