Our synchrotron radiation（SR）X-ray powder diffraction studies of accurate structure factors measurement and ab-initio structure determination during past couple of decades have been described with some details. These studies were carried out using SR powder profiles measured at SPring-8. This paper organized as follows：First the performance and an advantage of powder diffraction profile measured at SPring-8. Second, accurate structure factors measurement using SPring-8 together with recent topics. Third, we introduced the strong point of SPring-8 data for structure determination from powder diffraction with some examples. Finally, I will describe summary of this paper.
This review presents some of our studies on dynamic processes of molecules in crystals, which are related to orientational changes of organic molecules and photochromic reactions in crystals. The dynamic processes of molecules were studied by analyzing disorders in the crystal structures and their changes induced by temperature changes or photoreactions. Development of functional crystalline materials is also reviewed, especially focusing on plastic/ferroelectric molecular crystals that showed unique ferroelectric properties, which are due to the cubic crystal structures resulting from an isotropic molecular rotation in the plastic crystal phases.
The bottleneck in protein structure determination by X-ray crystallography is to obtain protein crystals with suitable size and sufficient diffracting power, and sometimes only microcrystals can be obtained. For such microcrystals, the use of X-ray microbeams is essential to collect diffraction data at high S/N ratio. However, radiation damage hampers complete and high-resolution data collection from a single microcrystal, and therefore multiple crystals are required. At microbeam beamline BL32XU, SPring-8, the workflow for protein microcrystals is established and automated. One of the key programs is SHIKA, which suggests microcrystal positions by finding diffraction spots from low-dose raster scan. Automatically collected datasets are processed and merged by KAMO, a new open-source data processing pipeline for automating the whole data processing tasks in the case of multiple datasets. These developments greatly facilitated the structure analyses from microcrystals.
A new method, called the direct derivation（DD） method, for quantitative phase analysis（QPA） can derive weight fractions of individual crystalline phases from sets of observed intensities and chemical composition data. The Patterson function plays an important role in replacing the sum of squared structure factors, calculated in the Rietveld method, with the sum of squared numbers of electrons belonging to the atoms in the chemical formula unit. Therefore, the DD method can conduct QPA of Rietveld equivalent without referencing to structure parameters. It can be applied to QPA of mixtures containing known structure, unknown structure, and high and low crystalline materials.
DNA is very attractive as bio-nanomaterials, since it is chemically stable, biocompatible, less toxic, environmentally friendly and easy to synthesize. In addition, the discovery of metal-mediated base pairs, such as T-Hg（II）-T and C-A（gI）-C, has inspired scientists to develop several nanodevices including heavy metal sensor and trapping beads. Recently, we have successfully developed a silver-DNA hybrid nanowire composed only of silver-mediated base pairs, in which Ag（I）make uninterrupted one-dimensional array along the DNA helical axis. In addition, its structure was solved by high-resolution X-ray crystallography. In this article, I present a variety of complicated and beautiful DNA structures and discuss the future outlook of “DNA structural bio-nanotechnology”.
Aptamers are nucleic acids that bind to a target molecule with high affinity and specificity, which are selected from systematic evolution of ligands by exponential enrichment （SELEX）. Because of their high affinity and specificity, aptamers are strong candidates of next generation molecular targeted agents. However, for the development of aptamer therapeutics, chemical modification of aptamers is required to improve their nuclease resistance. For the efficient modification, structural information could be important. In this review, I describe structural biology of aptamers.
LysR-type transcriptional regulators（LTTRs）are one of the most abundant transcriptional regulators in bacteria. CbnR derived from Cupriavidus necator NH9 is an LTTR involved in transcriptional activation of the cbnABCD genes that encode chlorocatechol degradative enzymes. The crystal structure of the DNA binding domain of CbnR（CbnR_DBD）in complex with recognition binding site（RBS）of the cbnA promoter showed details of interaction between the CbnR_DBD and RBS. We analyzed the sequence selectivity of CbnR by comparison of the CbnR_DBD-RBS and the BenM_DBD-RBS complexes.
Autotaxin is a plasma lysophospholipase D that hydrolyzes lysophosphatidylcholine to produce lysophosphatidic acid, and attractive target for treatment of Lung fibrosis. We developed anti- autotaxin DNA aptamers that inhibit autotaxin with high specificity and efficacy. We determined the crystal structure of autotaxin complexed with the anti-autotaxin aptamer RB011, and revealed the structural basis for the specific inhibition of autotaxin by the anti-autotaxin aptamer. We optimized RB011 based on the structural information to further improve its in vivo efficacy.