Before starting model building, the first set of protein phase, which is obtained with the isomorphous replacement method, the multiple wavelength anomalous dispersion method, and/or the molecular replacement method, should be improved by the phase improvement and density modification techniques. An insufficient quality of the electron density map might be a snag for model building. Methods of phase improvement and density modification techniques must usually be performed.
The protein's structure has to be refined to elucidate its biological function exactly, after it is approximately determined with the X-ray crystallography. Mathematically the conjugate gradient method is rapid and convenient to the refinement, giving the restraint in the structure as a gathering of parts of standard value. It would be possible to do the high accuracy in atomic level, because the high-quality data can have been observed.
Based on the results obtained for ceria nanocrystalline particles, the role of surface layers and the origin of anomalous lattice expansion in oxide nanoparticles are described in detail. The critical sizes and the anomalous dependence of lattice constants on particle size are discussed about ferroelectric and ferroelastic nanocrystallites. Consequently what are required for the research of oxide nanocrystallites in the near future are proposed.
The final goal of this research project is the understanding of all fundamental biological phenomena in terms of physical chemistry. As a model organism for the structural and functional studies, an extremely thermophilic bacterium, Thermus thermophilus HB8, is very promising because of the small genome size, the availability of genetic tools for functional analysis, and the thermostability of its proteins (http: //www.thermus.org/) . In this report, we summarize the recent progress of this research project toward the systems biology.
Extracellular proteins and receptor ectodomain fragments remain to be challenging targets for X-ray crystallography, due to the difficulties associated with the recombinant production as well as their intrinsic interdomain flexibility. We have determined crystal structures of the αIIbβ3 integrin headpiece fragment in complex with therapeutic antagonists. Unconventional tricks exploited during the course of the crystallization, including usage of a carbohydrate processing-deficient cell line, a“clasping”tag, extensive protease polishing, and the use of Fab fragment to rigidify the complex, are described.
Over a past few years, we have determined crystal structures of several metal-containing oxygenases including indoleamin-2, 3-dioxygenase and some P450s which have interesting chemistry and play important roles in metabolism. Molecular mechanisms of these oxygenases are discussed based on the crystal structures.
The charge ordered (CO) state in spinel A1V2O4, which appears below 700 K, was examined by electron and synchrotron x-ray diffraction experiments. It was found that the CO structure is characterized by the formation of V clusters (heptamers), each of which is consisting of 7 vanadium atoms and is in a spin-singlet state as a total. In addition, it was revealed that the Cr substitution for V in A1V2O4 suppressed the formation of the long-ranged CO structure and induced the charge disordered (CD) state. As a result, the coexisting state between the CO and CD states with the 20-30 nm size was stabilized in A1V2-xCrxO4 with x=0.125.
The crystal structure of the signaling complex of human granulocyte colony-stimulating factor (GCSF) and ligand binding region of human GCSF receptor (GCSF-R) has been determined to 2.8 Å resolution. The GCSF : GCSF-R complex formed a 2 : 2 stoichiometry via a crossover interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different to that between human GCSF and the CRH domain of mouse GCSF-R. This cross-over homodimerization necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational studies.