The second lesson in this tutorial course of SHELXL includes restraints and constraints of the geometrical as well as the atom displacement parameters, and the strategy of the modeling and refinement of the disordered structures. Treatment of a troublesome disorder of pentane around the special position will be illustrated. The effect of randomly distributed solvents may be corrected either by a bulk solvent approximation or by using PLATON/SQUEEZE as a filter. Some examples of disordered inorganic structures are shown, where the atom occupation factors have been restrained to maintain the electric neutrality of the crystals.
There have been remarkable developments in the methodology for protein structure analysis over the past few decades. Currently, single-wavelength anomalous diffraction phasing of a selenomethionyl derivative (Se-SAD) is used as a general method for determining protein structure, while the sulfur single-wavelength anomalous diffraction method (S-SAD) using native protein is evolving as a next-generation method. In this paper, we look back on the early applications of multi-wavelength anomalous diffraction phasing of a selenomethionyl derivative (Se-MAD) and introduce the study of ribosomal proteins as an example of the comprehensive analysis that took place in the 1990s. Furthermore, we refer to the current state of development of the S-SAD method as well as automatic structure determination.
Crystal structures of proteins and their complexes have become critical information for molecular-based life science. Biochemical and biological analysis based on tertiary structural information is a powerful tool to unveil complex molecular processes in the cell. Here, we present two examples of the structure-based life science study, structural biology studies of CagA, an effector protein from Helicobacter pylori, and histone chaperone CIA/ASF1, which is involved in transcription initiation.
Crystal structure is most important information to understand properties and behavior of target materials. Technique to analyze unknown crystal structures from powder diffraction data (ab initio powder diffraction analysis) enables us to reveal crystal structures of target materials even we cannot obtain a single crystal. In the present article, three examples are introduced to show the power of this technique in the field of materials sciences. The first example is dehydration/hydration of the pharmaceutically relevant material erythrocycin A. In this example, crystal structures of two anhydrous phases were determined from synchrotron X-ray powder diffraction data and their different dehydration/hydration properties were understood from the crystal structures. In the second example, a crystal structure of a three dimensional metal-organic-framework prepared by a mechanochemical reaction was determined from laboratory X-ray powder diffraction data and the reaction scheme has been revealed. In the third example, a crystal structure of a novel oxide-ion conductor of a new structure family was determined from synchrotron X-ray and neutron powder diffraction data which gave an important information to understand the mechanism of the oxide-ion conduction.
The organic crystal consisted of a methylene-bridged azobenzene dimer possessing long-chain alkoxy groups melts by UV light irradiation. This characteristic phase transition is named as the photoinduced crystal-melt transition and starts from the trans-cis photoisomerization of azobenzene moieties at a solid state. Herein, elucidation of detailed mechanism of the photoinduced crystal-melt transition in the crystal of the above target compound by single crystal X-ray structure analysis is described. In this crystal structure, azobenzene moieties are aligned via intermolecular π…π interactions for constructing three-dimensional periodic structure as a crystal. On the other hand, long-chain alkoxy groups are disturbed due to their thermal motion. This thermal motion of them mitigates the mechanical stress from geometrical change accompanying with trans-cis photoisomerization of azobenzene moieties and leads formation of an overall isotropic melt phase with sacrificing π…π interactions in the crystalline phase. Visualizing these structural features playing a role for photoinduced crystal-melt transition rationalizes phase transition induced by solid-state photoreaction with proposing a phase diagram.
Recently, there has been increasing attention on the design of nanostructured materials having gyroid structures due to their unique three-dimensionally ordered structures. In this paper, bicontinuous cubic liquid crystal, one of representative materials that form gyroid structure, is discussed. There have been only a small number of researches on liquid-crystalline molecules exhibiting thermotropic bicontinuous cubic phases, and therefore it is difficult to design bicontinuous cubic liquid crystals. We have succeeded in overcoming the difficulty by introducing designability of ionic liquids into liquid crystal design. In this paper, we describe self-organizing ionic liquids that show bicontinuous cubic liquid-crystalline phases. Furthermore, their potential application as novel nanochannel materials is described.
Autophagy is an intracellular bulk degradation system conserved from yeast to human. Assembly of the pre-autophagosomal structure (PAS) is one of the most important events in starvation-induced autophagy. Recently, the structures of the autophagy initiating Atg1 complex that constitutes the PAS core have been solved by X-ray crystallography. In this review, we summarize current knowledge regarding the structure and the molecular mechanism of starvation-induced assembly of the Atg1 complex and propose the current model of autophagy initiation.
X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal soaking experiment, which is usually performed manual. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, we developed a technique to anchor protein crystals to mounting loops by using gel and inkjet technology; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in designing a fully automated drug screening pipeline.