SynAggreg: A Multifunctional High-Throughput Technology for Precision Study of Amyloid Aggregation and Systematic Discovery of Synergistic Inhibitor Compounds.

Numerous proteins can coalesce into amyloid self-assemblies, which are responsible for a class of diseases called amyloidoses, but which can also fulfill important biological functions and are of great interest for biotechnology. Amyloid aggregation is a complex multi-step process, poorly prone to detailed structural studies. Therefore, small molecules interacting with amyloids are often used as tools to probe the amyloid aggregation pathway and in some cases to treat amyloidoses as they prevent pathogenic protein aggregation. Here, we report on SynAggreg, an in vitro high-throughput (HT) platform dedicated to the precision study of amyloid aggregation and the effect of modulator compounds. SynAggreg relies on an accurate bi-fluorescent amyloid-tracer readout that overcomes some limitations of existing HT methods. It allows addressing diverse aspects of aggregation modulation that are critical for pathomechanistic studies, such as the specificity of compounds toward various amyloids and their effects on aggregation kinetics, as well as the co-assembly propensity of distinct amyloids and the influence of prion-like seeding on self-assembly. Furthermore, SynAggreg is the first HT technology that integrates tailored methodology to systematically identify synergistic compound combinations-an emerging strategy to improve fatal amyloidoses by targeting multiple steps of the aggregation pathway. To this end, we apply analytical combinatorial scores to rank the inhibition efficiency of couples of compounds and to readily detect synergism. Finally, the SynAggreg platform should be suited for the characterization of a broad class of amyloids, whether of interest for drug development purposes, for fundamental research on amyloid functions, or for biotechnological applications.

Systematic study of the synthesis and coordination of 2-(1,2,3-triazol-4-yl)-pyridine to Fe(II), Ni(II) and Zn(II); ion-induced folding into helicates, mesocates and larger architectures, and application to magnetism and self-selection.

With its facile synthesis, the pyridine-1,2,3-triazole chelate is an attractive building block for coordination-driven self-assembly. When two such chelates are bridged by a spacer and exposed to cations of octahedral geometrical preference, they generally self-assemble into dinuclear triple-stranded structures in the solid state and in solution in the presence of non-coordinating counter-ions. In solution, a wider range of architectures may nevertheless form, depending on the nature of the spacer. A systematic study of the spacer and substitution pattern is therefore presented, which allows assessing the various factors affecting self-assembly around the pyridine-1,2,3-triazole chelate, as well as the stereochemical control in these architectures. Applications to chirality, magnetism and system selection are discussed, and involve Fe(ii), Ni(ii), Zn(ii) and Cu(i) cations.

Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study.

Tfb5 interacts with the Tfb2 subunit of the general transcription factor TFIIH to ensure efficient nucleotide-excision repair in eukaryotes. The crystal structure of the complex between Tfb5 and the C-terminal region of Tfb2 (Tfb2C) from Saccharomyces cerevisiae has recently been reported. Here, the structure-determination process is described as a case study. Although crystals were obtained readily, it was not possible to determine experimental phases from a first crystal form (Tfb2(412-513)-Tfb5(2-72)) that diffracted to 2.6 A resolution. Shortening of the Tfb2C from its N-terminus was decisive and modified the crystal packing, leading to a second crystal form (Tfb2(435-513)-Tfb5(2-72)). These crystals diffracted to 1.7 A resolution with excellent mosaicity and allowed structure determination by conventional approaches using heavy atoms. The refined structure from the second crystal form was used to solve the structure of the first crystal form by molecular replacement. Comparison of the two structures revealed that the N-terminal region of Tfb2C and (to a lesser extent) the C-terminal region of Tfb5 contributed to the crystal packing. A detailed analysis illustrates how variation in domain boundaries influences crystal packing and quality.

Automated overexpression and isotopic labelling of biologically active oncoproteins in the cyanobacterium Anabaena sp. PCC 7120.

We have previously shown the cyanobacterium Anabaena sp. PCC 7120 to be a suitable host for the production of isotopically labelled recombinant proteins using the nitrate-inducible nir expression system. However, the expression of toxic proteins such as oncoproteins proved to be difficult, as expression levels decreased shortly after induction, while growth continued. To overcome this limitation, we have developed a method of auto-induction of the nir promoter in which cells are grown to high cell density in a bioreactor in the presence of ammonium and nitrate. Since ammonium is the preferred nitrogen source and acts as a repressor of the nir promoter, induction occurs only when the ammonium had been depleted. Using this novel auto-induction method, both oncoproteins E6 and gankyrin were expressed at high levels in a folded conformation and were shown to be biologically active after purification. Furthermore, under similar conditions of growth in auto-inducing medium, the use of (15)N- and (13)C-labelled mineral salts yielded isotopic enrichment of these proteins at levels above 95%, making them suitable for NMR-based structural analysis in a cost-effective manner.

Supramolecular circular helicates formed by destabilisation of supramolecular dimers.

The effect of changes in the angles at the connection points of linear/circular helicates is explored as a route to control the nuclearity and architecture of metallo-supramolecular arrays. This effect is probed by changing the geometry of the metal centre used to assemble bis-pyridylimine ligands that contain a 1,3-bis(aminomethyl) benzene spacer group. Tetrahedral metal ions favour linear dimers, whereas octahedral nickel(II) predominantly gives a triangular circular helicate. Five-coordinate copper(II) falls in the middle of these extremes and results in the formation of solvent-dependent mixtures of dimer and trimer. The trinuclear, triangular, circular helicate structures, which result from coordination to copper(II) and nickel(II), are structurally characterised by X-ray crystallography and reveal that the units can aggregate into hexagonal arrays that contain anion-filled tube-like channels in the solid state.

Structural and functional characterization of a novel type of ligand-independent RXR-USP receptor.

Retinoid X receptor (RXR) and Ultraspiracle (USP) play a central role as ubiquitous heterodimerization partners of many nuclear receptors. While it has long been accepted that a wide range of ligands can activate vertebrate/mollusc RXRs, the existence and necessity of specific endogenous ligands activating RXR-USP in vivo is still matter of intense debate. Here we report the existence of a novel type of RXR-USP with a ligand-independent functional conformation. Our studies involved Tribolium USP (TcUSP) as representative of most arthropod RXR-USPs, with high sequence homology to vertebrate/mollusc RXRs. The crystal structure of the ligand-binding domain of TcUSP was solved in the context of the functional heterodimer with the ecdysone receptor (EcR). While EcR exhibits a canonical ligand-bound conformation, USP adopts an original apo structure. Our functional data demonstrate that TcUSP is a constitutively silent partner of EcR, and that none of the RXR ligands can bind and activate TcUSP. These findings together with a phylogenetic analysis suggest that RXR-USPs have undergone remarkable functional shifts during evolution and give insight into receptor-ligand binding evolution and dynamics.

Pathogenic and non-pathogenic polyglutamine tracts have similar structural properties: towards a length-dependent toxicity gradient.

Abnormally expanded polyglutamine (polyQ) tracts provide a gain of toxic functions to nine otherwise unrelated human proteins and induce progressive neurodegenerative diseases. Over the past ten years, it was suggested that only polyQ tracts longer than a specific threshold adopt a particular structure, which would be the cause of the apparent polyQ length-dependent toxicity threshold observed in polyQ diseases. We have used a combination of biochemical and biophysical approaches to compare the structural properties of polyQ of pathogenic and non-pathogenic lengths under various conditions. We observe that pathogenic and non-pathogenic polyQ, as soluble species and upon interaction with a partner, during aggregation, or as mature aggregates, display very similar structural properties. PolyQ length only influences the aggregation kinetics and, to a lesser extent, the stability of the aggregates. We thus propose that polyQ toxicity does not depend on a structural transition occurring above a specific threshold, but rather that polyQ tracts are inherently toxic sequences, whose deleterious effect gradually increases with their length. We discuss how polyQ properties and other cellular factors may explain the existence of an apparent polyQ length-dependent toxicity threshold.

Ruthenium(II) complexes with improved photophysical properties based on planar 4'-(2-pyrimidinyl)-2,2':6',2' '-terpyridine ligands.

A series of new tridentate polypyridine ligands, made of terpyridine chelating subunits connected to various substituted 2-pyrimidinyl groups, and their homoleptic and heteroleptic Ru(II) complexes have been prepared and characterized. The new metal complexes have general formulas [(R-pm-tpy)Ru(tpy)]2+ and [Ru(tpy-pm-R)2]2+ (tpy = 2,2':6',2' '-terpyridine; R-pm-tpy = 4'-(2-pyrimidinyl)-2,2':6',2' '-terpyridine with R = H, methyl, phenyl, perfluorophenyl, chloride, and cyanide). Two of the new metal complexes have also been characterized by X-ray analysis. In all the R-pm-tpy ligands, the pyrimidinyl and terpyridyl groups are coplanar, allowing an extended delocalization of acceptor orbital of the metal-to-ligand charge-transfer (MLCT) excited state. The absorption spectra, redox behavior, and luminescence properties of the new Ru(II) complexes have been investigated. In particular, the photophysical properties of these species are significantly better compared to those of [Ru(tpy)2]2+ and well comparable with those of the best emitters of Ru(II) polypyridine family containing tridentate ligands. Reasons for the improved photophysical properties lie at the same time in an enhanced MLCT-MC (MC = metal centered) energy gap and in a reduced difference between the minima of the excited and ground states potential energy surfaces. The enhanced MLCT-MC energy gap leads to diminished efficiency of the thermally activated pathway for the radiationless process, whereas the similarity in ground and excited-state geometries causes reduced Franck Condon factors for the direct radiationless decay from the MLCT state to the ground state of the new complexes in comparison with [Ru(tpy)2]2+ and similar species.

Biophysical characterization of an indolinone inhibitor in the ATP-binding site of DNA gyrase.

Fighting bacterial resistance is a challenging task in the field of medicinal chemistry. DNA gyrase represents a validated antibacterial target and has drawn much interest in recent years. By a structure-based approach we have previously discovered compound 1, an indolinone derivative, possessing inhibitory activity against DNA gyrase. In the present paper, a detailed biophysical characterization of this inhibitor is described. Using mass spectrometry, NMR spectroscopy, and fluorescence experiments we have demonstrated that compound 1 binds reversibly to the ATP-binding site of the 24 kDa N-terminal fragment of DNA gyrase B from Escherichia coli (GyrB24) with low micromolar affinity. Based on these data, a plausible molecular model of compound 1 in the active site of GyrB24 was constructed. The predicted binding mode explains the competitive inhibitory mechanism with respect to ATP and forms a useful basis for further development of potent DNA gyrase inhibitors.

Expression, purification, and characterization of a new heterotetramer structure of leucyl-tRNA synthetase from Aquifex aeolicus in Escherichia coli.

Aminoacyl-tRNA synthetases are key players in the interpretation of the genetic code. They constitute a textbook example of multi-domain proteins including insertion and terminal functional modules appended to one of the two class-specific active site domains. The non-catalytic domains usually have distinct roles in the aminoacylation reaction. Aquifex aeolicus leucyl-tRNA synthetase (LeuRS) is composed of a separated catalytic site and tRNA anticodon-binding site, which would represent one of the closest relics of the primordial aminoacyl-tRNA synthetase. Moreover, the essential catalytic site residues are split into the two different subunits. In all other class-I aminoacyl-tRNA synthetases, those two functional polypeptides are nowadays fused into a single protein chain. In this work, we report the isolation and the characterization, in Escherichia coli, of a novel oligomeric form (alphabeta)2 for A. aeolicus LeuRS, which is present in addition to the alphabeta heterodimer. A. aeolicus (alphabeta)2 LeuRS has been characterized by biochemical and biophysical methods. Native gel electrophoresis, mass spectrometry, analytical ultracentrifugation, and kinetic analysis confirmed that the (alphabeta)2 enzyme was a stable and active entity. By mass spectrometry we confirmed that the heterodimer alphabeta can bind one tRNALeu molecule whereas the heterotetramer (alphabeta)2 can bind two tRNALeu molecules. Active site titration and aminoacylation assays showed that two functional active sites are found per heterotetramer, suggesting that this molecular species might exist and be active in vivo. All those data suggest that the existence of the heterotetramer is certainly not an artifact of overexpression in E. coli.

Photoreaction of [Ru(hat)2phen]2+ with guanosine-5'-monophosphate and DNA: formation of new types of photoadducts.

[Ru(hat)2phen]2+ (HAT=1,4,5,8,9,12-hexaazatriphenylene, phen=1,10-phenanthroline) interacts with a good affinity with polynucleotides and DNA by intercalation, despite the presence of a second voluminous ancillary HAT ligand. It photoreacts with guanosine-5'-monophosphate (GMP). From HPLC, ESMS and NMR analyses, it can be concluded that this complex forms photoadducts with GMP. In contrast to the photoadducts isolated with Ru-TAP complexes (TAP=1,4,5,8-tetraazaphenanthrene), the photoadducts with [Ru(hat)2phen]2+ contain a covalent link between the oxygen atom of the guanine unit and a HAT ligand. Formation of oxidised photoadducts and compounds resulting from the addition of two GMP entities to the complex are also detected as side products. In the presence of oligo- and polynucleotides, [Ru(hat)2phen]2+ yields photoadducts when guanine bases are present.

A mixed-bridging ligand nonanuclear Ru(II) dendrimer containing a tris- chelating core. Synthesis and redox properties.

The first ligand-cored dendrimer based on branching Ru(II) centers and containing mixed polypyridine bridging ligands has been prepared; redox experiments suggest that the redox-active core is not reduced at the expected potential, probably as a consequence of shielding induced by the rigid dendritic array.

Dynamic behavior in diplatinum metalloreceptors.

Diplatinum metalloreceptors anti-4a and anti-4b exhibit dynamic behavior in solution that is modified by anion binding. An X-ray crystal structure determination of anti-4a supports its proposed solution structure.

Self-assembly, characterisation, and crystal structure of multinuclear metal complexes of the [2 x 3] and [3 x 3] grid-type.

The self-assembly of new multimetallic complexes of grid-type architecture is described. The binding of a set of tris-terdentate ligands, 1 a-1 d, based on terpyridine-like subunits, with different octahedrally coordinated metal ions leads to the formation of species whose structure depends strongly on the ligand, the metal ion, the counterion, the solvent, and the reaction conditions. Under suitable conditions, the [3 x 3] grid was obtained from the reaction of ligand 1 a with zinc tetrafluoroborate and from ligand 1 b with mercury triflate. The other ligands led to the formation of mainly one compound of composition [M(6)L(5)](12+), which has the structure of an incomplete [2 x 3] grid. The crystal structure of such a [2 x 3] grid, [Co(6)(1 d)(5)](12+), has been determined. In this complex, the three central pyrimidine-pyridine-pyrimidine non-coordinating sites adopt transoid NCbond;CN conformations. The much less stable cisoid conformations, the "pinching" of the coordination sites in the complex, the weaker donor strength of the central binding site, and the steric demand of the substituents are all factors contributing to the reluctance to produce the [3 x 3] structure. A subtle interplay between the nature of the metal, the steric demand of the ligand, the reaction conditions, and the type of counterion determine the product of self-assembly. The results obtained show that by tuning the parameters, complexes containing six or nine octahedrally coordinated metal ions in a well-defined grid-type arrangement are accessible. Both types of arrays, [2 x 3] and [3 x 3 ], are of interest as self-assembled inorganic architectures of well-defined structure and nuclearity that may be suitable prototypes for selective information storage media.

A strategy for improving the room-temperature luminescence properties of Ru(II) complexes with tridentate ligands.

Several ruthenium(II) complexes with new tridentate polypyridine ligands have been prepared, and their photophysical properties have been studied. The new tridentate ligands are tpy-modified systems (tpy = 2,2':6',2' '-terpyridine) in which aromatic substituents designed to be coplanar with the tpy moiety are introduced, with the aim of enhancing delocalization in the acceptor ligand of the potentially luminescent metal-to-ligand charge-transfer (MLCT) state and increasing the MLCT-MC energy gap (MC = metal-centered excited state). Indeed, the Ru(II) complexes obtained with this new family of tridentate ligands exhibit long-lived luminescence at room temperature (up to 200 ns). The enhanced luminescence properties of these complexes support this design strategy and are superior to those of the model Ru(tpy)22+ compound and compare favorably with those of the best Ru(II) complexes with tridentate ligands reported so far.

Characterization of multimetallic grid-type complexes by electrospray mass spectrometry.

The self-assembly of the terdentate ligands 1a-h, based on terpyridine-like binding sites, with octahedrally coordinated metal ions, such as Fe(II), Co(II), Cu(II), Zn(II), Cd(II), Hg(II) and Pb(II), leads to the formation of the supramolecular grid-type complexes 2a-c(M(II)), 3d-g(M(II)) and 4h(M(II)). The structures and compositions of these coordination complexes in solution were deduced from electrospray mass spectrometry (ESMS) measurements. The results agree with the data available from x-ray radiocrystallography in the solid state and/or NMR spectroscopy in solution. ESMS may be applied in cases where other methods are difficult to use or inconclusive. This study stresses the power of ESMS in supramolecular chemistry.