Kenji Sugase

NMR relaxation dispersion spectroscopy is a powerful technique to elucidate the mechanism of protein−protein binding reactions. However, it is difficult to optimize the concentration ratios that give relaxation dispersions of appropriate amplitude to determine accurate kinetic and thermodynamic parameters, especially in cases of very tight binding. In this study, we have obtained 15N R2 dispersions of Asn803-hydroxylated hypoxia-inducible factor-1α (HIF−OH) in the presence of a substoichiometric

In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8(+) T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an

Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. Here, we have carried out a semi-quantitative analysis of the dynamics of double-stranded DNA (dsDNA) containing var

Formation of protein aggregates or fibrils entails the conversion of soluble native protein monomers via multiple molecular states. No spectroscopic techniques have succeeded in capturing the transient molecular-scale events of fibrillation <i>in situ</i>. Here we report residue- and state-specific real-time monitoring of the fibrillation of amyotrophic lateral sclerosis-related SOD1 by rheology NMR (Rheo-NMR) spectroscopy. Under moderately denaturing conditions, where NMR signals of folded and

Compounds (2S,4S)- and (2S,4R)-4-(2'-guanidinoethyl)proline have been synthesized as a conformationally restricted arginine. Their backbones fit the i + 1 position in a turn, and the side chains are restricted compared to that of arginine. These analogues were incorporated into mini atrial natriuretic polypeptide, which has an important turnlike conformation at Gly(6)-Arg(7)()-Met(8)-Asp(9). Structural analysis revealed that the size of the conformational space of Arg(7) on binding to the recept

Amyloid fibril formation is associated with numerous neurodegenerative diseases. To elucidate the mechanism of fibril formation, the thioflavin T (ThT) fluorescence assay is widely used. ThT is a fluorescent dye that selectively binds to amyloid fibrils and exhibits fluorescence enhancement, which enables quantitative analysis of the fibril formation process. However, the detailed binding mechanism has remained unclear. Here we acquire real-time profiles of fibril formation of superoxide dismuta

Proteins and nucleic acids are central to all biological processes. NMR spectroscopy has proven to be excellent for studying the dynamics of these macromolecules over various timescales. Relaxation rates and heteronuclear nuclear Overhauser-effect values can resolve motion on pico- to nanosecond timescales, residual dipolar couplings provide information on submicro- to millisecond timescales, and even slower dynamics over seconds to hours can be resolved by hydrogen-exchange experiments. Relaxat

Major histocompatibility complex (MHC) molecules are loaded with a wide variety of self- and non-self-peptides in their binding grooves and present these to T cell receptors (TCRs) in order to activate the adaptive immune system. A large number of crystal structures of different MHC alleles with different bound peptides have been determined, and they have been found to be quite similar to one another regardless of the bound peptide sequence. The structures do not change markedly even when formin

Cryogenic-probe-based Rheo-NMR spectroscopy is a recently developed methodology to obtain solution NMR spectra of protein samples in situ under external shear. It is applicable to atomic-resolution monitoring of protein aggregation in situ, thereby aiding understanding of the transient structural changes and state conversion of amyloidogenic proteins, which are strongly associated with the both the onset and the progression of neurodegenerative diseases such as Alzheimer's disease and Parkinson'