Recent development of crystal structure determination methods enables us to produce ab initio solution for protein crystals. Some such methods are based on reciprocal space direct methods and some of them employs real space density modification methods. One of most successful methods called Shake & Bake is a hybrid of reciprocal and real space methods. This article introduces recently developed methods which have been successfully applied to protein crystals. Although many methods described here require atomic resolution data, it is getting possible to collect high resolution data for standard protein crystals with development of data collection technique at low temperature and strong synchrotron X-ray source such as Spring-8.
The structure of ribosomal protein S7 from Bacillus stearothermophilus has been solved at 2.5 Å resolution by multiwavelength anomalous diffraction method using selenomethionyl-substituted proteins. The molecule consists of a helical hydrophobic core domain and a β-ribbon arm extending from the hydrophobic core. The helical core domain is composed of a pair of entangled helix-turn-helix motifs; the fold of the core is similar to that of a DNA architectural factor. Highly conserved basic and aromatic residues are clustered on one face of the S7 molecule and create a 16S rRNA contact surface. The molecular structure of S7, together with the results of previous cross-linking experiments, suggests how this ribosomal protein binds to the 3' major domain of 16S rRNA and mediates the folding of 16S rRNA to create the ribosome decoding center.
The crystal structure of 8-HDF type photolyase from Anacystis nidulans showed the similarity of the backbone structure with MTHF type E. coli photolyase but completely different binding site of the light-harvesting cofactor. This is a first example that homologous primary and tertiary structures in closely related proteins recognize two different types of cofactors at different binding-sites. The structure and function of photolyase and its cofactor recoginition are reviewed and discussed.
The AuCd is one of the typical alloys which show martensitic transformation. There are two distinct martensites called γ2' and ζ2' phases appearing proximate to the composition of Au52.5Cd47.5 and Au50Cd50, respectively. The crystal structure of ζ2' martensite was solved and it was described to be a superposition of transverse waves whose poralization is ‹110› and wave vector is ‹110›. The phonon dispersion relations were observed for Au52.5Cd47.5 and Au50.5Cd49.5 overcoming the difficulty of strong absorption of neutron with an isotope 114Cd. The phonon softening behaviors were observed in addition to the peculiar behavior on Au52.5Cd47.5.
The optical second harmonic generation can be applied to the observation of ferroic domains. In particular, ferroelectric 180° domain structures were successfully observed using a nonlinear microscope termed SHG microscope. The principle utilizes the phase difference of the second harmonic waves produced in domains with opposite polarizations and the interference effect was utilized to make the intensity contrast. Other applications to the J-aagre-gate in monomolecular films and antiferromagnetic domain structure are also possible using the SHG microscope.
A new type of energy-tunable X-ray polarimeter has been developed by introducing a Hirano-Ishikawa-Kikuta's transmission-type X-ray phase retarder into an X-ray polarimeter consisting of Hart-Rodrigues' polarizer and analyzer. By using the new type of polarimeter, simultaneous detections of X-ray linear birefringence and dichroism, and simultaneous detections of X-ray linear triple refraction and trichroism, have been made for the first time. The Kramers-Kronig relation has been confirmed in the absolute scale of dielectric constant between linear birefringence and dichroism (and between linear triple refraction and trichroism), which correspond to the real and imaginary parts of dielectric anisotropy, respectively. Phase shift due to the birefringence (or the triple refraction) has been measured with a precision of 2π 110, 000, which is limited mainly by photon-counting statistics.