On 4th January 2018, a paper has been published from Nucleic Acids Research (IF=10.162) by the research team of Dr. Kota Kasahara (Ritsumeikan University), Dr. Masaaki Shiina, Prof. Kazuhiro Ogata (Yokohama City University), Prof. Junichi Higo and Prof. Haruki Nakamura (IPR, Osaka University), revealing the regulation mechanism of the intrinsically disordered region of Ets1 transcription factor due to phosphorylation of Ser residues by molecular simulation and biochemical studies.
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Dr. Ryo Yonehara of Nakagawa Lab., Institute for Protein Research (IPR), Osaka University and his collaborators have solved crystal structure of Ragulator complex by X-ray crystallography.
Nucleic Acids Research Breakthrough article describes the biological role of subtelomeric sequences in chromosome maintenance and chromatin structure.
Research teams led by Dr. Junko Kanoh at Osaka University and by Kunihiro Ohta at the University of Tokyo (Japan), have described a study of the biological function of subtelomeric homologous (SH) sequences (and of subtelomeres more generally) through phenotypic analysis of a Schizosaccharomyces pombe (fission yeast) mutant in which all SH sequences in the genome were deleted.
A paper”Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and its Inhibitor (http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b01127, DOI: 10.1021/acs.jctc.6b01127) by Dr. Gert-Jan Bekker, who is a Specially Appointed Assistant Professor in IPR, has been published from Journal of Chemical Theory and Computation (JCTC, IF=5.301) with its cover picture of the Issue 7, 2017.
A paper about the PDBj activities in our Institute has been published in Nucleic Acids Research:
“Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures”
A group of researchers reports on the structure and function of a novel protein named “Calredoxin”. Calredoxin binds calcium and catalyzes in dependence of its binding, redox reactions, particularly driving the detoxification of harmful oxygen species. The researchers are exploring how this protein functions at the crossroad of calcium- and redox-dependent reactions to promote efficient oxygenic photosynthesis.
A chromosome is composed of structurally and functionally distinct domains. However, the molecular mechanisms underlying the formation of chromatin structure and the function of subtelomeres, the telomere-adjacent regions, remain obscure. Here we report the roles of the conserved centromeric protein Shugoshin 2 (Sgo2) in defining chromatin structure and functions of the subtelomeres in the fission yeast Schizosaccharomyces pombe.
・Magic-angle spinning (MAS) NMR probe system with a closed-loop helium recirculation.
・Stable MAS for weeks at sample temperature T = 35 K without consuming helium.
・Multi-dimensional MAS NMR at T = 35 K at a low running cost for electricity 16 kW/h.
・An order of magnitude sensitivity gain at T = 40 K and B0 = 16.4 T.
5-Methylcytosine (5mC) is oxidized by ten-eleven translocation (TET) enzymes. This process followed by thymine DNA glycosylase is proposed to be the mechanism for methylcytosine demethylation. 5-Hydroxymethylcytosine (5hmC) is one of the most important key oxidative metabolites in the demethylation process, and therefore, simple and accurate method to determine 5hmC at single base resolution is desired. In the present study, we developed a mild catalytic oxidation of 5-hmC using micelle incarcerated oxidants that enables to determine the position of 5hmC at single base resolution.
In mammals, DNA methylation plays important roles in embryogenesis and terminal differentiation via regulation of the transcription-competent chromatin state. The methylation patterns are propagated to the next generation during replication by maintenance DNA methyltransferase, Dnmt1, in co-operation with Uhrf1.