Photosystem II (PSII) is a multi-subunit membrane protein complex. PSII performs a series of light-induced electron transfer reactions leading to the splitting of water and generation of molecular oxygen, the latter of which is essential for almost all life on the earth. The catalytic center is a Mn4CaO5-cluster, whose detailed structure has been successfully resolved in the 1.9 Å structure of PSII from Thermosynechococcus vulcanus. This structure also revealed the presence of nearly 2,800 water molecules, some of which are directly associated with the Mn4CaO5-cluster and thus may serve as the substrate water molecules for the oxygen-evolving reaction.
Epidote-group minerals are important rock-forming minerals and play a role as a reservoir of transition metal elements, strontium, rare-earth elements and water. They are formed under a variety of geological conditions. Both natural epidotes with complex chemical compositions and synthetic ones with idealized compositions have been investigated to understand their chemico-crystallographical features. In this paper, recent studies on synthetic and natural monoclinic epidotes are reviewed in terms of distributions of cations in coordination polyhedra and structural variations due to cation substitutions. New circumstances such as ‘ghost’ difference Fourier peak as an index of low-crystallinity epidotes and OH-free structure (oxyallanite) are introduced, and subjects for the future studies are proposed.
The molecular structure of collagen has long been believed to be that of a triple-stranded 10/3 helix (the Rich and Crick model). The meager X-ray diffraction data from native collagen can, however, also be explained in terms of a triple-stranded 7/2 helical model. The recent single-crystal study of the (Gly-Pro-Hyp)9 peptide confirmed that this peptide, which contains the Gly-Pro-Hyp sequence that is used as a basic repeating unit of the Rich and Crick model, does not adopt a 10/3 helix structure, but does adopt a 7/2 helix. The resulting structure will be useful for understanding molecular interactions involving collagen.
Cytochrome c (cyt c) is a stable globular protein which functions in a monomeric state as an electron donor for cytochrome c oxidase. It is also released to the cytosol when permeabilization of the mitochondrial outer membrane occurs at the early stage of apoptosis. For half a century, it has been known that cyt c forms polymers, but the polymerization mechanism remains unknown. In the crystal structures of dimeric and trimeric cyt c, the C-terminal helices are replaced by the corresponding domain of other cyt c molecules and Met80 is dissociated from the heme. The solution structures of dimeric, trimeric, and tetrameric cyt c were linear based on small-angle X-ray scattering measurements, where the trimeric linear structure shifted toward the cyclic structure by addition of PEG and (NH4)2HPO4. The absorption and CD spectra of high order oligomers (∼40 mer) were similar to those of dimeric and trimeric cyt c but different from those of monomeric cyt c. These results show that cyt c forms polymers by successive domain swapping, where the C-terminal helix is displaced from its original position in the monomer and Met-heme coordination is perturbed significantly. Successive domain swapping may be a common mechanism of protein polymerization.
An Origin of ferroelectricity in Perovskite-type oxides is discussed from a viewpoint of relation between lattice dynamics and chemical bonding state, through comprehensive study of a Ca-substitution effect on the ferroelectricity in CdTiO3. The result indicates covalency of constituent elements plays an important role on the ferroelectricity in the perovskite-type oxides.
“Cloverleaf” domain structures of six domains emerging from one point have been discovered in multiferroic hexagonal manganites RMnO3 (R = Y, Ho, and Er), by using transmission electron microscopy. The polarization orientations in 180° ferroelectric domains and phase relationships in structural antiphase domains distinctly characterize the domain pattern, which can be considered as a vortex structure. In addition, the antiphase boundaries and ferroelectric domain boundaries are found to be mutually locked, and this strong locking results in incomplete poling even when large electric fields are applied.
ACu3Fe4O12 (A = Ca and Sr) perovskites containing unusual high valence Fe4+ ions demonstrate charge disproportionation, charge ordering, and intersite charge transfer. CaCu3Fe4O12 perovskite shows charge disproportionation of 2Fe4+→Fe3++Fe5+ type, leading to the charge ordering of Fe3+ and Fe5+ in a rocksalt manner. SrCu3Fe4O12 perovskite exhibits crossover-like intersite charge transfer between Cu and Fe in the temperature range of 170∼270 K, resulting in a giant negative thermal expansion with a liner thermal expansion coefficient of −2.26×10−5 K−1, followed by the charge disproportionation at a ratio of Fe3+ : Fe5+≒4 : 1. The differences in the structural and electronic properties between CaCu3Fe4O12 and SrCu3Fe4O12 is attributed to the bond strains induced by A-site cation.
Deciphering structures of the multi-protein complexes is vital to understand biology. However, the large size, complexity, heterogeneity, and typically low abundance in their native sources, have often precluded successful structural analysis of the multi-protein machines. We have determined the crystal structure of the Mediator Head module (7 subunits, 223 kDa), an essential component in RNA polymerase II transcription. Our success depended on addressing series of challenges unique to structure determination of multi-protein complexes. We anticipate that our approach will serve as a paradigm for structural analysis of the eukaryotic multi-protein complexes that regulate vital cellular processes in the future.
High-throughput X-ray protein crystallography offers unprecedented facilitation to structure based drug discovery. The popular way to prepare crystals of target protein in complex with a candidate compound is the soaking method. However, the method often causes damage due to osmotic pressure to crystals, especially when a compound is dissolved in an organic solvent or solution with high ionic strength. These solutions damage protein crystals by osmotic shock. To overcome this difficulty, we have developed a novel technique to grow protein crystals in the concentrated hydrogel. Here, we demonstrate that protein crystals grown in hydrogel are stable to soaking and suffer less damage.