RootProf is a multi-purpose program which implements multivariate analysis of unidimensional profiles. Series of measurements, performed on related samples or on the same sample by varying some external stimulus, are analysed to find trends in data, classify them and extract quantitative information. Qualitative analysis is performed by using principal component analysis or correlation analysis. In both cases the data set is projected in a latent variable space, where a clustering algorithm classifies data points. Group separation is quantified by statistical tools. Quantitative phase analysis of a series of profiles is implemented by whole-profile fitting or by an unfolding procedure, and relies on a variety of pre-processing methods. Supervised quantitative analysis can be applied, provided a priori information on some samples is provided. RootProf can be applied to measurements from different techniques, which can be combined by means of a covariance analysis. A specific analysis for powder diffraction data allows estimation of the average size of crystal domains. RootProf borrows its graphics and data analysis capabilities from the Root framework, developed for high-energy physics experiments.
Crystallization still represents the bottleneck in the process of protein structure determination at high resolution, despite high-throughput structural genomics programs requiring optimized crystallization strategies regarding crystal quality, time, success rate, reproducibility, and used protein amount. On the other hand, the development of suitable materials for controlled heterogeneous nucleation might facilitate biomacromolecular crystallization in a variety of experimental conditions which are not conventionally fruitful. Here, the possibility to fabricate hydrogel membranes displaying controlled chemical composition and nanostructure and to use them as heterogeneous supports for biomacromolecular crystallization is demonstrated. Diverse gel morphologies are obtained by controlling phase separation kinetics during gel layer formation on membrane support. These composite materials are found to increase the effi ciency of the crystallization process so that crystals with enhanced diffraction properties are produced at lower protein concentration than conventional technique, thus affording the possibility to improve current approaches to protein crystallization and to be adapted to specifi c targets.
The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.
Supramolecular structure and properties of deep eutectic solvents (DESs) are known to be highly affected by the addition of water, and their use as solvents for poorly water-soluble macromolecules is being actively investigated. We report the first experimental investigation of protein crystallization in DESs. Different hydrophilic and hydrophobic eutectic mixtures, hydrated at different levels, have been screened as crystallization media. DESs were added to the solution containing the precipitant and the buffer required to crystallize three test proteins, and we observed that the volume ratio between DES and the corresponding solution is a key parameter for the crystallization process. Successful crystallization was achieved for the hen-egg white lysozyme when using choline chloride:urea, choline chloride:glycerol, and choline chloride:glutamic acid eutectic mixtures at a 1:2 molar ratio. High-resolution X-ray diffraction experiments disclosed the possibility to study the intriguing supramolecular network of the molecular complexes formed between protein and DES in the presence of water molecules. Individual DES components have been found to systematically occupy specific protein sites populated by solvent-exposed aromatic residues. Weak interactions between DES components, possibly mediated by water molecules, which resulted in being frozen in the ordered solvent surrounding the protein units in the crystal lattice, were reconstructed at atomic resolution. DESs were found to have a negligible effect on the protein conformation and its flexibility in the solid state. On the other hand, DESs greatly reduced solvent evaporation from the crystallization drop, thereby increasing the dissolution time of the protein crystals. Finally, DESs were found to serve as local modulators of the ordered solvent, and this resulted in a significant change of the protein solubility. In addition, we found that protein crystallization was sped up by tuning DES hydration. This enables the employment of these environmentally responsible solvents to improve biotechnological processes at the industrial level.
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