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.
In mammals, cytosine in the CpG sequence is often methylated by DNA methyltransferase (Dnmt). Methylated cytosine (5mC) plays crucial roles in gene silencing, genomic imprinting, X-chromosome inactivation and the stability of genomic DNA. Aberrant DNA methylation causes embryonic lethality and cancer. Recently, 5-hydoxymethylcytosine (5hmC) was discovered to be a new modification of cytosine, being an intermediate of the demethylation process, and thus is implicated in the pluripotency of stem cells, development, and disease. Therefore, it is quite important to develop the technique to analyze the position of 5hmC in genome. To determine 5hmC at single-base resolution, several techniques have been reported. However, each method has advantages and disadvantages.
The α, β and γ isoforms of mammalian heterochromatin protein 1 (HP1) selectively bind to methylated lysine 9 of histone H3 via their chromodomains. Although the phenotypes of HP1-knockout mice are distinct for each isoform, the molecular mechanisms underlying HP1 isoform-specific function remain elusive. In the present study, we found that in contrast to HP1α, HP1γ could not bind tri-methylated H3 lysine 9 in a reconstituted tetra-nucleosomes when the nucleosomes were in an uncompacted state. The hinge region connecting HP1’s chromodomain and chromoshadow domain contributed to the distinct recognition of the nucleosomes by HP1α and HP1γ.
The post-translational modification of histones plays an important role in gene expression. We report herein on a method for synthesizing such modified histones by ligating chemically prepared N-terminal peptides and C-terminal recombinant peptide building blocks. Based on their chemical synthesis, core histones can be categorized as two types; histones H2A, H2B and H4 which contain no Cys residues, and histone H3 which contains a Cys residue(s) in the C-terminal region. A combination of native chemical ligation and desulphurization can be simply used to prepare histones without Cys residues. For the synthesis of histone H3, the endogenous Cys residue(s) must be selectively protected, while keeping the N-terminal Cys residue of the C-terminal building block that is introduced for purposes of chemical ligation unprotected.