113 research outputs found
Solution NMR views of dynamical ordering of biomacromolecules.
No full textTo understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. Scope of Review In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. Major Conclusions Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1 MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. General Significance For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato
Making it Just in Time: Author-Creator Matsumoto Taiyō
No full textTranslated by Jon Holt and Teppei Fukuda
The first time I can remember encountering Matsumoto Taiyō’s work was probably when he released his short story collection, Blue Spring (Aoi haru - Matsumoto Taiyō tanpenshū [stories published from 1990 to 1993; Shōgakukan, 1993]). All of the stories concern a bunch of young dudes -- full of desires, frustrations, and violent tendencies -- and no chance they can ever get past those things. I thought to myself at that time, “Ah, I bet this stuff means a lot to readers in their teens, but they don’t really do anything for me.” After all, I was a man in my forties, so this stuff wasn’t on my radar as I was busy becoming a grown-up. Keep in mind that Taiyō himself was just in his early twenties. So, it really wasn’t that unnatural for him to write about life like that
Protein NMR Structure Refinement Based on Bayesian Inference for Dynamical Ordering of Biomacromolecules
No full textOn the Shafarevich conjecture (Algebraic Number Theory and Related Topics 2018)
No full textAlgebraic Number Theory and Related Topics 2018. November 26-30, 2018. edited by Takao Yamazaki and Shuji Yamamoto. The papers presented in this volume of RIMS Kôkyûroku Bessatsu are in final form and refereed.The Shafarevich conjecture, known as a geometric analogue of the Hermite-Minkowski theorem, states the finiteness of certain varieties over a fixed number field admitting good reduction away from a fixed finite set of finite places. In the abelian varieties of a fixed dimension case, this conjecture was proved by Faltings-Zarhin and applied to the Mordell conjecture. Moreover, the author proved a certain generalization of this conjecture in the K3 surfaces case. In the first part of this survey, we will sketch the proof of Faltings-Zarhin and its relation to the Mordell conjecture, and the second part we will present the result of the author
Protein structure determination in living cells
No full textTo date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works
Chapter 5. Protein Structure Determination in Living Cells from NOE-derived Distance Restraints
No full text1SDP-04 Dynamics of intrinsically disordered proteins in living cells(1SDP Protein Dynamics and Function in Cells elucidated by in-cell NMR and High Performance Computing,Symposium,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
No full text3P080 A refinement method for NMR protein structure determination based on Bayesian inference(01E. Protein: Measurement & Analysis,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
No full textTime to Re-Evaluate Taniguchi Jiro\u27s Pace in Manga
No full textNatsume Fusanosuke is Emeritus Professor of the Graduate Program of Cultural Studies in Corporeal and Visual Representation, Gakushūin University. Despite his recent retirement from Gakushūin in March, he is still very active in manga criticism and scholarship. Originally a manga artist himself in the 1980s, by the 1990s he began doing more writing about manga, although he often still employs his cartooning skills to assist in his analysis and explanation of his subjects, much like his American contemporary Scott McCloud. It is not a stretch to compare the latter’s Understanding Comics to Natsume\u27s work in the classic How to Read Manga (Manga no yomikata, 1995; co-authored with Takekuma Kentarō and others) and his subsequent Why Is Manga So Interesting? Its Expression and Grammar (Manga wa naze omoshiroi no ka: sono hyōgen to bunpō), which aired originally as a NHK [Japanese public broadcasting] ten-week lecture mini-series. Like McCloud, Natsume pioneered techniques to see and analyze comics that are still in use today by scholars. Although Natsume’s publications are too numerous to list here, he is author and co-author of approximately twenty books on manga and manga scholarship, including monographs like Where Is Tezuka Osamu? (Tezuka Osamu wa doko ni iru, 1992), the first full-length study on the manga giant. After the 1990s, Natsume went on to revise his early approaches to manga study, analysis, and scholarship, as seen in his New Challenges for the Field of Manga (Mangagaku e no chosen, 2004). He also co-edited with Takeuchi Osamu a new reader for Manga Studies, Mangagaku nyūmon (2009). In addition to these achievements, in his career he has been a television host for NHK’s public television show on comics (Broadcast Satellite Manga Night Talks [BS Manga yawa]), and author of other books on Japanese culture, including Grandson of Sōseki (Sōseki no mago, 2003), which tells the story of his family and his connection to Japan’s great modern novelist Natsume Sōseki. In 1999, he was the recipient of the prestigious Tezuka Osamu Culture Award.
In the following essay on Taniguchi Jirō, whom Natsume considers one of Japan’s most important manga creators, Natsume re-envisions the artist in the context of recent manga history. Taniguchi passed away in 2017, but his work suggests a path towards a new kind of “adult reading” of manga, which is a theme of Natsume’s recent writing on how Japanese people read their comic books and how perhaps they should read them. As his essay title suggests, he feels the time is now to reconsider Taniguchi’s artistic achievement. In fact, a recent exhibition of Taniguchi’s art ran again in his home prefecture, Tottori, from last January through February. His work continues to be popular with Japanese, such as The Solitary Gourmet (Kodoku no gurume, 1994-96; 2008-2015), which was adapted into a popular television and web series. (English-speaking audiences need only to wait until next year for the translated edition from Fanfare/Ponent Mon.)
- Jon Holt & Teppei Fukuda, translator
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