Structural and functional insights into thermally stable cytochrome c' from a thermophile

Thermophilic Hydrogenophilus thermoluteolus cytochrome c0 (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c0 (AVCP), which has a homo-dimeric structure and ligand-binding ability. To understand the thermal stability mechanism and ligand-binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo-dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 A ° . In the PHCP structure, six specific residues appeared to strengthen the heme-related and subunit–subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit–subunit interactions were more severely destabilized than ones having altered heme-related interactions. The PHCP structure further revealed a ligand-binding channel and a penta-coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme-related and subunit–subunit interactions with conservation of the ligand-binding ability.This work was performed under the Cooperative Research Program of the “Network Joint Research Center for Materials and Devices”

In Situ Synchrotron X-ray Analysis: Application of High-Pressure Sliding Process to Ti Allotropic Transformation

In this study, severe plastic deformation through high-pressure sliding (HPS) was applied for in situ high-energy X-ray diffraction analysis at SPring-8 in JASRI (Japan Synchrotron Radiation Research Institute). Allotropic transformation of pure Ti was examined in terms of temperatures, pressures and imposed strain using a miniaturized HPS facility. The true pressure applied on the sample was estimated from the peak shift. Peak broadening due to local variation of pressure was reduced using white X-rays. The phase transformation from α phase to ω phase occurred at a pressure of ∼4.5 GPa. Straining by the HPS processing was effective to promote the transformation to the ω phase and to maintain the ω phase even at ambient pressure. The reverse transformation from ω phase to α phase occurred at a temperature of ∼110°C under ambient pressure, while under higher pressure as ∼4 GPa, the ω phase remained stable even at ∼170°C covered in this study. It was suggested that the reverse transformation from the ω phase to the α phase is controlled by thermal energy

Structural basis for PPARγ transactivation by endocrine-disrupting organotin compounds

Harada, S., Hiromori, Y., Nakamura, S. et al. Structural basis for PPARγ transactivation by endocrine-disrupting organotin compounds. Sci Rep 5, 8520 (2015). https://doi.org/10.1038/srep08520

Structural basis for dimer formation of human condensin structural maintenance of chromosome proteins and its implications for single-stranded DNA recognition

Eukaryotic structural maintenance of chromosome proteins (SMC) are major components of cohesin and condensins that regulate chromosome structure and dynamics during cell cycle. We here determine the crystal structure of human condensin SMC hinge heterodimer with ∼30 residues of coiled coils. The structure, in conjunction with the hydrogen exchange mass spectrometry analyses, revealed the structural basis for the specific heterodimer formation of eukaryotic SMC and that the coiled coils from two different hinges protrude in the same direction, providing a unique binding surface conducive for binding to single-stranded DNA. The characteristic hydrogen exchange profiles of peptides constituted regions especially across the hinge-hinge dimerization interface, further suggesting the structural alterations upon single-stranded DNA binding and the presence of a half-opened state of hinge heterodimer. This structural change potentially relates to the DNA loading mechanism of SMC, in which the hinge domain functions as an entrance gate as previously proposed for cohesin. Our results, however, indicated that this is not the case for condensins based on the fact that the coiled coils are still interacting with each other, even when DNA binding induces structural changes in the hinge region, suggesting the functional differences of SMC hinge domain between condensins and cohesin in DNA recognition.Susumu Uchiyama, Kazuki Kawahara, Yuki Hosokawa, Shunsuke Fukakusa, Hiroya Oki, Shota Nakamura, Yukiko Kojima, Masanori Noda, Rie Takino, Yuya Miyahara, Takahiro Maruno, Yuji Kobayashi, Tadayasu Ohkubo, Kiichi Fukui. Structural Basis for Dimer Formation of Human Condensin Structural Maintenance of Chromosome Proteins and Its Implications for Single-stranded DNA Recognition. Journal of Biological Chemistry, Volume 290, Issue 49, 2015, Pages 29461-29477. https://doi.org/10.1074/jbc.M115.670794

The Fab portion of immunoglobulin G contributes to its binding to Fcγ receptor III

Most cells active in the immune system express receptors for antibodies which mediate a variety of defensive mechanisms. These receptors interact with the Fc portion of the antibody and are therefore collectively called Fc receptors. Here, using high-speed atomic force microscopy, we observe interactions of human, humanized, and mouse/human-chimeric immunoglobulin G1 (IgG1) antibodies and their cognate Fc receptor, FcγRIIIa. Our results demonstrate that not only Fc but also Fab positively contributes to the interaction with the receptor. Furthermore, hydrogen/deuterium exchange mass spectrometric analysis reveals that the Fab portion of IgG1 is directly involved in its interaction with FcγRIIIa, in addition to the canonical Fc-mediated interaction. By targeting the previously unidentified receptor-interaction sites in IgG-Fab, our findings could inspire therapeutic antibody engineering

Tensile properties of mechanically alloyed Zr added austenitic stainless steel

A mechanically alloyed austenitic stainless steel (MA304LZ) was produced from pre-alloyed SUS304L powder with a small amount of Zr addition. The yield stress of MA304LZ was more than 3 times larger than that of SUS304L or 316L, while total elongation was reduced to about one third of the conventional steels. Microstructure analysis revealed an average grain size of 0.42 µm in MA304LZ and about 34/30 µm in SUS304L/316 L. In MA304LZ, two types of precipitates were observed; inhomogeneously distributed fine precipitates with an average size of 6.0 nm and homogeneously distributed coarse precipitates (d > 20 nm) with an average size of 47 nm. The strengthening mechanism of MA304LZ was discussed on the bases of Hall-Petch and Orowan equations, and the strengthening of MA304LZ was attributed mostly to refined grains. The dislocation barrier strength factor, α, is estimated to be 0.277 for the Zr-rich precipitates in MA304LZ