Evaluation of crystal quality of thin protein crystals based on the dynamical theory of X-ray diffraction

Unraveling Polymorphism and Twisting in Near-Perfect Protein Crystals

Crystals ideally have well-formed shapes and periodic arrangements of constituent components, such as atoms and molecules. Twisting, an unconventional crystal morphology, presents itself as a puzzling and natural phenomenon. The coexistence of a continuous twisting structure and crystalline order poses a paradox. Numerous mechanisms to explain twisting have been proposed, and the elucidation of the underlying causes of spontaneous nonlong-range translational order twisting in crystals has been desired. Here, we demonstrate twisting and perfect crystals controlled by the crystal polymorphs of macromolecular crystals. We establish that the presence of either a perfectly periodic crystalline arrangement or twisting is linked to anisotropic interactions arising from salt bridges among protein molecules. Employing the dynamical theory of X-ray diffraction, we discern that twisting serves as an imperfection that cannot be attributed to conventional crystal defects within crystals. These insights suggest the origin of crystal twisting and methods for controlling crystal perfection.

Anisotropy-Driven Crystallization of Dimensionally Resolved Quasi-1D Van der Waals Nanostructures

Unusual behavior in solids emerges from the complex interplay between crystalline order, composition, and dimensionality. In crystals comprising weakly bound one-dimensional (1D) or quasi-1D (q-1D) chains, properties such as charge density waves, topologically protected states, and indirect-to-direct band gap crossovers have been predicted to arise. However, the experimental demonstration of many of these nascent physics in 1D or q-1D van der Waals (vdW) crystals is obscured by the highly anisotropic bonding between the chains, stochasticity of top-down exfoliation, and the lack of synthetic strategies to control bottom-up growth. Herein, we report the directed crystallization of a model q-1D vdW phase, Sb2S3, into dimensionally resolved nanostructures. We demonstrate the uncatalyzed growth of highly crystalline Sb2S3 nanowires, nanoribbons, and quasi-2D nanosheets with thicknesses in the range of 10 to 100 nm from the bottom-up crystallization of [Sb4S6]n chains. We found that dimensionally resolved nanostructures emerge from two distinct chemical vapor growth pathways defined by diverse covalent intrachain and anisotropic vdW interchain interactions and controlled precursor ratios in the vapor phase. At sub-100 nm nanostructure thicknesses, we observe the hardening of phonon modes, blue-shifting of optical band gaps, and the emergence of a new high-energy photoluminescence peak. The directional growth of weakly bound 1D ribbons or chains into well-resolved nanocrystalline morphologies provides opportunities to develop ordered nanostructures and hierarchical assemblies that are suitable for a wide range of optoelectronic and quantum devices.

Diffusion Coefficient of Intracrystalline Water in Intrinsic Hen Egg-White Lysozyme Crystals Determined by Confocal Raman Spectroscopy

Protein crystals composed of protein molecules are expected as a novel porous material. They have high porosity, and the knowledge of the diffusion of intracrystalline water is important. In this study, the diffusion coefficient of intracrystalline water in intrinsic hen egg-white lysozyme (HEWL) crystals was determined by a method that combines confocal Raman spectroscopy and air convection with controlled relative humidity. Similar to common porous materials, the drying process of the protein crystals includes three periods: constant-rate drying, falling-rate drying, and equilibrium state. During the falling-rate drying period, the drying rate depends on the diffusion of intracrystalline water in the protein crystal. The gradient of the water content was measured using confocal Raman spectroscopy. The diffusion coefficient of the intrinsic HEWL crystals was determined as 3.1 × 10^-7 cm²/s with a water content of 36.3 vol %. The estimated diffusion coefficients of the intrinsic HEWL crystals without cross-linking were in close agreement with those of the cross-linked protein crystals. This study is timely as the knowledge of the intrinsic diffusion coefficient is useful not only for understanding the mechanism of hydration of proteins but also in practical applications such as porous materials, drug binding, and cryoprotectant soaks.

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.

Identification of grown-in dislocations in protein crystals by digital X-ray topography

X-ray topography is a useful and nondestructive method for direct observation of crystal defects in nearly perfect single crystals. The grown-in dislocations from the cross-linked seed crystal in tetragonal hen egg-white lysozyme crystals were successfully characterized by digital X-ray topography. Digital X-ray topographs with various reflections were easily obtained by reconstruction of sequential rocking-curve images. The Burgers vector of the dislocation is different from those reported previously. Interestingly, one of the dislocations had a bent shape. The preferred direction of the dislocation line was analysed by the estimated dislocation energy based on the dislocation theory. The dislocation energy can be estimated by the dislocation theory even in protein crystals composed of macromolecules.