Synthesis, characterization, and magnetic properties of new homotrinuclear bis(oxamato) copper(II) complexes with an asymmetric central N,N′-bridge

The new mononuclear bis(oxamato) complex [n-Bu₄N]₂[Cu(obbo)] (1) (obbo=o-benzyl-bis(oxamato)) has been synthesized as a precursor for trinuclear oxamato-bridged transition metal complexes. Starting from 1 the homotrinuclear complexes [Cu₃(obbo)(pmdta)₂(NO₃)](NO₃)·CH₂Cl₂·H₂O (2) and [Cu₃(obbo)(tmeda)₂(NO₃)₂(dmf)] (3) have been prepared, where pmdta = N,N,N′,N″,N″-pentamethyldiethylenetriamine, tmeda = N,N,N′,N′-tetramethylethylenediamine and dmf = dimethylformamide. The crystal structures of 1-3 were solved. The magnetic properties of 2 and 3 were studied by susceptibility measurements versus temperature. For the intramolecular J parameter values of −111 cm⁻¹ (2) and −363 cm⁻¹ (3) were obtained.     

Investigation of iron-containing products from natural and laboratory cultivated Sphaerotilus-Leptothrix bacteria

Bacterial biomass collected from sheath-forming bacteria of the genera Sphaerotilus and Leptothrix was collected from a high-mountain natural stream water source. The elemental constitution and oxide phases of the products after selective cultivation of the bacteria on two different elective media using neutron activation analysis (NAA), electron microscopy (SEM, TEM), and X-ray diffraction (XRD) were studied. A high enrichment level of iron was revealed by the NAA technique in cultivated isolates as compared to the reference sample from nature. Three types of iron oxide compounds were established after cultivation in Adler’s medium: lepidocrocite (γ-FeOOH), magnetite (Fe₃O₄), and goethite (α-FeOOH). The cultivation in the Isolation medium yielded a single phase, that of goethite, excluding one sample with a distinguishable amount of lepidocrocite. XRD and EM investigations show that the biogenic oxides are nanosized. Our study exemplifies the possibilities of the biotechnology approach for obtaining, under artificial conditions, large quantities of iron-containing by-products that could be of further used in appropriate nano- and biotechnologies.     

Cation redistribution upon dehydration of Na58Y faujasite zeolite: a joint neutron diffraction and molecular simulation study

Using neutron scattering and Monte Carlo simulation, we investigate the distribution of cations in Na₅₈Y faujasite upon (de)hydration. We introduce a new method for the assignment of cations to specific sites in molecular simulations from their local environment. This allows us to bypass the need of the coordinates of crystallographic sites, which vary as water adsorption induces changes in the zeolite framework structure. Although the agreement between experiments and simulation is excellent at high temperature, some differences are observed below 150°C. We show that these differences are due to the presence of water and that temperature itself as well as adsorption-induced deformation of the framework play a less important role. We demonstrate the migration of sodium to sites III upon water adsorption, not observed for other Si:Al ratios.     

A new approach for structure analysis of two-dimensional membrane protein crystals using X-ray powder diffraction data

The application of powder diffraction methods to problems in structural biology is generally regarded as intractable because of the large number of unresolved, overlapping X‐ray reflections. Here, we use information about unit cell lattice parameters, space group transformations, and chemical composition as a priori information in a bootstrap process that resolves the ambiguities associated with overlapping reflections. The measured ratios of reflections that can be resolved experimentally are used to refine the position, the shape, and the orientation of low‐resolution molecular structures within the unit cell, in leading to the resolution of the overlapping reflections. The molecular model is then made progressively more sophisticated as additional diffraction information is included in the analysis. We apply our method to the recovery of the structure of the bacteriorhodopsin molecule (bR) to a resolution of 7 Å using experimental data obtained from two‐dimensional purple membrane crystals. The approach can be used to determine the structure factors directly or to provide reliable low‐resolution phase information that can be refined further by the conventional methods of protein crystallography.     

Analytical ultracentrifugation combined with X-ray and neutron scattering: Experiment and modelling

Analytical ultracentrifugation and solution scattering provide different multi-parameter structural and compositional information on proteins. The joint application of the two methods supplements high resolution structural studies by crystallography and NMR. We summarise the procedures required to obtain equivalent ultracentrifugation and X-ray and neutron scattering data. The constrained modelling of ultracentrifugation and scattering data is important to confirm the experimental data analysis and yields families of best-fit molecular models for comparison with crystallography and NMR structures. This modelling of ultracentrifugation and scattering data is described in terms of starting models, their conformational randomisation in trial-and-error fits, and the identification of the final best-fit models. Seven applications of these methods are described to illustrate the current state-of-the-art. These include the determination of antibody solution structures (the human IgG4 subclass, and oligomeric forms of human IgA and its secretory component), the solution structures of the complement proteins of innate immunity (Factor H and C3/C3u) and their interactions with macromolecular ligands (C-reactive protein), and anionic polysaccharides (heparin). Complementary features of joint ultracentrifugation and scattering experiments facilitate an improved understanding of crystal structures (illustrated for C3/C3u, C-reactive protein and heparin). If a large protein or its complex cannot be crystallised, the joint ultracentrifugation-scattering approach provides a means to obtain an overall macromolecular structure.     

Exploiting powder X-ray diffraction for direct structure determination in structural biology: the P2X4 receptor trafficking motif YEQGL

We report the crystal structure of the 5-residue peptide acetyl-YEQGL-amide, determined directly from powder X-ray diffraction data recorded on a conventional laboratory X-ray powder diffractometer. The YEQGL motif has a known biological role, as a trafficking motif in the C-terminus of mammalian P2X4 receptors. Comparison of the crystal structure of acetyl-YEQGL-amide determined here and that of a complex formed with the μ2 subunit of the clathrin adaptor protein complex AP2 reported previously, reveals differences in conformational properties, although there are nevertheless similarities concerning aspects of the hydrogen-bonding arrangement and the hydrophobic environment of the leucine sidechain. Our results demonstrate the potential for exploiting modern powder X-ray diffraction methodology to achieve complete structure determination of materials of biological interest that do not crystallize as single crystals of suitable size and quality for single-crystal X-ray diffraction.     

The fibrils of Ure2p homologs from Saccharomyces cerevisiae and Saccharoymyces paradoxus have similar cross-β structure in both dried and hydrated forms

The ability to convert into amyloid fibrils is a common feature of prion proteins. However, not all amyloid-forming proteins act as prions. Here, we compared two homologs of the yeast prion protein Ure2 from Saccharomyces cerevisiae and Saccharomyces paradoxus, ScUre2p and SpUre2p, which have different prion propensities in vivo. We also addressed the controversial issue of whether hydrated fibrils of Ure2 show a fundamentally different X-ray diffraction pattern than dried samples. Using Fourier transform infrared spectrometry (FTIR) and wide angle X-ray scattering of dried and concentrated hydrated fibrils, we compared the fibril structure of ScUre2p and SpUre2p. The results show that fibrils of ScUre2p and SpUre2 have a similar cross-β core under dried and hydrated conditions, with the same inter-strand and inter-sheet spacings. Given the different prion propensity of the two Ure2p homologs, this suggests that the detailed organization of the cross-β core may play an important role in the efficiency of prion propagation.     

FS36作为新型人源Hsp90抑制剂的发现

热休克蛋白90(Hsp90)通过对几百种蛋白质底物(客户蛋白质)进行合理的折叠、成熟其构象并且激活,在肿瘤细胞的生长和繁殖中发挥重要作用．因此,Hsp90成为非常有吸引力、有前途的抗肿瘤药物靶点,并且超过20种抑制剂已经进入临床实验阶段．我们在这里设计并合成了一个小分子抑制剂：FS36．收集了Hsp90^N-FS36复合物晶体结构的X射线衍射实验数据．高分辨率X射线晶体结构表明,FS36在ATP结合位点上与Hsp90^N相互作用,并且FS36可能替代核苷酸与Hsp90^N结合．FS36和Hsp90^N的复合物晶体结构和相互作用为后期设计和优化新型抗肿瘤药物奠定基础．     

Open Conformation of Ezrin Bound to Phosphatidylinositol 4,5-Bisphosphate and to F-actin Revealed by Neutron Scattering

Ezrin is a member of the ezrin-radixin-moesin family (ERM) of adapter proteins that are localized at the interface between the cell membrane and the cortical actin cytoskeleton, and they regulate a variety of cellular functions. The structure representing a dormant and closed conformation of an ERM protein has previously been determined by x-ray crystallography. Here, using contrast variation small angle neutron scattering, we reveal the structural changes of the full-length ezrin upon binding to the signaling lipid phosphatidylinositol 4,5-bisphosphate (PIP₂) and to F-actin. Ezrin binding to F-actin requires the simultaneous binding of ezrin to PIP₂. Once bound to F-actin, the opened ezrin forms more extensive contacts with F-actin than generally depicted, suggesting a possible role of ezrin in regulating the interfacial structure and dynamics between the cell membrane and the underlying actin cytoskeleton. In addition, using gel filtration, we find that the conformational opening of ezrin in response to PIP₂ binding is cooperative, but the cooperativity is disrupted by a phospho-mimic mutation S249D in the 4.1-ezrin/radixin/moesin (FERM) domain of ezrin. Using surface plasmon resonance, we show that the S249D mutation weakens the binding affinity and changes the kinetics of 4.1-ERM to PIP₂ binding. The study provides the first structural view of the activated ezrin bound to PIP₂ and to F-actin.