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The transporter associated with antigen processing (TAP) is an essential machine of the adaptive immune system that translocates antigenic peptides from the cytosol into the endoplasmic reticulum lumen for loading of major histocompatibility class I molecules. To examine this ABC transport complex in mechanistic detail, we have established, after extensive screening and optimization, the solubilization, purification, and reconstitution for TAP to preserve its function in each step. This allowed us to determine the substrate-binding stoichiometry of the TAP complex by fluorescence cross-correlation spectroscopy. In addition, the TAP complex shows strict coupling between peptide binding and ATP hydrolysis, revealing no basal ATPase activity in the absence of peptides. These results represent an optimal starting point for detailed mechanistic studies of the transport cycle of TAP by single molecule experiments to analyze single steps of peptide translocation and the stoichiometry between peptide transport and ATP hydrolysis.
Background: Nitric oxide (NO) is an essential vasodilator. In vascular diseases, oxidative stress attenuates NO signaling by both chemical scavenging of free NO and oxidation and down-regulation of its major intracellular receptor, the alpha/beta heterodimeric heme-containing soluble guanylate cyclase (sGC). Oxidation can also induce loss of sGC's heme and responsiveness to NO.
Results: sGC activators such as BAY 58-2667 bind to oxidized/heme-free sGC and reactivate the enzyme to exert disease-specific vasodilation. Here we show that oxidation-induced down-regulation of sGC protein extends to isolated blood vessels. Mechanistically, degradation was triggered through sGC ubiquitination and proteasomal degradation. The heme-binding site ligand, BAY 58-2667, prevented sGC ubiquitination and stabilized both alpha and beta subunits.
Conclusion: Collectively, our data establish oxidation-ubiquitination of sGC as a modulator of NO/cGMP signaling and point to a new mechanism of action for sGC activating vasodilators by stabilizing their receptor, oxidized/heme-free sGC.
PERIOD proteins are central components of the Drosophila and mammalian circadian clocks. The crystal structure of a Drosophila PERIOD (dPER) fragment comprising two PER-ARNT-SIM (PAS) domains (PAS-A and PAS-B) and two additional C-terminal alpha-helices (alphaE and alphaF) has revealed a homodimer mediated by intermolecular interactions of PAS-A with tryptophane 482 in PAS-B and helix alphaF. Here we present the crystal structure of a monomeric PAS domain fragment of dPER lacking the alphaF helix. Moreover, we have solved the crystal structure of a PAS domain fragment of the mouse PERIOD homologue mPER2. The mPER2 structure shows a different dimer interface than dPER, which is stabilized by interactions of the PAS-B beta-sheet surface including tryptophane 419 (equivalent to Trp482dPER). We have validated and quantitatively analysed the homodimer interactions of dPER and mPER2 by site-directed mutagenesis using analytical gel filtration, analytical ultracentrifugation, and co-immunoprecipitation experiments. Furthermore we show, by yeast-two-hybrid experiments, that the PAS-B beta-sheet surface of dPER mediates interactions with TIMELESS (dTIM). Our study reveals quantitative and qualitative differences between the homodimeric PAS domain interactions of dPER and its mammalian homologue mPER2. In addition, we identify the PAS-B beta-sheet surface as a versatile interaction site mediating mPER2 homodimerization in the mammalian system and dPER-dTIM heterodimer formation in the Drosophila system.
Single crystals of the title compound, C10H11NO4, an intermediate in the industrial synthesis of yellow azo pigments, were obtained from the industrial production. The molecules crystallize as centrosymmetic dimers connected by two symmetry-related N—H⋯O=C hydrogen bonds. Each molecule also contains an intramolecular N—H⋯O=C hydrogen bond. The dimers form stacks along the a-axis direction. Neighbouring stacks are arranged into a herringbone structure.
The light-harvesting complex of photosystem II (LHC-II) is the major antenna complex in plant photosynthesis. It accounts for roughly 30% of the total protein in plant chloroplasts, which makes it arguably the most abundant membrane protein on Earth, and binds about half of plant chlorophyll (Chl). The complex assembles as a trimer in the thylakoid membrane and binds a total of 54 pigment molecules, including 24 Chl a, 18 Chl b, 6 lutein (Lut), 3 neoxanthin (Neo) and 3 violaxanthin (Vio). LHC-II has five key roles in plant photosynthesis. It: (1) harvests sunlight and transmits excitation energy to the reaction centres of photosystems II and I, (2) regulates the amount of excitation energy reaching each of the two photosystems, (3) has a structural role in the architecture of the photosynthetic supercomplexes, (4) contributes to the tight appression of thylakoid membranes in chloroplast grana, and (5) protects the photosynthetic apparatus from photo damage by non photochemical quenching (NPQ). A major fraction of NPQ is accounted for its energy-dependent component qE. Despite being critical for plant survival and having been studied for decades, the exact details of how excess absorbed light energy is dissipated under qE conditions remain enigmatic. Today it is accepted that qE is regulated by the magnitude of the pH gradient (ΔpH) across the thylakoid membrane. It is also well documented that the drop in pH in the thylakoid lumen during high-light conditions activates the enzyme violaxanthin de-epoxidase (VDE), which converts the carotenoid Vio into zeaxanthin (Zea) as part of the xanthophyll cycle. Additionally, studies with Arabidopsis mutants revealed that the photosystem II subunit PsbS is necessary for qE. How these physiological responses switch LHC-II from the active, energy transmitting to the quenched, energy-dissipating state, in which the solar energy is not transmitted to the photosystems but instead dissipated as heat, remains unclear and is the subject of this thesis. From the results obtained during this doctoral work, five main conclusions can be drawn concerning the mechanism of qE: 1. Substitution of Vio by Zea in LHC-II is not sufficient for efficient dissipation of excess excitation energy. 2. Aggregation quenching of LHC-II does not require Vio, Neo nor a specific Chl pair. 3. With one exception, the pigment structure in LHC-II is rigid. 4. The two X-ray structures of LHC-II show the same energy transmitting state of the complex. 5. Crystalline LHC-II resembles the complex in the thylakoid membrane. Models of the aggregation quenching mechanism in vitro and the qE mechanism in vivo are presented as a corollary of this doctoral work. LHC-II aggregation quenching in vitro is attributed to the formation of energy sinks on the periphery of LHC-II through random interaction with other trimers, free pigments or impurities. A similar but unrelated process is proposed to occur in the thylakoid membrane, by which excess excitation energy is dissipated upon specific interaction between LHC-II and a PsbS monomer carrying Zea. At the end of this thesis, an innovative experimental model for the analysis of all key aspects of qE is proposed in order to finally solve the qE enigma, one of the last unresolved problems in photosynthesis research.
This thesis presents a 5.9 Å map of yeast FAS obtained by cryo-electron microscopy using single particle analysis (SPA). The EM-map has been analyzed both by quantitative and qualitative analysis to aid in understanding of the structure and dynamics of yeast FAS. This study approaches the factors limiting the resolution in EM (>20 Å) and further discusses the possibilities of achieving higher-resolutions (<10 Å) in cryo-EM by single particle analysis. Here, SPA is highlighted as a powerful tool for understanding the structure and dynamics of macro-molecular complexes at near native conditions. Though SPA has been used over the last four decades, the low-resolution range (20-30 Å) of the method has limited its use in structural biology. Over the last decade, sub nanometer resolution (<10 Å) structures solved by SPA have been reported --both in studies involving symmetric particles, such as GroEL (D7) and asymmetric particles, such as ribosomes (C1). Recently, near-atomic resolution in the range of 3.8-4.2 Å has been achieved in cases of highly symmetric icosahedral viral capsid structures as well. The yeast FAS structure (D3) presented here is one of two low symmetry structures submitted to the EM-database in a resolution range of 5-6 Å; the other being GroEL (D7). Fatty acid synthase (FAS) is the key enzyme for the biosynthesis of fatty acids in living organisms. There are two types of FAS, namely the type II FAS system in prokaryotes, consisting of a set of individual enzymes, and type I FAS found in eukaryotes as a multienzyme complex. Yeast fatty acid synthase (FAS) is a 2.6 MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a 3D map of yeast FAS at 5.9 Å resolution. Compared to the crystal structures of fungal FAS, the EM map reveals major differences and new features that indicate a considerably different arrangement of the complex in solution, as well as a high degree of variance inside the barrel. Distinct density regions in the reaction chambers next to each of the catalytic domains fit well with the substratebinding acyl carrier protein (ACP) domain. In each case, this resulted in the expected distance of ~18 Å from the ACP substrate binding site to the active site of the catalytic domains. The multiple, partially occupied positions of the ACP within the reaction chamber provide direct insight into the proposed substrate-shuttling mechanism of fatty acid synthesis in this large cellular machine.
Reciprocal t(9;22) ABL/BCR fusion proteins: leukemogenic potential and effects on B cell commitment
(2009)
Background: t(9;22) is a balanced translocation, and the chromosome 22 breakpoints (Philadelphia chromosome – Ph+) determine formation of different fusion genes that are associated with either Ph+ acute lymphatic leukemia (Ph+ ALL) or chronic myeloid leukemia (CML). The "minor" breakpoint in Ph+ ALL encodes p185BCR/ABL from der22 and p96ABL/BCR from der9. The "major" breakpoint in CML encodes p210BCR/ABL and p40ABL/BCR. Herein, we investigated the leukemogenic potential of the der9-associated p96ABL/BCR and p40ABL/BCR fusion proteins and their roles in the lineage commitment of hematopoietic stem cells in comparison to BCR/ABL. Methodology: All t(9;22) derived proteins were retrovirally expressed in murine hematopoietic stem cells (SL cells) and human umbilical cord blood cells (UCBC). Stem cell potential was determined by replating efficiency, colony forming - spleen and competitive repopulating assays. The leukemic potential of the ABL/BCR fusion proteins was assessed by in a transduction/transplantation model. Effects on the lineage commitment and differentiation were investigated by culturing the cells under conditions driving either myeloid or lymphoid commitment. Expression of key factors of the B-cell differentiation and components of the preB-cell receptor were determined by qRT-PCR. Principal Findings: Both p96ABL/BCR and p40ABL/BCR increased proliferation of early progenitors and the short term stem cell capacity of SL-cells and exhibited own leukemogenic potential. Interestingly, BCR/ABL gave origin exclusively to a myeloid phenotype independently from the culture conditions whereas p96ABL/BCR and to a minor extent p40ABL/BCR forced the B-cell commitment of SL-cells and UCBC. Conclusions/Significance: Our here presented data establish the reciprocal ABL/BCR fusion proteins as second oncogenes encoded by the t(9;22) in addition to BCR/ABL and suggest that ABL/BCR contribute to the determination of the leukemic phenotype through their influence on the lineage commitment.
Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis
(2009)
The bacterial PorB porin, an ATP-binding beta-barrel protein of pathogenic Neisseria gonorrhoeae, triggers host cell apoptosis by an unknown mechanism. PorB is targeted to and imported by host cell mitochondria, causing the breakdown of the mitochondrial membrane potential (delta psi m). Here, we show that PorB induces the condensation of the mitochondrial matrix and the loss of cristae structures, sensitizing cells to the induction of apoptosis via signaling pathways activated by BH3-only proteins. PorB is imported into mitochondria through the general translocase TOM but, unexpectedly, is not recognized by the SAM sorting machinery, usually required for the assembly of beta-barrel proteins in the mitochondrial outer membrane. PorB integrates into the mitochondrial inner membrane, leading to the breakdown of delta psi m. The PorB channel is regulated by nucleotides and an isogenic PorB mutant defective in ATP-binding failed to induce delta psi m loss and apoptosis, demonstrating that dissipation of delta psi m is a requirement for cell death caused by neisserial infection.
The CUG-binding protein 1 (CUG-BP1) is a member of the CUG-BP1 and ETR-like factors (CELF) family or the Bruno-like family and is involved in the control of splicing, translation and mRNA degradation. Several target RNA sequences of CUG-BP1 have been predicted, such as the CUG triplet repeat, the GU-rich sequences and the AU-rich element of nuclear pre-mRNAs and/or cytoplasmic mRNA. CUG-BP1 has three RNA-recognition motifs (RRMs), among which the third RRM (RRM3) can bind to the target RNAs on its own. In this study, we solved the solution structure of the CUG-BP1 RRM3 by hetero-nuclear NMR spectroscopy. The CUG-BP1 RRM3 exhibited a noncanonical RRM fold, with the four-stranded b-sheet surface tightly associated with the N-terminal extension. Furthermore, we determined the solution structure of the CUG-BP1 RRM3 in the complex with (UG)3 RNA, and discovered that the UGU trinucleotide is specifically recognized through extensive stacking interactions and hydrogen bonds within the pocket formed by the b-sheet surface and the N-terminal extension. This study revealed the unique mechanism that enables the CUG-BP1 RRM3 to discriminate the short RNA segment from other sequences, thus providing the molecular basis for the comprehension of the role of the RRM3s in the CELF/Bruno-like family.
This thesis describes the structural characterization of interactions between biological relevant ribonucleic acid biomacromolecules (RNAs) and selected ligands to optimize the methodologies for the design of pharmacological lead compounds. To achieve this aim, not only the structures of the RNA, the ligand and their complexes need to be known, but also information about the inherent dynamics, especially of the target RNA, are necessary. To determine the structure and dynamics of these molecules and their complexes, liquid state nuclear magnetic resonance spectroscopy (NMR) is a suitable and powerful method. The necessity for these investigations arises from the lack of knowledge in RNA-ligand interactions, e.g. for the development of new medicinal drugs targeting crucial RNA sequences. In the first chapters of this thesis (Chapters II to IV), an introduction into RNA research is given with a focus on RNA structural features (Chapter II), into the interacting molecules, the biology of the specific RNA targets and the further development of their ligands (Chapter III) and into the NMR theory and methodologies used within this thesis (Chapter IV). Chapter II begins with a description of RNA characteristics and functions, placing the focus on the increasing attention that these biomacromolecules have attracted in recent years due to their diverse biological functionalities. This is followed by a detailed description of general structural features of RNA molecules. The biological functions of the RNAs investigated in this thesis (Human immunodeficiency virus PSI- and TAR-RNA and Coxsackievirus B3 Stemloop D in the 5’-cloverleaf element), together with their known structural characteristics are introduced in Chapter III. Furthermore, a description of the investigated ligands is given, focusing on the methods how their affinity and specificity were determined. The introduction is completed in Chapter IV, where the relevant NMR theory and methodologies are explained. First, kinetics and thermodynamics of ligand binding are summarized from an NMR point of view. Subsequently, a detailed description of the resonance assignment procedures for RNAs and peptidic ligands is given. This procedure mainly concentrates on the assignment of the proton resonances, which are essential for the later structure calculation from NMR restraints. The procedure for NMR structure calculation of RNA and its complexes follows with a short introduction into the programs ARIA and HADDOCK. The final part of this chapter explains the relaxation theory and the methodology to extract dynamic information from autocorrelated relaxation rates via the model-free formalism. In the Chapters V to VII of this thesis, the original publications are included and grouped into three topics. Chapter V comprehends the publications on the investigations of HIV PSI-RNA and its hexapeptidic ligand. These three publications[1-3] focus on the characterization of the ligand and its binding properties, its structure and the optimization of its composition aiming to improve its usage for further spectroscopic investigations.
The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.
The molecular conformation of the title compound, C18H18N2O3S, is stabilized by an intramolecular N—H ... O hydrogen bond. The crystal packing shows centrosymmetric dimers connected by N—H ... S hydrogen bonds. The terminal ethoxy substituents are statistically disordered [occupancy ratio 0.527 (5):0.473 (5)].
The 3,5-methoxy groups in the title compound, C16H23NO4, are almost coplanar with the aromatic ring, whereas the 4-methoxy group is bent out of this plane. The three CH3—O—C—C torsion angles are -1.51 (18), 0.73 (19) and 75.33 (15)°. The cyclohexane ring adopts a chair conformation. In the crystal, molecules are connected by intermolecular N—H ... O hydrogen bonds into chains running along the b axis.
The asymmetric unit of the title compound, [K(C3H3N2)(C12H24O6)], is composed of a potassium cation bonded to the six O atoms of a crown ether molecule and the two N atoms of a pyrazolate anion. The K...O distances range from 2.8416 (8) to 3.0025 (8) Å, and the two K...N distances are 2.7441 (11) and 2.7654 (11) Å. The K cation is displaced by 0.8437 (4) Å from the best plane through the six O atoms. The latter plane is almost perpendicular to the plane of the pyrazolate ring [dihedral angle 83.93 (3)°]. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.026; wR factor = 0.066; data-to-parameter ratio = 16.5.
9,9-Dimethyl-9-silafluorene
(2009)
The title compound, C14H14Si, crystallizes with two almost identical molecules (r.m.s. deviation = 0.080 Å for all non-H atoms) in the asymmetric unit. All atoms of the silafluorene moiety lie in a common plane (r.m.s. deviations = 0.049 and 0.035 Å for the two molecules in the asymmetric unit). The Si-Cmethyl bonds are significantly shorter [1.865 (4)-1.868 (4) Å] than the Si-Caromatic bonds [1.882 (3)-1.892 (3) Å]. Owing to strain in the five-membered ring, the endocyclic C-Si-C angles are reduced to 91.05 (14) and 91.21 (14)°. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.005 A°; R factor = 0.061; wR factor = 0.157; data-to-parameter ratio = 16.3.
In the title compound, C17H12F2N2OS, the planar thiazole ring (r.m.s. deviation = 0.012 Å) makes dihedral angles of 15.08 (9) and 81.81 (6)° with the 4-fluorophenyl and 2-fluorophenyl rings, respectively. The 2-fluorophenyl ring is disordered over two orientations with site-occupancy factors of 0.810 (3) and 0.190 (3). The structure contains intermolecular C-H...O hydrogen bonds. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.003 Å; disorder in main residue; R factor = 0.034; wR factor = 0.082; data-to-parameter ratio = 16.1.
In the title compound, C16H16BrNO4, the dihedral between the planes of the aromatic rings is 7.74 (18)°. The amide group is tilted with respect to the bromo- and methoxy-substituted aromatic rings by 36.3 (8) and 35.2 (8)°, respectively. The meta-methoxy groups are essentially in-plane with the aromatic ring [dihedral angles CH3-O-C-C = -4.6 (4) and -2.5 (4)°]. The para-methoxy group is markedly displaced from the ring plane [dihedral angle CH3-O-C-C = -72.5 (4)°]. The crystal packing is stabilized by N-H...O hydrogen bonds linking the molecules into chains running along the b axis. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.004 Å; R factor = 0.033; wR factor = 0.076; data-to-parameter ratio = 14.6.
4-Chloro-N-m-tolylbenzamide
(2009)
In the title compound, C14H12ClNO, the dihedral angle between the two aromatic rings is 11.29 (15)°. The crystal packing is stabilized by N-H...O hydrogen bonds linking the molecules into chains running along the c axis. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.004 Å; R factor = 0.066; wR factor = 0.178; data-to-parameter ratio = 13.7.
2-Chloro-5-nitroaniline
(2009)
The molecule of the title compound, C6H5ClN2O2, is close to being planar (rms deviation = 0.032 Å for all non-H atoms), with a maximum deviation of -0.107 (3) Å for an O atom. In the crystal structure, intermolecular N-H...O and N-H...N interactions link the molecules into a three-dimensional network. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.023; wR factor = 0.061; data-to-parameter ratio = 11.8.
The title compound, C21H16N2O2, was derived from 1-(2-hydroxyphenyl)-3-(-methoxyphenyl)propane-1,3-dione. The molecular structure of the title compound is stabilized by an intramolecular O-H...N hydrogen bond. The dihedral angle between the hydroxyphenyl ring involved in this intramolecular hydrogen bond and the pyrazole ring is significantly smaller [10.07 (6)°] than the dihedral angle between the pyrazole and the other hydroxyphenyl ring [36.64 (5)°]. The benzene ring makes a dihedral angle of 54.95 (3)° with the pyrazole ring. The crystal packing is stabilized by O-H...O and O-H...N hydrogen bonds. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 Å; R factor = 0.039; wR factor = 0.101; data-to-parameter ratio = 16.2.