Crystal Chemistry of the Copper Oxalate Biomineral Moolooite: The First Single-Crystal X-ray Diffraction Studies and Thermal Behavior.

Moolooite, Cu(C2O4)·nH2O, is a typical biomineral which forms due to Cu-bearing minerals coming into contact with oxalic acid sources such as bird guano deposits or lichens, and no single crystals of moolooite of either natural or synthetic origin have been found yet. This paper reports, for the first time, on the preparation of single crystals of a synthetic analog of the copper-oxalate biomineral moolooite, and on the refinement of its crystal structure from the single-crystal X-ray diffraction (SCXRD) data. Along with the structural model, the SCXRD experiment showed the significant contribution of diffuse scattering to the overall diffraction data, which comes from the nanostructural disorder caused by stacking faults of Cu oxalate chains as they lengthen. This type of disorder should result in the chains breaking, at which point the H2O molecules may be arranged. The amount of water in the studied samples did not exceed 0.15 H2O molecules per formula unit. Apparently, the mechanism of incorporation of H2O molecules governs the absence of good-quality single crystals in nature and a lack of them in synthetic experiments: the more H2O content in the structure, the stronger the disorder will be. A description of the crystal structure indicates that the ideal structure of the Cu oxalate biomineral moolooite should not contain H2O molecules and should be described by the Cu(C2O4) formula. However, it was shown that natural and synthetic moolooite crystals contain a significant portion of "structural" water, which cannot be ignored. Considering the substantially variable amount of water, which can be incorporated into the crystal structure, the formula Cu(C2O4)·nH2O for moolooite is justified.

Solid Solutions of Lindbergite-Glushinskite Series: Synthesis, Ionic Substitutions, Phase Transformation and Crystal Morphology.

To clarify the crystal chemical features of natural and synthetic oxalates Me2+(C2O4)∙2H2O (Me2+ = Fe, Mn, Mg, Zn), including minerals of the humboldtine group, solid solutions of lindbergite Mn(C2O4)∙2H2O−glushinskite Mg(C2O4)∙2H2O were precipitated under various conditions, close to those characteristic of mineralization in biofilms: at the stoichiometric ratios ((Mn + Mg)/C2O4 = 1) and non-stochiometric ratios ((Mn + Mg)/C2O4 < 1), in the presence and absence of citrate ions. Investigation of precipitates was carried out by powder X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Thermodynamic modelling was performed in order to evaluate the lindbergite−glushinskite equilibrium. It was shown that glushinskite belongs to the orthorhombic ß-modification (sp. Gr. Fddd), while lindbergite has a monoclinic α-modification (sp. gr. C2/c). Mg ions incorporate lindbergite in much higher quantities than Mn ions incorporate glushinskite; moreover, Mn glushinskites are characterized by violations of long-range order in their crystal structure. Lindbergite−glushinskite transition occurs abruptly and can be classified as a first-order isodimorphic transition. The Me2+/C2O4 ratio and the presence of citric acid in the solution affect the isomorphic capacity of lindbergite and glushinskite, the width of the transition and the equilibrium Mg/Mn ratio. The transition is accompanied by continuous morphological changes in crystals and crystal intergrowths. Given the obtained results, it is necessary to take into account in biotechnologies aimed at the bioremediation/bioleaching of metals from media containing mixtures of cations (Mg, Mn, Fe, Zn).

Exploring Structural Flexibility and Stability of α-Synuclein by the Landau-Ginzburg-Wilson Approach.

α-Synuclein (αS) is the principal protein component of the Lewy body and Lewy neurite deposits that are found in the brains of the victims of one of the most prevalent neurodegenerative disorders, Parkinson's disease. αS can be qualified as a chameleon protein because of the large number of different conformations that it is able to adopt: it is disordered under physiological conditions in solution, in equilibrium with a minor α-helical tetrameric form in the cytoplasm, and is α-helical when bound to a cell membrane. Also, in vitro, αS forms polymorphic amyloid fibrils with unique arrangements of cross-ß-sheet motifs. Therefore, it is of interest to elucidate the origins of the structural flexibility of αS and what makes αS stable in different conformations. We address these questions here by analyzing the experimental structures of the micelle-bound, tetrameric, and fibrillar αS in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is illustrated that without molecular dynamics simulations the kinks are capable of identifying the key residues causing structural flexibility of αS. Also, the stability of the experimental structures of αS is investigated by simulating heating/cooling trajectories using the Glauber algorithm. The findings are consistent with experiments.

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.

Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218-62.

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.

Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in ∼15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of ß-strands in folding, misfolding, and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D, and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. We show that the formation of each ß-strand in folding trajectories is accompanied by the emergence of kinks in internal coordinate space as well as a decrease in local free energy. In particular, the decrease in downhill folding trajectory is ∼7 kcal/mol, while it varies between 31 and 48 kcal/mol for the three-state folding trajectory. The kink analyses of the experimental structures give new insights into formation of intermediates, which may become a useful tool for preventing aggregation.