Existence of twisting in dislocation-free protein single crystals.

The growth of high-quality protein crystals is a prerequisite for the structure analysis of proteins by X-ray diffraction. However, dislocation-free perfect crystals such as silicon and diamond have been so far limited to only two kinds of protein crystals, such as glucose isomerase and ferritin crystals. It is expected that many other high-quality or dislocation-free protein crystals still exhibit some imperfection. The clarification of the cause of imperfection is essential for the improvement of crystallinity. Here, we explore twisting as a cause of the imperfection in high-quality protein crystals of hen egg-white lysozyme crystals with polymorphisms (different crystal forms) by digital X-ray topography with synchrotron radiation. The magnitude of the observed twisting is 10−6 to 10−5°/µm which is more than two orders smaller than 10−3 to 104°/µm in other twisted crystals owing to technique limitations with optical and electron microscopy. Twisting is clearly observed in small crystals or in the initial stage of crystal growth. It is uniformly relaxed with crystal growth and becomes smaller in larger crystals. Twisting is one of main residual defects in high-quality crystals and determines the crystal perfection. Furthermore, it is presumed that the handedness of twisting can be ascribed to the anisotropic interaction of chiral protein molecules associated with asymmetric units in the crystal forms. This mechanism of twisting may correspond to the geometric frustration proposed as a primary mechanism of twisting in molecular crystals. Our finding provides insights for the understanding of growth mechanism and the growth control of high-quality crystals.

Radiation-induced defects in protein crystals observed by X-ray topography.

The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.

Control of strain in subgrains of protein crystals by the introduction of grown-in dislocations.

It is important to reveal the exact cause of poor diffractivity in protein crystals in order to determine the accurate structure of protein molecules. It is shown that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality is rather high, as shown by clear equal-thickness fringes in X-ray topography. Thus, a large stress is exerted on the subgrains of protein crystals, which could significantly lower the resistance of the crystals to radiation damage. It is also demonstrated that this local strain can be reduced through the introduction of dislocations in the crystal. This suggests that the introduction of dislocations in protein crystals can be effective in enhancing the crystal quality of subgrains of protein crystals. By exploiting this effect, the radiation damage in subgrains could be decreased, leading to the collection of X-ray diffraction data sets with high diffractivity.

Structural transformations of growing thin colloidal crystals in confined space via convective assembly.

The structural evolution of growing thin colloidal crystals in a confined space via the convective assembly technique has been investigated. The thin colloidal crystals were grown in a wedge-shaped cell, where the height of the cell increased with increased crystal growth. Triangle and square patterns, denoted as [111]- and [100]-oriented grains, respectively, were formed alternately as the height of the cell increased. The structural transformation was associated with an increase in the number of layers when the n-layer [100]-oriented grains changed to n + 1-layer [111]-oriented grains. Between the different grain structures, a stripe pattern was observed, which was a transitional region, where particle configuration gradually changed. The structural transformation occurred through the continuous change of particle configuration rather than through the abrupt formation of a grain boundary. The interval of the strip pattern lengthened as the number of layers increased, which is understood to be the structure with the highest packing density. The findings of the study give a better insight into convective assembly in a confined space, and also contribute to the greater structural control of colloidal crystals, useful for a number of applications.

Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals.

High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, there is no report yet on protein crystals showing clear dynamical diffraction. We wonder whether the perfection of protein crystals might still be low compared with that of high-quality Si crystals. Here, we present observations of the oscillatory profile of rocking curves for protein crystals such as glucose isomerase crystals. The oscillatory profiles are in good agreement with those predicted by the dynamical theory of diffraction. We demonstrate that dynamical diffraction occurs even in protein crystals. This suggests the possibility of the use of dynamical diffraction for the determination of the structure and charge density of proteins.

Heterogeneous Nucleation of Colloidal Crystals on a Glass Substrate with Depletion Attraction.

The heterogeneous nucleation of colloidal crystals with attractive interactions has been investigated via in situ observations. We have found two types of nucleation processes: a cluster that overcomes the critical size for nucleation with a monolayer, and a method that occurs with two layers. The Gibbs free energy changes (ΔG) for these two types of nucleation processes are evaluated by taking into account the effect of various interfacial energies. In contrast to homogeneous nucleation, the change in interfacial free energy, Δσ, is generated for colloidal nucleation on a foreign substrate such as a cover glass in the present study. The Δσ and step free energy of the first layer, γ1, are obtained experimentally based on the equation deduced from classical nucleation theory (CNT). It is concluded that the ΔG of q-2D nuclei is smaller than of monolayer nuclei, provided that the same number of particles are used, which explains the experimental result that the critical size in q-2D nuclei is smaller than that in monolayer nuclei.

Two-Dimensional Nucleation on the Terrace of Colloidal Crystals with Added Polymers.

Understanding nucleation dynamics is important both fundamentally and technologically in materials science and other scientific fields. Two-dimensional (2D) nucleation is the predominant growth mechanism in colloidal crystallization, in which the particle interaction is attractive, and has recently been regarded as a promising method to fabricate varieties of complex nanostructures possessing innovative functionality. Here, polymers are added to a colloidal suspension to generate a depletion attractive force, and the detailed 2D nucleation process on the terrace of the colloidal crystals is investigated. In the system, we first measured the nucleation rate at various area fractions of particles on the terrace, ϕarea. In situ observations at single-particle resolution revealed that nucleation behavior follows the framework of classical nucleation theory (CNT), such as single-step nucleation pathway and existence of critical size. Characteristic nucleation behavior is observed in that the nucleation and growth stage are clearly differentiated. When many nuclei form in a small area of the terrace, a high density of kink sites of once formed islands makes growth more likely to occur than further nucleation because nucleation has a higher energy barrier than growth. The steady-state homogeneous 2D nucleation rate, J, and the critical size of nuclei, r*, are measured by in situ observations based on the CNT, which enable us to obtain the step free energy, γ, which is an important parameter for characterizing the nucleation process. The γ value is found to change according to the strength of attraction, which is tuned by the concentration of the polymer as a depletant.

Impurity partitioning during colloidal crystallization.

We have found that an impurity partitioning takes place during growth of colloidal crystals, which was recognized by the fact that the impurity concentration in the solid (CS) was different from that in the initial solution (C0). The effective partition coefficient k(eff) (=CS/C0) was investigated for pure polystyrene and polystyrene dyed with fluorescent particles by changing the ratio of particle diameters d(imp)/d(cryst) and growth rate V. At each size ratio for the polystyrene impurity, k(eff) was less than unity and increased to unity with increasing V, whereas at a given growth rate, k(eff) increased to unity as d(imp)/d(cryst) approached unity. These results were consistent with the solute behavior analyzed using the Burton, Prim, and Slichter (BPS) model. The obtained k0, equilibrium partition coefficient, from a BPS plot increased as d(imp)/d(cryst) approached unity. In contrast, while the fluorescent particles also followed the BPS model, they showed higher k0 values than those of the same size of polystyrene particles. A k0 value greater than unity was obtained for impurities that were similar in size to the host particle. This behavior is attributed to the positive free energy of fusion associated with the incorporation of the fluorescent particles into the host matrix. Such positive free energy of fusion implies the presence of the enthalpy associated with interaction between particles.