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Tomoto Ura

Bio: Tomoto Ura is an academic researcher from University of Tsukuba. The author has contributed to research in topics: Medicine & Chemistry. The author has an hindex of 2, co-authored 5 publications receiving 14 citations. Previous affiliations of Tomoto Ura include National Institute of Advanced Industrial Science and Technology.

Papers
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Journal ArticleDOI
TL;DR: A review of the effect of additives on the formation of liquid droplets and aggregates of proteins can be found in this article, where the authors summarized the effects of various additives on protein aggregation.
Abstract: This review briefly summarizes the effect of additives on the formation of liquid droplets and aggregates of proteins. Proteins have the property of forming liquid droplets and aggregates both in vivo and in vitro. The liquid droplets of proteins are mainly stabilized by electrostatic and cation-π interactions, whereas the amorphous aggregates are mainly stabilized by hydrophobic interactions. Crowders usually stabilize liquid droplets, whereas ions and hexandiols destabilize the droplets. Additives such as kosmotropes, sugars, osmolytes, and crowders promote the formation of amorphous aggregates, whereas additives such as arginine and chaotropes can prevent the formation of amorphous aggregates. Further, amyloid has a different mechanism for its formation from amorphous aggregates because it is primarily stabilized by a cross-β structure. These systematic analyses of additives will provide clues to controlling protein aggregations and will aid the true understanding of the transition of proteins from liquid droplets and aggregates.

22 citations

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TL;DR: In this article, a model LLPS system coupled with a sequential glycolytic enzymatic reaction was developed to reproduce the dynamic control of liquid droplets; the droplets, which consist of poly-L-lysine and nucleotides, compartmentalize two different enzymes (hexokinase and glucose-6-phosphate dehydrogenase) individually, accelerating the overall reaction.

6 citations

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TL;DR: It is reported that cations, including arginine, guanidine and sodium ions, enhance the retention of uncharged aromatic solutes on a cation-exchange resin, i.e., a negatively charged resin, with carboxyl groups.

4 citations

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TL;DR: In this article , the authors investigated the affinity of phenolic compounds for transition metal ions by varying the number and position of PHO groups and using different transition metals on various IMACs, in which the columns were fabricated by equilibrating the cation exchange column with transition metal solutions.

3 citations

Posted ContentDOI
09 Dec 2020-bioRxiv
TL;DR: This study demonstrates a new mechanism of enzyme activation in the droplets using Llactate oxidase (LOX), and represents the first report for increasing kcat by the formation of the liquid droplet.
Abstract: Liquid droplets formed by liquid-liquid phase separation are attracting attention as functional states of proteins in living cells. Liquid droplets are thought to activate enzymatic reactions by assembling the required molecules. Thus, liquid droplets usually increase the affinity of an enzyme to its substrates, leading to decreased KM values. In this study, we demonstrate a new mechanism of enzyme activation in the droplets using Llactate oxidase (LOX). In the presence of poly-L-lysine (PLL), LOX formed droplets with diameters of hundreds of nanometers to tens of micrometers, stabilized by electro-static interaction. The enzyme activity of LOX in the droplets was significantly enhanced by a fourfold decrease in KM and a tenfold increase in kcat. To our knowledge, this represents the first report for increasing kcat by the formation of the liquid droplet. Interestingly, the conformation of LOX changed in the liquid droplet, probably leading to increased kcat value. Understanding enzyme activation in the droplets provides essential information about enzyme function in living cells in addition to biotechnology applications.

2 citations


Cited by
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Journal ArticleDOI
TL;DR: The authors identify reversible amyloid cores from the LC of hnRNPA1, based on which they elucidate the structural basis of reversible fibrillation and its interplay with hn RNPA1 droplet formation.
Abstract: Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of amyloid fibril. The former mirrors biological granule assembly, while the latter is usually associated with neurodegenerative disease. Here, we observe a reversible amyloid formation of hnRNPA1 that synchronizes with liquid-liquid phase separation, regulates the fluidity and mobility of the liquid-like droplets, and facilitates the recruitment of hnRNPA1 into stress granules. We identify the reversible amyloid-forming cores of hnRNPA1 (named hnRACs). The atomic structures of hnRACs reveal a distinct feature of stacking Asp residues, which contributes to fibril reversibility and explains the irreversible pathological fibril formation caused by the Asp mutations identified in familial ALS. Our work characterizes the structural diversity and heterogeneity of reversible amyloid fibrils and illuminates the biological function of reversible amyloid formation in protein phase separation.

154 citations

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TL;DR: This study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.
Abstract: Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.

26 citations

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TL;DR: The nature and goals of this program are outlined before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.
Abstract: This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members.

16 citations

Journal ArticleDOI
TL;DR: Th4+ tuned aggregation-induced emission, for sequential ultrasensitive detection and separation of Th4+ and Hg2+ was developed successfully and the THTA-G could be used as a writable smart light-emitting material.

10 citations

Journal ArticleDOI
TL;DR: Ionic liquids have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties as mentioned in this paper.

9 citations