Researcher basic information

• Doctor of Engineering, University of Tsukuba, Mar. 2023

• https://researchmap.jp/nishinami?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202301018835072317
• https://orcid.org/0009-0005-7534-4881

• https://orcid.org/0009-0005-7534-4881

• 202301018835072317

• Biomolecular solutions
• Protein solutions
• Co-solute/solvent
• Additives
• Prediction

• Life Science, Applied biochemistry
• Life Science, Biophysics

Research activity information

• Mar. 2023, University of Tsukuba, Dean’s Award for Outstanding Doctoral Dissertation
  Suguru Nishinami
• May 2022, Cheminas 45, Best Research Award
  Mao Fukuyama;Suguru Nishinami;Shunsuke Tomita;Yumiko Ohhashi;Motohiro Kasuya;Eri Chatani;Yoko Maruyama;Kentaro Shiraki;Akihide Hibara
• Mar. 2020, University of Tsukuba, Dean’s Award for Outstanding Master’s Thesis
  Suguru Nishinami

• Local aromatic interactions define temperature sensitivity of phase separation in an intrinsically disordered protein
  Yumiko Ohhashi; Suguru Nishinami; Yoko Maruyama; Mao Fukuyama; Kentaro Shiraki; Eri Chatani; Hideki Taguchi
  bioRxiv, openRxiv, 08 May 2026
  Liquid liquid phase separation (LLPS) of intrinsically disordered proteins is highly sensitive to environmental conditions, yet the molecular basis of sharp temperature responsiveness remains poorly understood. Here, we investigate a sequence encoded mechanism underlying the pronounced temperature sensitivity of phase separation using Sup35NM, the intrinsically disordered domain of the yeast prion Sup35. We show that a tyrosine rich local structural region within this domain encodes strong temperature responsiveness of droplet formation. Mutational analyses reveal that tyrosine residues mediate both intramolecular interactions that stabilize local structure and intermolecular interactions required for LLPS. Substitution of the tyrosine residues with alanine disrupts local structure and weakens intermolecular interactions, thereby diminishing temperature sensitivity. In contrast, substitution with phenylalanine promotes rapid droplet gelation, abolishes internal fluidity, suppresses amyloid formation, and confers resistance to temperature induced dissolution. Based on these findings, we propose a molecular model in which finely tuned, moderately weak aromatic interactions among tyrosines enable reversible local compaction that is sensitive to temperature, thereby generating a sharp phase transition. These results suggest that amino acid sequences encode not only phase separation propensity but also the sensitivity of condensates to environmental perturbations, providing a framework for understanding how intrinsically disordered proteins act as molecular sensors of cellular conditions.
• Effects of Arginine on Hierarchical Protein Aggregation
  Suguru Nishinami; Yoshiki Kihara; Teruo Akuta; Kentaro Shiraki; Tsutomu Arakawa
  The Protein Journal, Springer Science and Business Media LLC, 20 Feb. 2026, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Differences and Similarities in Protein and Nucleic Acid Structures and Their Biological Interactions
  Tsutomu Arakawa; Taiji Oyama; Tomoto Ura; Suguru Nishinami; Kentaro Shiraki; Teruo Akuta
  Current Issues in Molecular Biology, 47, 12, 1019, 1019, MDPI AG, 06 Dec. 2025, [Peer-reviewed]
  Scientific journal, Protein and nucleic acid play central roles in biology and pharmaceuticals. Both share a similar architecture made of a backbone and side chains. Protein has a peptide backbone and various side chains, whereas nucleic acid has a phosphate backbone and aromatic side chains. However, they are significantly different in the chemical properties of the backbone and side chains. The protein backbone is uncharged, while nucleic acid backbone is negatively charged. The protein side chains comprise widely different chemical properties. On the other hand, the nucleic acid side chains comprise a uniform chemical property of aromatic bases. Such differences lead to fundamentally different folding, molecular interactions and co-solvent interactions, which are the focus of this review. In regular protein secondary structures, the peptide groups form polar hydrogen bonds, making the interior hydrophilic. The side chains of different chemical properties are exposed on the outside of the protein secondary structures and participate in molecular and co-solvent interactions. On the other hand, hydrophobic/aromatic nucleobase side chains are located inside the typical double helix or quadruplex structures. The charged phosphate groups of the nucleic acid backbone are located outside, participating in electrostatic interactions. The nucleobases are also involved in molecular interactions, when exposed in breaks, hairpins, kinks and loops. These structural differences between protein and nucleic acid confer different interactions with commonly used co-solvents, such as denaturants, organic solvents and polymers.
• Low-complexity domains in phase-separated droplets suppress the amyloid formation of yeast prion Sup35
  Yumiko Ohhashi; Suguru Nishinami; Kentaro Shiraki; Eri Chatani; Hideki Taguchi
  npj Biosensing, 2, 13, Apr. 2025, [Peer-reviewed]
• Inter-molecular Interactions of High Concentration Antibody Formulation Resulting in Problems of Viscosity, Opalescence and Phase Separation
  Tsutomu Arakawa; Suguru Nishinami; Kentaro Shiraki; Yui Tomioka; Teruo Akuta
  Preprints, 03 Jul. 2024
• High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular L-Lactate
  Saaya Hario; Giang N. T. Le; Hikaru Sugimoto; Kei Takahashi-Yamashiro; Suguru Nishinami; Hirofumi Toda; Selene Li; Jonathan S. Marvin; Shinya Kuroda; Mikhail Drobizhev; Takuya Terai; Yusuke Nasu; Robert E. Campbell
  ACS Central Science, American Chemical Society (ACS), 30 Jan. 2024, [Peer-reviewed]
  Scientific journal
• Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging
  Yusuke Nasu; Abhi Aggarwal; Giang N. T. Le; Camilla Trang Vo; Yuki Kambe; Xinxing Wang; Felix R. M. Beinlich; Ashley Bomin Lee; Tina R. Ram; Fangying Wang; Kelsea A. Gorzo; Yuki Kamijo; Marc Boisvert; Suguru Nishinami; Genki Kawamura; Takeaki Ozawa; Hirofumi Toda; Grant R. Gordon; Shaoyu Ge; Hajime Hirase; Maiken Nedergaard; Marie-Eve Paquet; Mikhail Drobizhev; Kaspar Podgorski; Robert E. Campbell
  Nature Communications, 14, 1, Springer Science and Business Media LLC, 27 Oct. 2023, [Peer-reviewed]
  Scientific journal, Abstract
  
  l-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. However, investigations of the inter- and intra-cellular dynamics of l-lactate are currently hampered by the limited selection and performance of l-lactate-specific genetically encoded biosensors. Here we now report a spectrally and functionally orthogonal pair of high-performance genetically encoded biosensors: a green fluorescent extracellular l-lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellular l-lactate biosensor, designated R-iLACCO1. eLACCO2.1 exhibits excellent membrane localization and robust fluorescence response. To the best of our knowledge, R-iLACCO1 and its affinity variants exhibit larger fluorescence responses than any previously reported intracellular l-lactate biosensor. We demonstrate spectrally and spatially multiplexed imaging of l-lactate dynamics by coexpression of eLACCO2.1 and R-iLACCO1 in cultured cells, and in vivo imaging of extracellular and intracellular l-lactate dynamics in mice.
• Detection of Fibril Nucleation in Micrometer-Sized Protein Condensates and Suppression of Sup35NM Fibril Nucleation by Liquid–Liquid Phase Separation
  Mao Fukuyama; Suguru Nishinami; Yoko Maruyama; Taiki Ozawa; Shunsuke Tomita; Yumiko Ohhashi; Motohiro Kasuya; Masao Gen; Eri Chatani; Kentaro Shiraki; Akihide Hibara
  Analytical Chemistry, American Chemical Society (ACS), 22 Jun. 2023, [Peer-reviewed]
  Scientific journal
• Kinetic quantitative analysis reveals the suppression of Sup35NM amyloid fibril nucleation by liquid-liquid phase separation
  Mao Fukuyama; Suguru Nishinami; Yoko Maruyama; Taiki Ozawa; Shunsuke Tomita; Yumiko Ohhashi; Motohiro Kasuya; Masao Gen; Eri Chatani; Kentaro Shiraki; Akihide Hibara
  ChemRxiv, 01 Nov. 2022
• Affinity of aromatic amino acid side chains in amino acid solvents.
  Akira Nomoto; Suguru Nishinami; Kentaro Shiraki
  Biophysical chemistry, 287, 106831, 106831, Aug. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The affinity between amino acid and water is important for understanding how proteins behave in aqueous solutions. For example, the hydrophobicity of amino acid side chains determines a protein's solubility. However, the affinity of amino acid side chains in amino acid solvents should be determined in order to understand the propensity of protein condensates induced by multivalent amino acid interactions. Here we measured the transfer free energy of amino acid side chains (ΔGSC) from water to amino acid solvents. The ΔGSC of aromatic amino acids showed a different value depending on the type and the pH of amino acid solvent. Interestingly, the propensity of ΔGSC was completely different from the hydrophobicity of amino acids. This indicate that the ΔGSC describes the affinity between amino acid side chains involving the existence of water. The ΔGSC is a significant parameter for understanding whether amino acid side chains prefer bulk or protein condensate.
• Opalescence Arising from Network Assembly in Antibody Solution.
  Yoshitaka Nakauchi; Suguru Nishinami; Yusuke Murakami; Toshihiko Ogura; Hideaki Kano; Kentaro Shiraki
  Molecular pharmaceutics, 19, 4, 1160, 1167, 04 Apr. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Opalescence of therapeutic antibody solutions is one of the concerns in drug formulation. However, the mechanistic insights into the opalescence of antibody solutions remain unclear. Here, we investigated the assembly states of antibody molecules as a function of antibody concentration. The solutions of bovine gamma globulin and human immunoglobulin G at around 100 mg/mL showed the formation of submicron-scale network assemblies. The network assembly resulted in the appearance of opalescence with a transparent blue color without the precipitates of antibodies. Furthermore, the addition of trehalose and arginine, previously known to act as protein stabilizers and protein aggregation suppressors, was able to suppress the opalescence arising from the network assembly. These results will provide an important information for evaluating and improving protein formulations.
• Arginine and its Derivatives Suppress the Opalescence of an Antibody Solution.
  Shogo Oki; Suguru Nishinami; Yoshitaka Nakauchi; Toshihiko Ogura; Kentaro Shiraki
  Journal of pharmaceutical sciences, 111, 4, 1126, 1132, Apr. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Opalescence is a problem concerned with the stability of an antibody solution. It occurs when a high concentration of a protein is present. Arginine (Arg) is a versatile aggregation suppressor of proteins, which is among the candidates that suppress opalescence in antibody solutions. Here, we investigated the effect of various types of small molecular additives on opalescence to reveal the mechanism of Arg in preventing opalescence in antibody solution. As expected, Arg suppressed the opalescence of the immunoglobulin G (IgG) solution. Arg also concentration dependently inhibited the formation of microstructures in IgG molecules. Interestingly, the intrinsic fluorescence spectra of highly concentrated IgG solutions differed from those having low concentrations, even though IgG retained a distinct tertiary structure. Arginine ethylester was more effective in suppressing the opalescence of IgG solutions than Arg, whereas lysine and γ-guanidinobutyric acid were less effective. These results indicated that positively charged groups of both α-amine and guanidinium actively influence Arg as an additive for suppressing opalescence. Diols, which are the suppressors of the liquid-liquid phase separation of proteins were also effective in suppressing the opalescence. These results therefore provide insight into the control of opalescence of antibody solutions at high concentrations using solution additives.
• Classification of protein solubilizing solutes by fluorescence assay.
  Suguru Nishinami; Tsutomu Arakawa; Kentaro Shiraki
  International journal of biological macromolecules, 203, 695, 702, 01 Apr. 2022, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Aromatic interaction plays a crucial role in controlling protein interaction by additives. Here we investigated the interaction of protein salting-in (solubilizing) additives with tryptophan (Trp), tyrosine (Tyr), indole, and proteins based on their fluorescence spectra. Five salting-in additives, i.e., arginine (Arg), urea, guanidine (Gdn), ethylene glycol (EG), and magnesium chloride (MgCl2), showed different effects on the fluorescence properties of Trp and Tyr. Arg significantly reduced fluorescence intensity of Trp and Tyr, as was the case for glycine to a lesser extent. MgCl2 and calcium chloride (CaCl2) showed little effect on the aromatic fluorescence spectra. Gdn also showed little effect on the aromatic fluorescence spectra of Trp and Tyr even at high concentrations. EG increased the aromatic fluorescence intensity of Trp and Tyr with blue-shifted emission wavelength. Urea enhanced fluorescence of Trp and Tyr without altering emission wavelength. These results indicate that the protein solubilizing additives interact with aromatic groups differently.
• Aromatic interaction of hydantoin compounds leads to virucidal activities.
  Suguru Nishinami; Keiko Ikeda; Tamiko Nagao; A Hajime Koyama; Tsutomu Arakawa; Kentaro Shiraki
  Biophysical chemistry, 275, 106621, 106621, Aug. 2021, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Virus inactivation or disinfection is the first line of protection against virus infection. Here, we report for the first time the virus inactivation (virucidal) activities of hydantoin and its derivative, 1-methylhydantoin against enveloped herpes simplex virus type-1. These hydantoin compounds showed favorable interaction with aromatic amino acids, similarly to arginine hydrochloride also exhibiting aromatic interaction and virucidal activities on the same virus. Among them, 1-methylhydantoin demonstrated a greater virucidal activity. Solubility measurements in organic solvents and salting-out salt solutions showed that 1-methylhydantoin is more hydrophobic than others, suggesting that the hydrophobic nature and aromatic interaction play a role in interaction with viral proteins and thereby virucidal activity.
• Aggregation of hen egg white proteins with additives during agitation
  Taehun Hong; Kazuki Iwashita; Jeungmin Han; Suguru Nishinami; Akihiro Handa; Kentaro Shiraki
  LWT, 146, 111378, 111378, Elsevier BV, Jul. 2021, [Peer-reviewed]
  Scientific journal
• Glass-like protein condensate for the long-term storage of proteins.
  Yoshitaka Nakauchi; Suguru Nishinami; Kentaro Shiraki
  International journal of biological macromolecules, 182, 162, 167, 01 Jul. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Long-term storage of proteins at ambient temperature is required for applications in pharmaceutics and biotechnology. Lyophilization is a versatile approach for stabilizing proteins at ambient temperature, although its freezing and drying processes negatively affect the protein structure. In this study, we show a glass-like protein condensate (GLPC) as a new method for protein stabilization at ambient temperature. Various protein types, including immunoglobulin G, gamma globulin, albumin, and chymotrypsin, formed a glassy state during ultracentrifugation and natural drying, while proteins that tend to crystalize, such as hen egg-white lysozyme, did not. The GLPCs were characterized by a transparent solid state, similar to a dry glass ball. Importantly, the GLPCs were dissolved easily in saline solution at a physiological concentration, thereby retaining their native structures and functions. The GLPCs preserved their native structures even after 1 year of incubation at ambient temperature. These results provide a framework for the development of protein preservation methods at ambient temperature other than lyophilization.
• Solubility Parameters of Amino Acids on Liquid-Liquid Phase Separation and Aggregation of Proteins.
  Akira Nomoto; Suguru Nishinami; Kentaro Shiraki
  Frontiers in cell and developmental biology, 9, 691052, 691052, 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, The solution properties of amino acids determine the folding, aggregation, and liquid-liquid phase separation (LLPS) behaviors of proteins. Various indices of amino acids, such as solubility, hydropathy, and conformational parameter, describe the behaviors of protein folding and solubility both in vitro and in vivo. However, understanding the propensity of LLPS and aggregation is difficult due to the multiple interactions among different amino acids. Here, the solubilities of aromatic amino acids (SAs) were investigated in solution containing 20 types of amino acids as amino acid solvents. The parameters of SAs in amino acid solvents (PSASs) were varied and dependent on the type of the solvent. Specifically, Tyr and Trp had the highest positive values while Glu and Asp had the lowest. The PSAS values represent soluble and insoluble interactions, which collectively are the driving force underlying the formation of droplets and aggregates. Interestingly, the PSAS of a soluble solvent reflected the affinity between amino acids and aromatic rings, while that of an insoluble solvent reflected the affinity between amino acids and water. These findings suggest that the PSAS can distinguish amino acids that contribute to droplet and aggregate formation, and provide a deeper understanding of LLPS and aggregation of proteins.
• Effect of additives on liquid droplets and aggregates of proteins.
  Kentaro Shiraki; Masahiro Mimura; Suguru Nishinami; Tomoto Ura
  Biophysical reviews, 12, 2, 587, 592, Apr. 2020, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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.
• Hydantoin and Its Derivatives Reduce the Viscosity of Concentrated Antibody Formulations by Inhibiting Associations via Hydrophobic Amino Acid Residues
  Suguru Nishinami; Tomoshi Kameda; Tsutomu Arakawa; Kentaro Shiraki
  Industrial & Engineering Chemistry Research, 58, 36, 16296, 16306, American Chemical Society (ACS), 11 Sep. 2019, [Peer-reviewed], [Lead author]
  Scientific journal
• Effects of allantoin and dimethyl sulfoxide on the thermal aggregation of lysozyme.
  Suguru Nishinami; Atsushi Hirano; Tsutomu Arakawa; Kentaro Shiraki
  International journal of biological macromolecules, 119, 180, 185, Nov. 2018, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Allantoin is used to suppress protein aggregation without decreasing the melting temperature. However, the solubility of allantoin in water or buffer solutions is too low (approximately 30 mM at ambient temperature) to be used as a protein aggregation suppressor in various situations. Here we show that a high-concentration solution of allantoin in neat dimethyl sulfoxide (DMSO) is useful as a stock solution for the additive that controls protein aggregation. The allantoin concentration from 10 to 100 mM in 10% (v/v) DMSO significantly suppressed the thermal aggregation of hen egg white lysozyme as a model protein, with increasing allantoin concentration. The residual activity of lysozyme in 10% DMSO and 100 mM allantoin after heating at 90 °C for 10 min was increased >3-fold compared to that without allantoin. Thus, it was concluded that allantoin in DMSO is an effective stock solution for practical application in enhancing the recovery of enzymatic activity and suppressing the formation of small aggregate of protein.
• Arginine suppresses opalescence and liquid-liquid phase separation in IgG solutions.
  Shogo Oki; Suguru Nishinami; Kentaro Shiraki
  International journal of biological macromolecules, 118, Pt B, 1708, 1712, 15 Oct. 2018, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Antibody formulation often necessitates the protein concentration to be increased above 100 mg/ml, because of the large therapeutic doses of antibodies required and the volume limitations of subcutaneous injections. However, high concentrations of antibody lead to opalescent states in solution, resulting in safety and application problems. In this study, we investigated the effect of additives on opalescence in IgG solutions. Arginine (Arg) was observed to most effectively suppress opalescence in IgG solutions among the additives tested, which included guanidine hydrochloride, NaCl, and other amino acids. Moreover, Arg also suppressed liquid-liquid phase separation (LLPS) of highly concentrated IgG solutions during incubation at low temperature. Comparative analysis showed that the effects of Arg on opalescence and LLPS in IgG solutions result from its unique structure, which comprises an amino acid main chain, a guanidinium group, and a counter ion. These results indicate that Arg has high potency as an excipient in antibody drug formulations for the suppression of opalescence and LLPS as well as protein aggregation.
• Allantoin and hydantoin as new protein aggregation suppressors.
  Suguru Nishinami; Shunsuke Yoshizawa; Tsutomu Arakawa; Kentaro Shiraki
  International journal of biological macromolecules, 114, 497, 503, 15 Jul. 2018, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, Allantoin is widely used in pharmaceutical and cosmetic products, and is composed of a hydantoin ring and a ureido group. Recent reports showed that allantoin suppresses thermal aggregation of hen egg white lysozyme (LYZ). However, structural insight into the properties of allantoin on protein aggregation and whether allantoin controls the aggregation of other proteins under different stress conditions remain unclear. Here we studied the structural properties of allantoin in terms of its effects on protein aggregation by comparing allantoin with urea and hydantoin. Furthermore, we analyzed the effects of allantoin and its derivatives on the aggregation of LYZ, carbonic anhydrase from bovine erythrocytes (BCA), albumin from chicken egg white (OVA), and immunoglobulin G (IgG) by various stresses in comparison with arginine. These four proteins are widely different in charged state and molecular size. Allantoin suppressed the aggregation and inactivation of LYZ comparing to arginine without affecting the melting temperature of proteins, and was responsible for the slightly improved formation of soluble oligomers and insoluble aggregates of IgG with thermal and acidic stresses. In contrast, hydantoin increased the solubility of aromatic amino acids more effectively than arginine and allantoin. The structural properties underlying the observed effects of allantoin as an aggregation suppressor include hydrophobic interactions between hydantoin moiety and aromatic ring on the surface of proteins, which is reflected on the difference between allantoin and arginine. These results show that the backbone of hydantoin ring may be a new category of additives for development of small aggregation suppressors.
• One-Step Identification of Antibody Degradation Pathways Using Fluorescence Signatures Generated by Cross-Reactive DNA-Based Arrays.
  Shunsuke Tomita; Ayumi Matsuda; Suguru Nishinami; Ryoji Kurita; Kentaro Shiraki
  Analytical chemistry, 89, 15, 7818, 7822, 01 Aug. 2017, [Peer-reviewed], [International Magazine]
  English, Scientific journal, Therapeutic antibodies are prone to degradation via a variety of pathways during each stage of the manufacturing process. Hence, a low-cost, rapid, and broadly applicable tool that is able to identify when and how antibodies degrade would be highly desirable to control the quality of therapeutic antibody products. With this goal in mind, we have developed signature-based sensing system to discriminate differently degraded therapeutic antibodies. The use of arrays consisting of conjugates between nanographene oxide and fluorophore-modified single-stranded DNAs under acidic pH conditions generated unique fluorescence signatures for each state of the antibodies. Multivariate analyses of the thus obtained signatures allowed identifying (i) common features of native, denatured, and visibly aggregated antibodies, (ii) complicated degradation pathways of therapeutic omalizumab upon time-course heat-treatment, and (iii) the individual compositions of differently degraded omalizumab mixtures. As the signature-based sensing has the potential to identify a broad range of degraded antibodies formed by different kinds of realistic stress types, this system may serve as the basis for high-throughput assays for the screening of antibody manufacturing processes.

• タンパク質溶液の状態はシミュレーションできるのか?
  西奈美 卓; 白木 賢太郎, アンサンブル 分子シミュレーション学会誌, 24, 4, 220, 224, Oct. 2022, [Lead author]
• 低分子化合物によるタンパク質溶液粘度の制御法
  西奈美 卓; 白木 賢太郎, バイオサイエンスとインダストリー (B&I), 80, 1, 42, 43, Jun. 2022, [Lead author]
• Phasing Biology Reveals the Role of Prion Protein
  西奈美 卓; 白木 賢太郎, 日本物理学会誌, 75, 4, 192, 200, Apr. 2020, [Lead author]

• 相分離生物学の全貌
  西奈美 卓; 大橋 祐美子, プリオンと相分離現象
  白木 賢太郎 編, 東京化学同人, Nov. 2020, 9784807913466, xi, 402p, Japanese, [Contributor]

• Sleep-inducing peptide Nemuri arrests ribosomal phase separation to inhibit bacterial translation
  Suguru Nishinami
  第12回IGM研究会, 24 Oct. 2025, Oral presentation
• リボソーム相分離を標的とした新規抗菌ペプチド
  西奈美 卓
  第4回IGM生理研ジョイントシンポジウム, 08 Oct. 2025, Poster presentation
• 細菌内の分子集合体を標的とする新規抗菌ペプチド
  西奈美 卓
  第36回高遠分子細胞生物学シンポジウム, Aug. 2025, Poster presentation
• 細菌内のリボソーム物性を標的とする新規抗菌ペプチド
  西奈美卓; Moynul Hasan; 五十嵐雅之; 戸田浩史; 野田展生
  第62回日本生化学会北海道支部例会, Jul. 2025, Poster presentation
  Jul. 2025 - Jul. 2025
• Antimicrobial peptides that target phase separation of ribosomes
  Suguru Nishinami
  The 16th HOPE Meeting with Nobel Laureates, Mar. 2025, Poster presentation
  Mar. 2025 - Mar. 2025
• Several C-terminal fragments of NEMURI function as non-lytic antimicrobial peptide
  Moynul Hasan; Yuta Ogasawara; Yuko Fujioka; Suguru Nishinami; Hirofumi Toda; Nobuo Noda
  The 24th Annual Meeting of the Protein Science Society of Japan, Jun. 2024, Poster presentation
• Structural studies of protein condensates prepared by ultracentrifugation/air-drying
  Ryuga Someya; Akira Nomoto; Suguru Nishinami; Hiroka Sugai; Kentaro Shiraki
  The 21st IUPAB & The 62nd BSJ Joint Congress 2024, Jun. 2024, Poster presentation
• Mechanism of membrane activity of NEMURI protein
  Moynul Hasan; Yuta Ogasawara; Yuko Fujioka; Suguru Nishinami; Hirofumi Toda; Nobuo N. Noda
  The 61st Annual Meeting of the Biophysical Society of Japan, Nov. 2023, Poster presentation
• 液–液相分離に高い温度感受性をもたらすSup35天然変性領域の局所構造
  大橋 祐美子; 西奈美 卓; 白木 賢太郎; 茶谷 絵理
  第46回分子生物学会, Nov. 2023, Oral presentation
• Development of a microfluidic device for long-term observation of protein condensates for amyloid nucleation analysis
  Taiki Ozawa; Suguru Nishinami; Shunsuke Tomita; Yumiko Ohhashi; Motohiro Kasuya; Eri Chatani; Yoko Maruyama; Kentaro Shiraki; Akihide Hibara; Mao Fukuyama
  The 103rd CSJ Annual Meeting, Mar. 2023, Oral presentation
• プリオンタンパク質濃縮相内アミロイド核生成の速度論的解析に向けた溶媒条件検討
  小澤 大樹; 西奈美 卓; 冨田 峻介; 大橋 祐美子; 粕谷 素洋; 茶谷 絵里; 丸山 洋子; 白木 賢太郎; 火原 彰秀; 福山 真央
  第22回東北大学多元物質科学研究所研究発表会, Dec. 2022, Poster presentation
• Local structure of an intrinsically disordered region of Sup35 causes temperature sensitivity of liquid-liquid phase separation
  Yumiko Ohhashi; Suguru Nishinami; Kentaro Shiraki; Eri Chatani
  Proteostasis & Disease Symposium 2022, Nov. 2022, Poster presentation
  Nov. 2022 - Nov. 2022
• Liquid-liquid phase separation and amyloid formation of Sup35 from three different yeast species
  大橋 祐美子; 西奈美 卓; 白木 賢太郎; 茶谷 絵里
  日本生物物理学会年会, Sep. 2022, Poster presentation
  Sep. 2022 - Sep. 2022
• Study on solvent conditions of prion protein droplet formation of amyloid nucleation analysis
  Taiki Ozawa; Suguru Nishinami; Shunsuke Tomita; Yumiko Ohhashi; Motohiro Kasuya; Eri Chatani; Yoko Maruyama; Kentaro Shiraki; Akihide Hibara; Mao Fukuyama
  Joint Meeting of the Tohoku Area Chemistry Societies, Sep. 2022, Poster presentation
• Characterization of protein solubilizing additive by fluorescence assay
  Suguru Nishinami; Tsutomu Arakawa; Kentaro Shiraki
  2022 Colorado Protein Stability Conference, Aug. 2022, Poster presentation
  Aug. 2022 - Aug. 2022
• Network association and glass-like condensation of highly concentrated proteins
  Suguru Nishinami; Yoshitaka Nakauchi; Kentaro Shriaki
  2022 Colorado Protein Stability Conference, Aug. 2022, Poster presentation
  Aug. 2022 - Aug. 2022
• Hydantoin and its derivative recover the virucidal activity of umezu phenolics from the inhibition by proteins
  Keiko Ikeda; Suguru Nishinami; Tamiko Nagao; Takahiko Mitani; Kentaro Shiraki; Tsutomu Arakawa; A. Hajime Koyama
  International Union of Microbiological Societies (IUMS 2022), Jul. 2022, Poster presentation
  Jul. 2022 - Jul. 2022
• マイクロサイズプリオンタンパク質集合液滴中からのアミロイド核生成速度解析
  福山 真央; 西奈美 卓; 冨田 峻介; 大橋 祐美子; 粕谷 素洋; 茶谷 絵理; 丸山 洋子; 白木 賢太郎; 火原 彰秀
  第82回分析化学討論会, May 2022, Oral presentation
  May 2022 - May 2022
• A local structure of intrinsically disordered region governs the environmental response of Sup35 liquid–liquid phase separation
  Yumiko Ohhashi; Suguru Nishinami; Kentaro Shiraki; Eri Chatani
  日本蛋白質科学会年会プログラム・要旨集, Jun. 2022, Oral presentation
  2022 - 2022
• Size dependence of the amyloid nucleation in protein condensates formed by liquid-liquid phase separation
  福山 真央; 西奈美 卓; 冨田 峻介; 大橋 祐美子; 粕谷 素洋; 茶谷 絵理; 丸山 洋子; 白木 賢太郎; 火原 彰秀
  化学とマイクロ・ナノシステム学会第45回研究会 (Cheminas 45), May 2022
  2022 - 2022
• プリオンタンパク質濃縮相内アミロイド核生成の速度論的解析に向けた溶媒条件検討
  小澤大樹; 小澤大樹; 西奈美卓; 冨田峻介; 大橋祐美子; 粕谷素洋; 茶谷絵里; 丸山洋子; 白木賢太郎; 火原彰秀; 福山真央; 火原彰秀; 福山真央; 火原彰秀; 福山真央
  東北大学多元物質科学研究所研究発表会講演予稿集, 2022
  2022 - 2022
• Amino acid side chain parameters on phase separation of protein
  野本 晃; 西奈美 卓; 白木 賢太郎
  第59回日本生物物理学会年会, Nov. 2021, Poster presentation
  Nov. 2021 - Nov. 2021
• 蛋白質の液 - 液相分離や凝集に対するアミノ酸の溶解度パラメーター
  野本 晃; 西奈美 卓; 白木 賢太郎
  日本蛋白質科学会年会プログラム・要旨集, Jun. 2021, Poster presentation
  Jun. 2021 - Jun. 2021
• Sup35の液-液相分離におけるプリオンドメインの役割
  大橋 祐美子; 西奈美 卓; 白木 賢太郎; 茶谷 絵理
  日本蛋白質科学会年会プログラム・要旨集, Jun. 2021, Poster presentation
  Jun. 2021 - Jun. 2021
• Characterization of virucidal activities of hydantoin and its derivative
  Keiko Ikeda; Suguru Nishinami; Tamiko Nagao; Nishide Zyuutoku; Kentaro Shiraki; Tsutomu Arakawa; A. Hajime Koyama
  The 44th Annual Meeting of the Molecular Biology Society of Japan, 2021, Poster presentation
  2021 - 2021
• 添加剤を用いたプリオンの相分離現象の理解
  西奈美 卓; 白木 賢太郎
  日本生化学会大会(Web) 93rd, 16 Sep. 2020, Invited oral presentation
• Solubility of aromatic amino acids in amino acid solutions
  野本 晃; 西奈美 卓; 白木 賢太郎
  第58回日本生物物理学会年会, Sep. 2020, Poster presentation
  Sep. 2020 - Sep. 2020
• プリオンの相分離現象と添加剤による制御
  西奈美 卓; 白木 賢太郎
  大阪大学蛋白質研究所セミナー／新学術領域「分子夾雑の生命科学」／研究拠点形成事業「蛋白質凝集の先端研究ネットワーク形成」共催セミナー／第3回LLPS研究会, 12 Sep. 2019, Invited oral presentation
• The effects of molecular crowding on phase separation and fibrillization of yeast prion Sup35
  Suguru Nishinami; Yumiko Ohhashi; Kentaro Shiraki
  2019 Colorado Protein Stability Conference: 25th Anniversary, Jul. 2019, Poster presentation
  Jul. 2019 - Jul. 2019
• Hydantoin and its derivatives modulate the aggregation, solubility, and viscosity in protein solutions
  Suguru Nishinami; Tsutomu Arakawa; Kentaro Shiraki
  2019 Colorado Protein Stability Conference: 25th Anniversary, Jul. 2019, Poster presentation
  Jul. 2019 - Jul. 2019
• 抗体溶液のオパレッセンスは凝集ではなく分子ネットワークに由来する
  仲内 喜大; 西奈美 卓; 白木 賢太郎
  日本蛋白質科学会年会 19th／日本細胞生物学会年会 71st／合同年次大会, Jun. 2019, Poster presentation
  Jun. 2019 - Jun. 2019
• 酵母プリオンタンパク質Sup35のNMドメインにおける液-液相分離と線維化
  西奈美 卓; 大橋 祐美子; 白木 賢太郎
  日本蛋白質科学会年会 19th／日本細胞生物学会年会 71st／合同年次大会, Jun. 2019, Poster presentation
  Jun. 2019 - Jun. 2019
• 添加剤を用いた液-液相分離とアミロイドへの成熟プロセスの理解
  白木 賢太郎; 西奈美 卓; 大橋 祐美子
  Dementia Japan, 2019, Invited oral presentation
  2019 - 2019
• 単一タンパク質がつくるオパレッセンスのメカニズムと制御
  西奈美 卓; 仲内 喜大; 白木 賢太郎
  第1回LLPS研究会, 31 Oct. 2018, Invited oral presentation
• 新しい凝集抑制剤としてのアラントインとヒダントイン
  西奈美 卓; 吉澤 俊介; 荒川 力; 白木 賢太郎
  日本蛋白質科学会年会プログラム・要旨集, Jun. 2018, Poster presentation
  Jun. 2018 - Jun. 2018
• 抗体の劣化情報をフィンガープリントとして出力するDNA/酸化グラフェン複合体アレイ
  冨田 峻介; 松田 あゆみ; 西奈美 卓; 栗田 僚二; 白木 賢太郎
  高分子学会予稿集, 2018, Poster presentation
  2018 - 2018
• DNA/酸化グラフェン複合体アレイによる抗体劣化経路の指紋ベース同定
  冨田 峻介; 松田 あゆみ; 西奈美 卓; 栗田 僚二; 白木 賢太郎
  分析化学討論会講演要旨集, 2018, Poster presentation
  2018 - 2018

• 2019 - Present
  The Biophysical Society of Japan
• 2018 - Present
  Protein Science Society of Japan
• The Japanese Biochemical Society
• The Molecular Biology Society of Japan

• N-ミリストイルトランスフェラーゼによるストレス依存的な睡眠の制御機構
  Grant in Aid for Early-Career Scientists
  Apr. 2024 - Mar. 2027
  Suguru Nishinami
  Japan Society for the Promotion of Science (JSPS), Hokkaido University, 24K18076
• Nemuriの包括的研究から迫る液-液相分離による睡眠制御機構
  Grant-in-Aid for JSPS Research Fellow
  Apr. 2024 - Mar. 2027
  Suguru Nishinami
  Japan Society for the Promotion of Science (JSPS), Hokkaido University, 24KJ0004
• IIIS Start-up Grant
  May 2023 - Mar. 2024
  Suguru Nishinami
  International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba
• Graduate Student Fellowship
  Oct. 2020 - Mar. 2023
  Suguru Nishinami
  Nakatani Foundation, University of Tsukuba
• 酵母プリオンタンパク質Sup35の線維化を制御する新規添加剤の開発
  Grant-in-Aid for JSPS Research Fellow
  Apr. 2020 - Mar. 2023
  Suguru Nishinami
  プリオンドメインが形成する液滴の溶液状態の理解を深めるため、液滴形成に対する溶媒効果の網羅的な解析をおこなった。実験には、飢餓ストレスに応じて液-液相分離することが知られている酵母由来の翻訳終結因子であるプリオンタンパク質Sup35の天然変性領域を用いた。溶媒のpHやイオン強度などの基礎的な条件の検討から、Sup35の天然変性領域のうち、N末端側のプリオンドメインが液滴やアミロイドの形成に関わることがわかった。Sup35のプリオンドメインが形成する液滴に対して、天然の低分子化合物であるアルコールやコスモトロープ、カオトロープ、オスモライト、アミノ酸、および高分子クラウダーを幅広い濃度で添加したところ、液滴を抑制するものと促進するものにわかれることがわかった。液滴を抑制した添加剤のうち、球状タンパク質の変性によるアモルファス凝集の形成を促進するものがあり、溶媒効果によってタンパク質の液滴に特有のふるまいが起こることを発見した。
  このように制御された液滴は、その後の成熟過程が異なる可能性があるため、チオフラビンT蛍光を用いてアミロイド化の様子を調べた。ほとんどの場合、液滴を抑制すると、アミロイドの形成も抑制されることが分かった。プリオンドメインが駆動する液滴は、アミロイド化と関連することが示唆された。さらに、プリオンドメインの液体性が観察された。プリオンドメインが形成する会合体は、高濃度の添加剤を加えても液滴のままであり、他の球状タンパク質や荷電性ポリマーとは異なる性質を持つことを見出した。
  Japan Society for the Promotion of Science (JSPS), University of Tsukuba, 20J21732
• Overseas Study Support Project
  Aug. 2022 - Aug. 2022
  Suguru Nishinami
  University of Tsukuba, University of Tsukuba

• 細菌内の相分離現象の観察
  31 Oct. 2025
  Others
  札幌シニア大学
• 生命分子機構分野 ～生命の仕組みを調べる研究へのご招待～
  08 Jun. 2024
  Others
  第66回北大祭 IGM一般公開

• Mar. 2023
  Outstanding Achievements Awards, Japan Student Services Organization (JASSO)