Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions

We use the MM/GBSA method to calculate the free energies of dimer formation by binding two monomers with different combinations of precipitant ions, both embedded in the structure of monomers and in the crystallization solution. It shows that the largest difference in free energy values corresponds to the most accurate dimer model, which considers all precipitant ions in their structure. In addition, it shows that in the absence of precipitant ions in the solution of lysozyme molecules, a monomer is a more energetically favorable state.

Review of crystallization processes applied for diagnosis and homeopathic research

Background: The present study makes part of the project ‘Systematic Review of Crystallization Processes Applied for Medical Purposes (SyRCrysMed)’. SyRCrysMed is planned to lead to a publication of three review articles: (i) on crystallization of blood and its derivatives (serum, plasma) for diagnostic purposes, (ii) on crystallization of other biological fluids for diagnostic purposes, and (iii) on crystallization applied to homeopathy (both, basic and clinical research). Medical crystallization is a wide, however fragmented and little known field of science. It embraces different crystallization methodologies and applications. The commune scope of most of the crystallization-based methods is to access a more complex (or different) kind of information on the diagnosed/analyzed subject than it is possible by the use of conventional methods. The underlying thought to this analysis possibility provided by crystallization is that crystallization is an extremely sensitive process and is able to visualize not only the material dimension of the sample (e.g. composition), but also immaterial forces (e.g. force-like effects, sample’s vitality). This sensitivity of crystallization encouraged some researchers (both in the past and nowadays) to apply this process also in homeopathic research. Here we present a first summary of the crystallization-based methodologies with focus on these applied in homeopathy. Materials and methods: 177 articles, books, and book chapters on medical crystallization have been collected from scientific databases, university libraries, and the library at the Goetheanum in Dornach/Switzerland. The collected literature was divided into experimental studies and other literature. All methodologies described in the experimental studies were summarized in accordance to following criteria: type of the biological fluid, dilution degree of the fluid in the crystallizing solution, presence and type of reagent in the crystallizing solution, amount of the crystallizing solution per pattern, type of diagnosed disorder, and sensitivity and specificity of the method. Results: The different diagnostic methodologies concerned mainly the crystallization of blood, plasma, serum and saliva, however also tears, urine, cerebrospinal fluid, vaginal mucosa, and sweat were used. The concentration of the sample in the crystallizing solution ranged from 100% to trace amounts. In case of diluted samples additions of salts, amino acids, neurotransmitters were used. The volume of the crystallization solution per pattern ranged from 3 μl to 6ml. The evaporation took place on a glass surface in forms of droplets, smears, or on round dishes (10cm diameter). The methodologies were applied for the diagnoses of cancer (different types and stages, including pre-symptomatic diagnosis), other diseases (e.g. diabetes, hepatitis B&C, multiple sclerosis, tuberculosis, cystic fibrosis, Sjogren’s syndrome, gastro-intestinal disorders, colon polyps, senile dementia), and physiological stages (fertility days and pregnancy in women, differences before and after physical activity). Finally, the mean sensitivity of the methods amounted to 82.1% (from 40.6% to 100%) and the mean specificity to 84.9% (from 62.3% to 96.7%). In overall the experimental methodologies can be divided into following groups: - Evaporation of droplets of an undiluted biological fluid, - Evaporation of droplets of a diluted biological fluid with addition of salts, - Evaporation of droplets of a diluted biological fluid with addition of salts and amino acids, - Evaporation of droplets containing salts, amino acids and neurotransmitters, - Evaporation of droplets of a watery solution of ashes of a biological fluid (spagyric crystallization), - Evaporation of films/smears of an undiluted biological fluid (ferning tests), - Evaporation of larger amounts of crystallizing solution of a strongly diluted biological fluid with addition of copper chloride placed on dishes (Pfeiffer’s crystallization), Within the analyzed literature there were 10 works on crystallization applied for homeopathy. They concerned three different crystallization approaches, all characterized by a low concentration of the analyzed sample in the crystallization solution (from 1% to trace amounts), or even its absence. These methodologies, besides blood, concerned also plant models and crystallization of the homeopathic preparations by themselves (without a biological sample). In these approaches the crystallization took place with or without the addition of a reagent (salt). Summary & Conclusions: Our preliminary results indicate that crystallization based methods might constitute in future valid, non-invasive, and cost-saving tools enabling, inter alia, pre-symptomatic cancer diagnosis. The studies on crystallization based methods applied to homeopathic research point at a great potential of these methodologies for both basic research and possibly also clinical applications and screening tests. Disclosure Information: The Authors declare that there is no conflict of interest.

Viscosity effect on the strategic kinetic overgrowth of molecular crystals in various morphologies: concave and octapod fullerene crystals

A kinetic overgrowth allowing organic molecular crystals in various morphologies is induced by temperature-dependent viscosity change of crystallization solution.

Allanites in the Sin Quyen IOCG deposit, North Vietnam

Allanite minerals are the principal host of REEs in the Sin Quyen, Iron Oxide Copper Gold (IOCG) type deposit. The geochemical characteristics of these minerals are discussed in this work. The studied allanites have an unstable concentration of all major elements, such as REE (14-27 wt%), Ca (9-16 wt%), Al (8-19 wt%), Si (26-34 wt%) and Fe (12-21 wt%). Two different varieties of these minerals are documented, the older with higher REE concentrations ranging from 20 to 27 wt%, and younger with lower total REE concentration ranging from 14 to 19 wt%, which occur as a rim surrounding the older. Differences between the two groups of allanites are documented by Raman spectra and optical properties. The WDS chemical composition indicate that the allanites belong to the Ce-La-ferriallanite family, with low ƩHREE with an average of 0.21 wt.%. This work also supports the estimated timing of the deposit development focusing on detailed petrological study, and documented chemical composition of allanites confirmed by simplified statistical analysis. Temperature 355ºC which was calculated using value of δ34S isotopes is interpreted as a temperature of the second crystallization stage of allanite group. The pressure of crystallization solution was calculated and is ranging from 0.98 to 5.88 MPa.

Polysaccharide-Based Injection Matrix for Serial Crystallography

Serial crystallography (SX) provides an opportunity to observe the molecular dynamics of macromolecular structures at room temperature via pump-probe studies. The delivery of crystals embedded in a viscous medium via an injector or syringe is widely performed in synchrotrons or X-ray free-electron laser facilities with low repetition rates. Various viscous media have been developed; however, there are cases in which the delivery material undesirably interacts chemically or biologically with specific protein samples, or changes the stability of the injection stream, depending on the crystallization solution. Therefore, continued discovery and characterization of new delivery media is necessary for expanding future SX applications. Here, the preparation and characterization of new polysaccharide (wheat starch (WS) and alginate)-based sample delivery media are introduced for SX. Crystals embedded in a WS or alginate injection medium showed a stable injection stream at a flow rate of < 200 nL/min and low-level X-ray background scattering similar to other hydrogels. Using these media, serial millisecond crystallography (SMX) was performed, and the room temperature crystal structures of glucose isomerase and lysozyme were determined at 1.9–2.0 Å resolutions. WS and alginate will allow an expanded application of sample delivery media in SX experiments.

In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices

Although prevalent in the determination of protein structures; crystallography always has the bottleneck of obtaining high-quality protein crystals for characterizing a wide range of proteins; especially large protein complexes. Stable fragments or domains of proteins are more readily to crystallize; which prompts the use of in situ proteolysis to remove flexible or unstable structures for improving crystallization and crystal quality. In this work; we investigated the effects of in situ proteolysis by chymotrypsin on the crystallization of the XcpVWX complex from the Type II secretion system of Pseudomonas aeruginosa. Different proteolysis conditions were found to result in two distinct lattices in the same crystallization solution. With a shorter chymotrypsin digestion at a lower concentration; the crystals exhibited a P3 hexagonal lattice that accommodates three complex molecules in one asymmetric unit. By contrast; a longer digestion with chymotrypsin of a 10-fold higher concentration facilitated the formation of a compact P212121 orthorhombic lattice with only one complex molecule in each asymmetric unit. The molecules in the hexagonal lattice have shown high atomic displacement parameter values compared with the ones in the orthorhombic lattice. Taken together; our results clearly demonstrate that different proteolysis conditions can result in the generation of distinct lattices in the same crystallization solution; which can be exploited in order to obtain different crystal forms of a better quality

Structural Analyses of Helicobacter Pylori FolC Conducting Glutamation in Folate Metabolism

FolC plays important roles in the folate metabolism of cells by attaching l-Glu to dihydropteroate (DHP) and folate, which are known activities of dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS), respectively. Here, we determined the crystal structure of Helicobacter pylori FolC (HpFolC) at 1.95 Å resolution using the single-wavelength anomalous diffraction method. HpFolC has globular N- and C-terminal domains connected by a single loop, and a binding site for ATP is located between the two domains. Apo-HpFolC was crystallized in the presence of citrate in a crystallization solution, which was held in the ATP-binding site. Structural motifs such as the P-loop and Ω-loop of HpFolC for binding of ATP and two magnesium ions are well conserved in spite of the low overall sequence similarity to other FolC/FPGSs. The Ω-loop would also recognize a folate molecule, and the DHP-binding loop of HpFolC is expected to exhibit a unique recognition mode on DHP, compared with other FolCs. Because human FolC is known to only exhibit FPGS activity, the DHFS activity of bacterial FolC is an attractive target for the eradication of pathogenic bacteria. Consequently, our structural analyses of HpFolC provide a valuable foundation for a universal antibacterial strategy against H. pylori as well as other pathogenic bacteria.

Regioselective synthesis and characterization of monovanadium-substituted β-octamolybdate [VMo7O26]5−

The monovanadium-substituted polyoxometalate anion [VMo7O26]5−, exhibiting a β-octamolybdate archetype structure, was selectively prepared as pentapotassium [hexaikosaoxido(heptamolybdenumvanadium)]ate hexahydrate, K5[VMo7O26]·6H2O (VMo7 ), by oxidation of a reduced vanadomolybdate solution with hydrogen peroxide in a fast one-pot approach. X-ray structure analysis revealed that the V atom occupies a single position in the cluster that differs from the other positions by the presence of one doubly-bonded O atom instead of two terminal oxide ligands in all other positions. The composition and structure of VMo7 was also confirmed by elemental analyses and IR spectroscopy. The selectivity of the synthesis was inspected by a 51V NMR investigation which showed that this species bound about 95% of VV in the crystallization solution. Upon dissolution of VMo7 in aqueous solution, the [VMo7O26]5− anion is substantially decomposed, mostly into [VMo5O19]3−, α-[VMo7O26]4− and [V2Mo4O19]4−, depending on the pH.

The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome

The structure of the γ subunit of archaeal translation initiation factor 2 (aIF2) fromSulfolobus solfataricus(SsoIF2γ) was determined in complex with GDPCP (a GTP analog). Crystals were obtained in the absence of magnesium ions in the crystallization solution. They belonged to space groupP1, with five molecules in the unit cell. Four of these molecules are related in pairs by a common noncrystallographic twofold symmetry axis, while the fifth has no symmetry equivalent. Analysis of the structure and its comparison with other known aIF2 γ-subunit structures in the GTP-bound state show that (i) the magnesium ion is necessary for the formation and the maintenance of the active form of SsoIF2γ and (ii) in addition to the two previously known structural switches 1 and 2, eukaryotic translation initiation factor 2 (eIF2) and aIF2 molecules have another flexible region (switch 3), the function of which may consist of initiation of the hydrolysis of GTP and the removal of e/aIF2 from the ribosome after codon–anticodon recognition.