Crystal growth and crystallography

Solubility of Organic Salts in Solvent-Antisolvent Mixtures: A Combined Experimental and Molecular Dynamics Simulations Approach

We combine molecular dynamics simulations with experiments to estimate solubilities of an organic salt in complex growth environments. We predict the solubility by simulations of the growth and dissolution of ions at the crystal surface kink sites at different solution concentrations. Thereby, the solubility is identified as the solution's salt concentration, where the energy of the ion pair dissolved in solution equals the energy of the ion pair crystallized at the kink sites. The simulation methodology is demonstrated for the case of anhydrous sodium acetate crystallized from various solvent-antisolvent mixtures. To validate the predicted solubilities, we have measured the solubilities of sodium acetate in-house, using an experimental setup and measurement protocol that guarantees moisture-free conditions, which is key for a hygroscopic compound like sodium acetate. We observe excellent agreement between the experimental and the computationally evaluated solubilities for sodium acetate in different solvent-antisolvent mixtures. Given the agreement and the rich data the simulations produce, we can use them to complement experimental tasks, which in turn will reduce time and capital in the design of complicated industrial crystallization processes of organic salts.

Semi-empirical model to estimate ideal conditions for the growth of large protein crystals

A large high-quality crystal is required to specify the positions of H atoms in neutron structural analysis. Consequently, several methods have been proposed for obtaining such large crystals, and theoretical considerations for growing them have been presented. However, further investigation is required to obtain a numerical model that can provide quantitative experimental conditions for obtaining a single large crystal. In the case of protein crystallization experiments, the amount of sample is often limited. Therefore, it is more realistic to make a rough estimation from a small number of experiments. This paper proposes a method of estimating the optimum experimental conditions for the growth of large protein crystals by performing a small number of experiments using a micro-batch method and reporting a numerical model based on nucleation theory and a linear approximation of the crystal-growth rate. Specifically, micro-batch experiments are performed to provide the empirical parameters for the model and to help to estimate the conditions for the growth of a crystal of a predetermined size using a certain sample concentration and volume. This method is offered as a step on the path towards efficiently and rationally producing large crystals that can be subjected to neutron diffraction without depending on luck or on performing many experiments. It is expected to contribute to drug design and the elucidation of protein molecular functions and mechanisms by obtaining positional information on H atoms in the protein molecule, which is an advantage of neutron diffraction.

Methods for Obtaining Better Diffractive Protein Crystals: From Sample Evaluation to Space Crystallization

In this paper, we present a summary on how to obtain protein crystals from which better diffraction images can be produced. In particular, we describe, in detail, quality evaluation of the protein sample, the crystallization conditions and methods, flash-cooling protection of the crystal, and crystallization under a microgravity environment. Our approach to protein crystallization relies on a theoretical understanding of the mechanisms of crystal growth. They are useful not only for space experiments, but also for crystallization in the laboratory.

Oscillations and accelerations of ice crystal growth rates in microgravity in presence of antifreeze glycoprotein impurity in supercooled water

The free growth of ice crystals in supercooled bulk water containing an impurity of glycoprotein, a bio-macromolecule that functions as ‘antifreeze’ in living organisms in a subzero environment, was observed under microgravity conditions on the International Space Station. We observed the acceleration and oscillation of the normal growth rates as a result of the interfacial adsorption of these protein molecules, which is a newly discovered impurity effect for crystal growth. As the convection caused by gravity may mitigate or modify this effect, secure observations of this effect were first made possible by continuous measurements of normal growth rates under long-term microgravity condition realized only in the spacecraft. Our findings will lead to a better understanding of a novel kinetic process for growth oscillation in relation to growth promotion due to the adsorption of protein molecules and will shed light on the role that crystal growth kinetics has in the onset of the mysterious antifreeze effect in living organisms, namely, how this protein may prevent fish freezing.

Numerical model of protein crystal growth in a diffusive field such as the microgravity environment

It is said that the microgravity environment positively affects the quality of protein crystal growth. The formation of a protein depletion zone and an impurity depletion zone due to the suppression of convection flow were thought to be the major reasons. In microgravity, the incorporation of molecules into a crystal largely depends on diffusive transport, so the incorporated molecules will be allocated in an orderly manner and the impurity uptake will be suppressed, resulting in highly ordered crystals. Previously, these effects were numerically studied in a steady state using a simplified model and it was determined that the combination of the diffusion coefficient of the protein molecule (D) and the kinetic constant for the protein molecule (β) could be used as an index of the extent of these depletion zones. In this report, numerical analysis of these depletion zones around a growing crystal in a non-steady (i.e. transient) state is introduced, suggesting that this model may be used for the quantitative analysis of these depletion zones in the microgravity environment.

High-Quality Protein Crystal Growth of Mouse Lipocalin-Type Prostaglandin D Synthase in Microgravity

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) catalyzes the isomerization of PGH(2) to PGD(2) and is involved in the regulation of pain and of nonrapid eye movement sleep and the differentiation of male genital organs and adipocytes, etc. L-PGDS is secreted into various body fluids and binds various lipophilic compounds with high affinities, acting also as an extracellular transporter. Mouse L-PGDS with a C65A mutation was previously crystallized with citrate or malonate as a precipitant, and the X-ray crystallographic structure was determined at 2.0 Å resolution. To obtain high-quality crystals, we tried, unsuccessfully, to crystallize the C65A mutant in microgravity under the same conditions used in the previous study. After further purifying the protein and changing the precipitant to polyethylene glycol (PEG) 8000, high-quality crystals were grown in microgravity. The precipitant solution was 40% (w/v) PEG 8000, 100 mM sodium chloride, and 100 mM HEPES-NaOH (pH 7.0). Crystals grew on board the International Space Station for 11 weeks in 2007, yielding single crystals of the wild-type L-PGDS and the C65A mutant, both of which diffracted at around 1.0 Å resolution. The crystal quality was markedly improved through the use of a high-viscosity precipitant solution in microgravity, in combination with the use of a highly purified protein.

High-quality crystals of human haematopoietic prostaglandin D synthase with novel inhibitors

Human haematopoietic prostaglandin D synthase (H-PGDS; EC 5.3.99.2) produces prostaglandin D(2), an allergic and inflammatory mediator, in mast cells and Th2 cells. H-PGDS has been crystallized with novel inhibitors with half-maximal inhibitory concentrations (IC(50)) in the low nanomolar range by the counter-diffusion method onboard the Russian Service Module on the International Space Station. The X-ray diffraction of a microgravity-grown crystal of H-PGDS complexed with an inhibitor with an IC(50) value of 50 nM extended to 1.1 A resolution at 100 K using SPring-8 synchrotron radiation, which is one of the highest resolutions obtained to date for this protein.

Crystallization of soluble proteins in vapor diffusion for x-ray crystallography

The preparation of protein single crystals represents one of the major obstacles in obtaining the detailed 3D structure of a biological macromolecule. The complete automation of the crystallization procedures requires large investments in terms of money and labor, which are available only to large dedicated infrastructures and is mostly suited for genomic-scale projects. On the other hand, many research projects from departmental laboratories are devoted to the study of few specific proteins. Here, we try to provide a series of protocols for the crystallization of soluble proteins, especially the difficult ones, tailored for small-scale research groups. An estimate of the time needed to complete each of the steps described can be found at the end of each section.

In vitro modeling of matrix vesicle nucleation: synergistic stimulation of mineral formation by annexin A5 and phosphatidylserine

Annexins A5, A2, and A6 (Anx-A5, -A2, and -A6) are quantitatively major proteins of the matrix vesicle nucleational core that is responsible for mineral formation. Anx-A5 significantly activated the induction and propagation of mineral formation when incorporated into synthetic nucleation complexes made of amorphous calcium phosphate (ACP) and Anx-A5 or of phosphatidylserine (PS) plus ACP (PS-CPLX) and Anx-A5. Incorporation of Anx-A5 markedly shortened the induction time, greatly increasing the rate and overall amount of mineral formed when incubated in synthetic cartilage lymph. Constructed by the addition of Ca(2+) to PS, emulsions prepared in an intracellular phosphate buffer matched in ionic composition to the intracellular fluid of growth plate chondrocytes, these biomimetic PS-CPLX nucleators had little nucleational activity. However, incorporation of Anx-A5 transformed them into potent nucleators, with significantly greater activity than those made from ACP without PS. The ability of Anx-A5 to enhance the nucleation and growth of mineral appears to stem from its ability to form two-dimensional crystalline arrays on PS-containing monolayers. However, some stimulatory effect also may result from its ability to exclude Mg(2+) and HCO(-)(3) from nucleation sites. Comparing the various annexins for their ability to activate PS-CPLX nucleation yields the following: avian cartilage Anx-A5 > human placental Anx-A5 > avian liver Anx-A5 > or = avian cartilage Anx-A6 >> cartilage Anx-A2. The stimulatory effect of human placental Anx-A5 and avian cartilage Anx-A6 depended on the presence of PS, since in its absence they either had no effect or actually inhibited the nucleation activity of ACP. Anx-A2 did not significantly enhance mineralization.

Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions

The transcription termination factor NusA from Aeropyrum pernix was crystallized using a counter-diffusion technique in both terrestrial and microgravity environments. Crystallization under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 A, with similar unit-cell parameters. Based on a comparison of the crystal parameters, the effect of microgravity on protein crystallization is discussed.

Numerical analysis of the depletion zone formation around a growing protein crystal

It is expected that a protein depletion zone and an impurity depletion zone are formed around a crystal during protein crystal growth if the diffusion field around the crystal is not disturbed. The growth rate of the crystal may be decreased and the impurity uptake may be suppressed to result in highly ordered crystals if these zones are not disturbed. It is well known that a microgravity environment can reduce convective fluid motion, and this is thought to disturb the depletion zones. Therefore, we expect that crystals grown in space can attain better quality than those grown on the ground. In this study, we estimate the depletion zone formation numerically and discuss the results of crystallization in space experiments. In case of alpha-amylase, most of the crystals form a cluster-like morphology on the ground using PEG 8000 as a precipitant. However, in space, we have obtained a single and high-quality crystal grown from the same sample compositions. We have measured the viscosity of the solution, the diffusion coefficient, and the growth rate of protein crystals on the ground. Applying numerical analysis to these values a significant depletion zone was expected to form mainly due to higher values of the viscosity. This might be one of the main reasons for better quality single crystals grown in space, where the depletion zone is thought to remain undisturbed. For protein crystallization experiments, salts are widely used as a precipitant. However, in that case, reduced concentration depletion zone effects can be expected because of a low viscosity. Therefore, if it is possible to increase the viscosity of the protein solution by means of an additive, the depletion zone formation effect would be enhanced to provide a technique that would be especially effective in space.

Crystallization mechanisms of hemoglobin C in the R state

Crystallization of the mutated hemoglobin, HbC, which occurs inside red blood cells of patients expressing betaC-globin and exhibiting the homozygous CC and the heterozygous SC (in which two mutant beta-globins, S and C, are expressed) diseases, is a convenient model for processes underlying numerous condensation diseases. As a first step, we investigated the molecular-level mechanisms of crystallization of this protein from high-concentration phosphate buffer in its stable carbomonoxy form using high-resolution atomic force microscopy. We found that in conditions of equilibrium with the solution, the crystals' surface reconstructs into four-molecule-wide strands along the crystallographic a (or b) axis. However, the crystals do not grow by the alignment of such preformed strands. We found that the crystals grow by the attachment of single molecules to suitable sites on the surface. These sites are located along the edges of new layers generated by two-dimensional nucleation or by screw dislocations. During growth, the steps propagate with random velocities, with the mean being an increasing function of the crystallization driving force. These results show that the crystallization mechanisms of HbC are similar to those found for other proteins. Therefore, strategies developed to control protein crystallization in vitro may be applicable to pathology-related crystallization systems.

Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV). Growth of the (101) face of TYMV crystals proceeded by two-dimensional nucleation. The molecular structure of the step edges and adsorption of individual virus particles and their aggregates on the crystalline surface were recorded. The surfaces of individual virions within crystals were visualized and seen to be quite distinctive with the hexameric and pentameric capsomers of the T = 3 capsids being clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions. In some cases areas of a single crystal surface were recorded in which were captured successive phases of the transition. We believe this provides the first visual record of a cooperative restructuring of the surface of a supramolecular crystal.