Study on Protein Solution

Shiraki Lab, Univ Tsukuba

Protein Solution Landscape

Research in this group is focused on understanding all protein-solution phenomena that span classic solubilization/aggregation to modern industrial application. Specifically, we aim to control the protein solution by a designed solvent with conventional additives.

Protein Solution Design

Proteins are prone to inactivation in aqueous solutions because chemical modification and aggregation usually occur, particularly at high temperature. This review focuses on the recent advance in practical application with amine compounds that prevent the heat-induced inactivation and aggregation of proteins. Coexistence of amine solutes, typically diamines, polyamines, amino acid esters, and amidated amino acids decreases the heat-induced inactivation rate of proteins by one order of magnitude compared with that in the absence of additives under low concentrations of proteins at physiological pH. The amine compounds mainly suppress chemical modification, typically the β-elimination of disulfide bond and deamidation of asparagine side chain, thereby preventing heat-induced inactivation of proteins. Polyamines do not improve the refolding yield of proteins, owing to decrease in the solubility of unfolded proteins. In contrast, arginine is the most versatile additive for various situations, such as refolding of recombinant proteins, solubilized water-insoluble compounds, and prevention of nonspecific binding to solid surfaces; however, it is not always effective for preventing heat-induced aggregation. Amine compounds will be a key to prevent protein inactivation in solution additives.
Curr Pharm Biotechnol. 2016;17(2):116-25. review

Viscosity Control by Additives

Viscosity of protein solution is one of the most troublesome issues for the high-concentration formulation of protein drugs. In this review, we summarize the practical methods that suppress the viscosity of protein solution using small molecular additives. The small amount of salts decreases the viscosity that results from electrostatic repulsion and attraction. The chaotrope suppresses the hydrophobic attraction and cluster formation, which can lower the solution viscosity. Arginine hydrochloride (ArgHCl) also suppresses the solution viscosity due to the hydrophobic and aromatic interactions between protein molecules. The small molecular additives are the simplest resolution of the high viscosity of protein solution as well as understanding of the primary cause in complex phenomena of protein interactions.
Curr Protein Pept Sci. review

Wrap-Strip Technology

A polyelectrolyte is a polymer composed of repeating units of an electrolyte group that enables reversible complex formation with proteins in aqueous solutions. This review introduces "wrap-and-strip" technology of protein-polyelectrolyte complex (PPC) by noncovalent interaction. Storage: protein is stabilized against physical and chemical stresses. Enrichment: precipitation through PPC can be used as an enrichment method without irreversible unfolding. Catalytic activity switch: a complementary charged pair of polyelectrolytes functions as a reversible enzyme activity switch. Hyperactivation: a specific combination of a polyelectrolyte and substrate enhances enzyme activity by one order of magnitude compared with an enzyme alone. Stabilization: PPC increases protein stability against chemical and physical stresses, such as covalently modified polyethylene glycosylated protein. Simple PPC-based technology can expand the applicable fields of soluble proteins in aqueous solutions.
Curr Med Chem. 2016;23(3):276-89. review

Aggregative Protein Formulation

Aggregative protein-polyelectrolyte complex (PPC) has been proposed as a concentrated state of protein with a great potential for biopharmaceutical application. In this review article, we introduce a unique concentration method of protein formulation using PPC for a dozen types of pharmaceutical antibodies, hormones, and enzymes. Aggregative PPC can be obtained only by mixing poly(amino acid)s with proteins under low salt concentration conditions at an ambient temperature. The aggregative PPC is in a stabilized state against shaking, heating, and oxidation. More importantly, the aggregative PPC can be fully redissolved by the addition of physiological saline without denaturation and activity loss for many proteins. In addition, the general toxicity and pharmacokinetic profiles of the aggregative PPC are identical to those of the control antibody formulation. Thus, the protein formulation produced by aggregative PPC would be applicable for biomedical use as a kind of concentrated-state protein.
Int J Biol Macromol. 2016 Jun 7. review

Recent Advances

KEY WORDS; phase separation, coacervation, coaggregation, aggregation, condensation, concentration, aggregation, hyperactivation, opalescence, Arg technology, high concentration protein formulation, protein-polyelectrolyte complex formation

Peer-Reviewed Articles

  1. Atsushi Hirano, Kazuki Iwashita, Tomoto Ura, Shun Sakuraba, Kentaro Shiraki, Tsutomu Arakawa, Tomoshi Kameda. Binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations through cation–pai interaction: the case of sodium ion and arginine
  2. Kazuki Iwashita, Masahiro Mimura, Kentaro Shiraki. Control of aggregation, co-aggregation, and liquid droplet of proteins by small additives. Curr. Pharm. Biotechnol.
  3. Masahiro Mimura, Keisuke Tsumura, Ayumi Matsuda, Naoki Akatsuka, and Kentaro Shiraki. Effect of additives on liquid droplet of protein–polyelectrolyte complex for high-concentration formulations. J Chem Phys. 150, 064903 (2019)
  4. Kazuki Iwashita, Akihiro Handa, Kentaro Shiraki. Co-aggregation of ovotransferrin and lysozyme. Food Hydrocolloids
  5. Miki Nemoto, Kazunori Sugihara, Tsubasa Adachi, Kazuki Murata, Kentaro Shiraki, and Seiya Tsujimura. Effect of electrolyte ions on stability of flavin adenine dinucleotide-dependent glucose dehydrogenase, ChemElectroChem
  6. Masahiro Mimura, Shunsuke Tomita, Ryoji Kurita, and Kentaro Shiraki. Array-based generation of response fingerprints with common fluorescent dyes for identification of proteins and cells. Anal Sci. 35, 99-102 (2019)
  7. Takahiro Nonaka, Noriko Tsurui, Teruhisa Mannem, Yoshimi Kikuchi, Kentaro Shiraki. Non-chromatographic purification of teriparatide with a pH-responsive CspB tag. Protein Expr. Purif. 155, 66-71 (2019)
  8. Tsutomu Arakawa, Masao Tokunaga, Takuya Maruyama, Kentaro Shiraki. Two Elution Mechanisms of MEP Chromatography. Curr Protein Pept Sci. 20, 28-33 (2019)
  9. Atsushi Hirano, Kentaro Shiraki, and Tomoshi Kameda. Effects of Arginine on Multimodal Chromatography: Experiments and Simulations, Curr Protein Pept Sci. 20, 40-48 (2019)
  10. Shogo Oki, Suguru Nishinami, Kentaro Shiraki. Arginine suppresses opalescence and liquid–liquid phase separation in IgG solutions. Int. J. Biol. Macromol. 118, 1708-1712 (2018)
  11. Ayumi Matsuda, Masahiro Mimura, Takuya Maruyama, Takaaki Kurinomaru, Shiuhei Mieda, and Kentaro Shiraki. Liquid Droplet of Protein–Polyelectrolyte Complex for High-Concentration Formulations. Journal of Pharmaceutical Sciences, 107, 2713-2719 (2018)
  12. Tomohito Nakayama, Takeshi Tanaka, Kentaro Shiraki, Muneaki Hase, and Atsushi Hirano. Suppression of single-wall carbon nanotube redox reaction caused by protein adsorption. Applied Physics Express 11, 075101 (2018)
  13. Akihiro Endo, Takaaki Kurinomaru, and Kentaro Shiraki. Hyperactivation of serine protease by the Hofmeister effect. Molecular Catalysis, 455, 32-37 (2018)
  14. Kazuki Iwashita, Akihiro Handa, Kentaro Shiraki. Coacervates and coaggregates: Liquid-liquid and liquid-solid phase transitions by native and unfolded protein complexes. Int. J. Biol. Macromol. 120, 10-18 (2018)
  15. Suguru Nishinami, Atsushi Hirano, Tsutomu Arakawa, and Kentaro Shiraki. Effects of allantoin and dimethyl sulfoxide on the thermal aggregation of lysozyme. Int. J. Biol. Macromol., 119, 180-185 (2018)
  16. Suguru Nishinami, Shunsuke Yoshizawa, Tsutomu Arakawa and Kentaro Shiraki. Allantoin and hydantoin as new protein aggregation suppressors. Int. J. Biol. Macromol., 114, 497-503 (2018)
  17. Taehun Hong, Kazuki Iwashita, Kentaro Shiraki. Viscosity Control of Protein Solution by Small Solutes: A Review. Current Protein and Peptide Science, 19, 746-758 (2018)
  18. Atsushi Hirano, Kazuki Iwashita, Shun Sakuraba, Kentaro Shiraki, Tsutomu Arakawa, Tomoshi Kameda. Salt-dependent Elution of Uncharged Aromatic Solutes in Ion-exchange Chromatography. Journal of Chromatography A, 1546, 46-55 (2018)
  19. Shogo Oki, Takahiro Nonaka, Kentaro Shiraki. Specific solubilization of aromatic impurities in culture media: Arg solution improves purification of pH-responsive tag CspB50 with Teriparatide. Protein Expression and Purification 146, 85-90 (2018)
  20. Takahiro Nonaka, Noriko Tsurui, Teruhisa Mannem, Yoshimi Kikuchi, Kentaro Shiraki. A new pH-responsive peptide tag for protein purification. Protein Expression and Purification 146, 91-96 (2018)
  21. Shunsuke Yoshizawa, Shogo Oki, Tsutomu, Arakawa, and Kentaro Shiraki. Trimethylamine N-oxide (TMAO) is a counteracting solute of benzyl alcohol for multi-dose formulation of immunoglobulin. Int. J. Biol. Macromol., 107, 984-989 (2018)
  22. Shogo Oki, Kazuki Iwashita, Masahiro Kimura, Hideaki Kano, Kentaro Shiraki. Mechanism of co-aggregation in a protein mixture with small additives. Int. J. Biol. Macromol., 107, 1428-1437 (2018)
  23. Shunsuke Tomita, Ayumi Matsuda, Suguru Nishinami, Ryoji Kurita, Kentaro Shiraki. One-step identification of antibody degradation pathways using fluo-rescence signatures generated by cross-reactive DNA-based arrays. Anal. Chem. 89, 7818-7822 (2017)
  24. Tomohito Nakayama, Shunsuke Yoshizawa, Atsushi Hirano, Takeshi Tanaka, Kentaro Shiraki, Muneaki Hase. Vibrational Energy Transfer from Photo-Excited Carbon Nanotubes to Proteins Observed by Coherent Phonon Spectroscopy. Applied Physics Express, 10 (12), 125101 (2017)
  25. Shunsuke Yoshizawa, Tsutomu Arakawa, and Kentaro Shiraki. Thermal Aggregation of Human Immunoglobulin G in Arginine Solutions: Contrasting Effects of Stabilizers and Destabilizers, Int. J. Biol. Macromol., 104, 650–655 (2017)
  26. Takaaki Kurinomaru, Kengo Kuwada, Shunsuke Tomita, Tomoshi Kameda and Kentaro Shiraki. Noncovalent PEGylation through Protein-Polyelectrolyte Interaction: Kinetic Experiment and Molecular Dynamics Simulation, J. Phys. Chem. B. 121, 6785-6791 (2017)
  27. Kazuki Iwashita, Akihiro Handa, Kentaro Shiraki. Co-aggregation of ovalbumin and lysozyme. Food Hydrocolloids, 67 206-215 (2017)
  28. Atsushi Hirano, Takuya Maruyama, Kentaro Shiraki, Tsutomu Arakawa, and Tomoshi Kameda. A Study of the Small-Molecule System Used to Investigate the Effect of Arginine on Antibody Elution in Hydrophobic Charge-Induction Chromatography. Protein Expr Purif, 129, 44-52 (2017)
  29. Taehun Hong, Kazuki Iwashita, Akihiro Handa, Kentaro Shiraki. Arginine prevents thermal aggregation of hen egg white proteins. Food Research International, 97, 272-279 (2017)
  30. Takaaki Kurinomaru and Kentaro Shiraki. Aggregative protein-polyelectrolyte complex for high-concentration formulation of protein drug. Int. J. Biol. Macromol.,100 (2017) 11–17
  31. Akihiro Endo, Takaaki Kurinomaru, and Kentaro Shiraki. Hyperactivation of α-chymotrypsin by the Hofmeister effect. J. Mol. Catal. B: Enzymatic, 133, 432-438 (2016)
  32. Kazuki Iwashita, Motoki Sumida, Kazuya Shirota, and Kentaro Shiraki. A recovery method of surimi wash-water protein by pH shift and heat treatment. Food Science and Technology Research, 22 (6), 743-749 (2016)
  33. Shogo Oki, Tsutomu Arakawa, Kentaro Shiraki. The effects of n-acetyltryptophan and caprylic acid on protein aggregation. J. Biol. Macromol. 16, 3-7 (2016)
  34. Kengo Kuwada, Takaaki Kurinomaru, Shunsuke Tomita, and Kentaro Shiraki. Noncovalent PEGylation-based enzyme switch in physiological saline conditions using quaternized polyamines. Colloid and Polymer Science, 296, 1551-1556 (2016)
  35. Shunsuke Yoshizawa, Tsutomu Arakawa, and Kentaro Shiraki. Effect of counter ions of arginine as an additive for the solubilization of protein and aromatic compounds. Int. J. Biol. Macromol. 91, 471-476 (2016)
  36. Katsuyoshi Aoki, Kentaro Shiraki, and Toshiaki Hattori. Salt effects on the picosecond dynamics of lysozyme hydration water investigated by terahertz time-domain spectroscopy and an insight into Hofmeister series for protein stability and solubility. Physical Chemistry Chemical Physics, 18, 15060-15069 (2016)
  37. Kazuki Iwashita, Kentaro Shiraki, Rieko Ishii, Takeshi Tanaka, Atsushi Hirano. Arginine Suppresses the Adsorption of Lysozyme on Single-Wall Carbon Nanotube. Chem. Lett. 45, 952-954 (2016)
  38. Takumi Miyatake, Shunsuke Yoshizawa, Tsutomu Arakawa, Kentaro Shiraki. Charge state of arginine as an additive on heat-induced protein aggregation. Int. J. Biol. Macromol. 87, 563-569 (2016)
  39. Kentaro Shiraki, Takaaki Kurinomaru, and Shunsuke Tomita. Wrap-and-Strip Technology of Protein-Polyelectrolyte Complex for Biomedical Application. Curr. Med. Chem., 23, 276-289 (2016), review
  40. Kentaro Shiraki, Shunsuke Tomita, and Naoto Inoue. Small Amine Molecules: Solvent Design Toward Facile Improvement of Protein Stability Against Aggregation and Inactivation. Curr. Pharm. Biotechnol. 17, 116-125 (2016), review
  41. Kazuki Iwashita, Kentaro Shiraki, Rieko Ishii, Takeshi Tanaka, Atsushi Hirano. Liquid chromatographic analysis of the interaction between amino acids and aromatic surfaces using single-wall carbon nanotubes. Langmuir. 31, 8923-8929 (2015)
  42. Shunsuke Izaki, Takaaki Kurinomaru, Kenji Handa, Tomoaki Kimoto, and Kentaro Shiraki. Stress Tolerance of Antibody-Poly(amino acid) Complexes for Improving the Stability of High Concentration Antibody Formulations. J. Pharm. Sci. 104, 2457-2463 (2015)
  43. Kazuki Iwashita, Naoto Inoue, Akihiro Handa, and Kentaro Shiraki. Thermal aggregation of hen egg white proteins in the presence of salts. Protein J. 34, 212-219 (2015)
  44. Takuya Maruyama, Shunsuke Izaki, Takaaki Kurinomarua, Kenji Handa, Tomoaki Kimoto, and Kentaro Shiraki. Protein-poly(amino acid) precipitation stabilizes a therapeutic protein of L-asparaginase against physicochemical stress. J. Biosci. Bioeng. 120, 720-723 (2015)
  45. Takaaki Kurinomaru, Tomoshi Kameda, and Kentaro Shiraki. Effects of Hydrophobicity and Multivalency of Polyamines on Enzyme Hyperactivation of alpha-Chymotrypsin. J. Mol. Catal. B: Enzymatic. 115, 135-139 (2015)
  46. Shunsuke Izaki, Takaaki Kurinomaru, Takuya Maruyama, Kenji Handa, Tomoaki Kimoto and Kentaro Shiraki. Feasibility of Antibody-Poly(amino acid) Complexes: Preparation of High-concentration Antibody Formulations and their Pharmaceutical Properties. J. Pharm. Sci. 104, 1929-37 (2015)
  47. Masato Shimada, Eisuke Takai, Daisuke Ejima, Tsutomu Arakawa and Kentaro Shiraki. Heat-induced formation of myosin oligomer-soluble filament complex in high salt solution. Int. J. Biol. Macromol. 73, 17-22 (2015)
  48. Takaaki Kurinomaru and Kentaro Shiraki. Non-covalent PEGylation of L-Asparaginase Using PEGylated Polyelectrolyte. J. Pharm. Sci. 104, 587-592 (2015)
  49. Atsushi Hirano, Takuya Maruyama, Kentaro Shiraki, Tsutomu Arakawa, and Tomoshi Kameda. Mechanism of Protein Desorption from 4-Mercaptoethylpyridine Resins by Arginine Solutions. J. Chromato. A, 1373, 141-148 (2014)
  50. Toru Nakayama, Taro Sakuraba, Shunsuke Tomita, Akira Kaneko, Eisuke Takai, Kentaro Shiraki, Kentaro Tashiro, Noriyuki Ishii, Yuri Hasegawa, Yoichi Yamada, Reiji Kumai, and Yohei Yamamoto. Charge-Separated Fmoc-Peptide beta-Sheets: Sequence-Secondary Structure Relationship for Arranging Charged Side Chains on Both Sides .Asian J. Org. Chem., 3, 1182-1188 (2014)
  51. Eisuke Takai, Tsuyoshi Kitamura, Junpei Kuwabara, Satoshi Ikawa, Shunsuke Yoshizawa, Kentaro Shiraki, Hideya Kawasaki, Ryuichi Arakawa, and Katsuhisa Kitano. Chemical Modification of Amino Acids by Atmospheric-Pressure Cold Plasma in Aqueous Solution. J. Phys. D: Appl. Phys. 47, 285403 (2014)
  52. Shunsuke Tomita, Tomohiro Soejima, Kentaro Shiraki and Keitaro Yoshimoto. Enzymatic fingerprinting of structurally similar homologous proteins using polyion complex library constructed by tuning PEGylated polyamine functionalities. Analyst. 139, 6100-6103 (2014)
  53. Naoto Inoue, Eisuke Takai, Tsutomu Arakawa, and Kentaro Shiraki. Specific decrease in solution viscosity of antibodies by arginine for therapeutic formulations. Molecular Pharmaceutics 11, 1889-1896 (2014)
  54. Katsuhisa Murakami, Tianchen Dong, Yuya Kajiwara, Takaki Hiyama, Teppei Takahashi, Eisuke Takai, Gai Ohashi, Kentaro Shiraki, and Jun-ichi Fujita. Synthesis of graphene nanoribbons from amyloid templates by gallium vapor-assisted solid-phase graphitization. Appl. Phys. Lett. 104, 243101 (2014)
  55. Takaaki Kurinomaru, Takuya Maruyama, Shunsuke Izaki, Kenji Handa, Tomoaki Kimoto, and Kentaro Shiraki. Protein-Poly(amino acid) Complex Precipitation for High-concentration Protein Formulation. J. Pharm. Sci. 103, 2248-2254 (2014)
  56. Shunsuke Yoshizawa, Tsutomu Arakawa, and Kentaro Shiraki. Dependence of ethanol effects on protein charges. Int. J. Biological Macromolecules. 68, 169-172 (2014)
  57. Takaaki Kurinomaru, Shunsuke Tomita, Yoshihisa Hagihara, and Kentaro Shiraki. Enzyme Hyperactivation System Based on Generated Reaction Field by Polyelectrolyte. Langmuir 30, 3826-3831 (2014)
  58. Eisuke Takai, Gai Ohashi, Ryuichi Ueki, Yoichi Yamada, Jun-ichi Fujita, Kentaro Shiraki. Scanning Electron Microscope Imaging of Amyloid Fibrils. Am. J. Biochem. Biotechnol. 10, 31-39, (2014)
  59. Eisuke Takai, Ken Uda, Shuhei Matsushita, Yui Shikiya, Yoichi Yamada, Tamotsu Zako, Mizuo Maeda, Kentaro Shiraki, Cysteine Inhibits Amyloid Fibrillation of the Lysozyme and Directs the Formation of Small Worm-like Aggregates through Non-Covalent Interactions. Biotechnol. Prog. 30, 470-478 (2014)
  60. Eisuke Takai, Ken Uda, Tomonori Yoshida, Tamotsu Zako, Mizuo Maeda, Kentaro Shiraki, Cysteine Inhibits the Fibrillisation and Cytotoxicity of Amyloid-beta 40 and 42: Implications for the Contribution of the Thiophilic Interaction. Physical Chemistry Chemical Physics 16, 3566 - 3572 (2014)
  61. Eisuke Takai, Gai Ohashi, Tomonori Yoshida, Karin Margareta Sorgjerd, Tamotsu Zako, Mizuo Maeda, Katsuhisa Kitano, Kentaro Shiraki, Degeneration of Amyloid-beta Fibrils Caused by Exposure to Low-Temperature Atmospheric-Pressure Plasma in Aqueous Solution. Applied Physics Letters, 104, 023701 (2014)
  62. Naoto Inoue, Eisuke Takai, Tsutomu Arakawa, and Kentaro, Arginine and Lysine Reduce the High Viscosity of Serum Albumin Solutions for Pharmaceutical Injection, J. Biosci. Bioeng. 117, 539-543 (2014)
  63. Katsuyoshi Aoki, Kentaro Shiraki, and Toshiaki Hattori. Observation of salt effects on hydration water of lysozyme in aqueous solution using terahertz time-domain spectroscopy. Applied Physics Letters. 103, 173704 (2013)
  64. Naohisa Sugimoto Yasuaki Takakura, Kentaro Shiraki, Shinya Honda, Naoki Takaya, Takayuki Hoshino, and Akira Nakamura. Directed Evolution for Thermostabilization of a Hygromycin B Photphotransferase from Streptomyces hygroscopicus. Bioscience, Biotechnology, and Biochemistry 77, 2234-2241 (2013)
  65. Shunsuke Tomita, Yumiko Tanabe, and Kentaro Shiraki. Oligoethylene glycols prevent thermal aggregation of alpha-chymotrypsin in a temperature-dependent manner: implications for design guidelines. Biotechnol. Prog. 29, 1325-1330 (2013)
  66. Eisuke Takai, Shunsuke Yoshizawa, Daisuke Ejima, Tsutomu Arakawa, and Kentaro Shiraki. Synergistic Solubilization of Porcine Myosin in Physiological Salt Solution by Arginine. Int. J. Biological Macromolecules. 62, 647-651 (2013)
  67. Atsushi Hirano, Tomoshi Kameda, Daisuke Shinozaki, Tsutomu Arakawa, Kentaro Shiraki. Molecular Dynamics Simulation of Arginine-Assisted Solubilization of Caffeic Acid: Intervention in the Interaction. J. Phys. Chem. B 117, 7518-7528 (2013)
  68. Yui Shikiya, Shunsuke Tomita, Tsutomu Arakawa, and Kentaro Shiraki. Arginine inhibits proteins adsorption on polystyrene surface. PLoS One 8(8): e70762 (2013)
  69. Shunsuke Tomita, Yukio Nagasaki, and Kentaro Shiraki. Different mechanisms of action of poly(ethylene glycol) and arginine on thermal inactivation of proteins. Biotechnology and Bioengineering, 109, 2543-2542 (2012)
  70. Hiroki Yoshikawa, Atsushi Hirano, Tsutomu Arakawa, and Kentaro Shiraki. Effects of alcohol on the solubility and structure of native and disulfide-modified bovine serum albumin. Int. J. Biological Macromolecules 50, 1286-1291 (2012)
  71. Atsushi Hirano, Hiroki Yoshikawa, Shuhei Matsushita, Yoichi Yamada, and Kentaro Shiraki. Adsorption and disruption of lipid bilayers by nanoscale protein aggregates. Langmure 28, 3887-3895 (2012)
  72. Takaaki Kurinomaru, Shunsuke Tomita, Shinpei Kudo, Sumon Ganguli, Yukio Nagasaki, and Kentaro Shiraki. Improved Complementary Polymer Pair System: Switching for Enzyme Activity by PEGylated Polymers. Langmuir 28, 4334-4338 (2012)
  73. Len Ito, Masaki Okumura, Kohsaku Tao, Yusuke Kasai, Shunsuke Tomita, Akiko Oosuka, Hidetoshi Yamada, Tomohisa Shibano, Kentaro Shiraki, Takashi Kumasaka, Hiroshi Yamaguchi. Glutathione ethylester, a novel protein refolding reagent, enhances both the efficiency of refolding and correct disulfide formation. Protein J. 31, 499-503 (2012)
  74. Hiroki Yoshikawa, Atsushi Hirano, Tsutomu Arakawa, and Kentaro Shiraki. Mechanistic insights into protein precipitation by alcohol. Int. J. Biological Macromolecules 50, 865-871 (2012)
  75. Tsutomu Arakawa, Atsushi Hirano, Kentaro Shiraki, Takako Niikura and Yoshiko Kita. Advances in characterization of neuroprotective peptide, Humanin. Curr. Med. Chem. 18, 5554-5563 (2011)
  76. Atsushi Hirano, Kentaro Shiraki, and Tsutomu Arakawa. Polyethylene glycol behaves like weak organic solvent. Biopolymers, 97, 117-122 (2012)
  77. Eisuke Takai, Katsuhisa Kitano, Junpei Kuwabara, Kentaro Shiraki. Protein Inactivation by Low-Temperature Atmospheric Pressure Plasma in Aqueous Solution. Plasma Processes and Polymers, 9, 77-82 (2012)
  78. Ryosuke Ariki, Atsushi Hirano, Tsutomu Arakawa, Kentaro Shiraki. Drug solubilization effect of lauroyl-L-glutamate. J. Biochemistry, 151, 27-33 (2012)
  79. Shunsuke Tomita and Kentaro Shiraki. Poly(acrylic acid) is a common non-competitive inhibitor for cationic enzymes with high affinity and reversibility. Journal of Polymer Science Part A: Polymer Chemistry. 49, 3835-3841 (2011)
  80. Shunsuke Tomita, Hiroki Yoshikawa, and Kentaro Shiraki. Arginine controls heat-induced cluster-cluster aggregation of lysozyme at around the isoelectric point. Biopolymers, 95, 695-701 (2011)
  81. Tsutomu Arakawa, Yoshiko Kita, Kentaro Shiraki and Satoshi Ohtake. The mechanism of protein precipitation by salts, polymers and organic solvents. Global J. Anal. Chem. 2, 152-167 (2011)
  82. Shunsuke Tomita and Kentaro Shiraki. Why do solution additives suppress the heat-induced inactivation of proteins? Biotechnol. Prog., 27, 855-862 (2011).
  83. Eisuke Takai, Atsushi Hirano, and Kentaro Shiraki. Effects of alkyl chain length of gallate on self-association and membrane-binding. J Biochemistry 150, 165-171 (2011)
  84. Kiyouhisa Ohnishi, Kumiko Nakahira, Satoru Unzai, Kouta Mayanagi, Hiroshi Hashimoto, Kenataro Shiraki, Takeshi Honda and Itaru Yanagihara. Relationship between heat-induced fibrillogenicity and hemolytic activity of thermostable direct hemolysin and a related hemolysin of Vibrio parahaemolyticus. FEMS Microbiology Letters 318, 10-17 (2011)
  85. Ryosuke Ariki, Atsushi Hirano, Tsutomu Arakawa, Kentaro Shiraki. Arginine increases solubility of alkyl gallates through interaction with the aromatic ring. J. Biochemistry149, 389-394 (2011)
  86. Len Ito, Kentaro Shiraki, Takanori Matsuura, Masaki Okumura, Kazuya Hasegawa, Seiki Baba, Hiroshi Yamaguchi, and Takashi Kumasaka. High-resolution X-ray analysis revealing binding of arginine to aromatic residues of lysozyme surface: Implication of suppression of protein aggregation by arginine, Protein Engineering Design and Selection, 24, 269-274 (2011)
  87. Atsushi Hirano, Kentaro Shiraki, Takako Niikura, Tsutomu Arakawa and Yoshiko Kita. Structure of three Humanin peptides with different activities upon interaction with liposome. Int. J. Biological Macromolecules. 48, 360-363 (2011)
  88. Len Ito, Kentaro Shiraki, Masatomo Makino, Kazuya Hasegawa, and Takashi Kumasaka. Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation. FEBS letters 585, 550-560 (2011)
  89. Atsushi Hirano, Ken Uda, Yutaka Maeda, Takeshi Akasaka, and Kentaro Shiraki. One-Dimensional Protein-Based Nanoparticles Induce Lipid Bilayer Disruption: Carbon Nanotube Conjugates and Amyloid Fibrils. Langmuir, 26, 17256-17259 (2010)
  90. Atsushi Hirano, Yutaka Maeda, Xiaofei Yuan, Ryuuichi Ueki, Yosuke Miyazawa, Jun-ichi Fujita, Takeshi Akasaka, and Kentaro Shiraki. Controlled dispersion and purification of protein-CNT conjugates by guanidine hydrochloride. Chemistry, 16, 12221-12228 (2010)
  91. Len Ito, Kentaro Shiraki, Tatsuya Uchida, Masaki Okumura and Hiroshi Yamaguchi. Crystallization and preliminary crystallographic analysis of the Achromobacter Protease I mutants. Acta Crystallographica Section F, 66, 1531-1532 (2010)
  92. Kentaro Shiraki, Atsushi Hirano, Yoshiko Kita, A. Hajime Koyama and Tsutomu Arakawa. Potential application of arginine in interaction analysis. Drug Discoveries and Therapeutics, review, 4, 326-333 (2010)
  93. Atsushi Hirano, Tomoshi Kameda, Tsutomu Arakawa, Kentaro Shiraki. Arginine-Assisted Solubilization System for Drug Substances: Solubility Experiment and Simulation. J. Phys. Chem. B, 114, 13455-13462 (2010)
  94. Sumon Ganguli, Keitaro Yoshimoto, Shunsuke Tomita, Hiroshi Sakuma, Tsuneyoshi Matsuoka, Kentaro Shiraki, and Yukio Nagasaki "Improving the Heat Resistance of Ribonuclease A by the Addition of Poly(N,N-diethylaminoethyl methacrylate)-graft-poly(ethylene glycol) (PEAMA-g-PEG)" Macromolecular Bioscience, 10, 853-859 (2010)
  95. Atsushi Hirano, Yutaka Maeda, Takeshi Akasaka, and Kentaro Shiraki. Mechanism of enhanced dispersion of single-walled carbon nanotubes with proteins by alcohols and chaotropes. Japanese Journal of Applied Physics, 49, 06GJ10 (2010)
  96. Shunsuke Tomita, Len Ito, Hiroshi Yamaguchi, Gen-ichi Konishi, Yukio Nagasaki, and Kentaro Shiraki. Enzyme switch by complementary polymer pair system (CPPS). Soft Matter 6, 5320-5326 (2010)
  97. Len Ito, Kentaro Shiraki and Hiroshi Yamaguchi. Comparative analysis of amino acids and amino-acid derivatives in protein crystallization. Acta Cryst. F66, 744-749 (2010)
  98. Len Ito, Kentaro Shiraki and Hiroshi Yamaguchi. Amino acids and glycine ethyl ester as new crystallization reagents for lysozyme. Acta Cryst. F66, 750-754 (2010)
  99. Yoshihiro Fujiwara, Yasuhiko Aiki, Lijun Yang, Fumio Takaiwa, Akemi Kosaka, Noriko M. Tsuji, Kentaro Shiraki, and Kenji Sekikawa. Extraction and purification of human interleukin-10 from transgenic rice seeds. Protein Expression and Purification, 72, 125-130 (2010).
  100. Atsushi Hirano, Hiroko Tokunaga, Masao Tokunaga, Tsutomu Arakawa, and Kentaro Shiraki. The solubility of nucleobases in aqueous arginine solutions. Archives of Biochemistry and Biophysics. 497, 90-96 (2010)
  101. Akiko Fujimoto, Atsushi Hirano, and Kentaro Shiraki. Ternary system of solution additives with arginine and salt for refolding of beta-galactosidase. Protein J. 29, 161-166 (2010)
  102. Kentaro Shiraki and Soichiro Kayano. Thermal-assisted refolding: Dilution Folding Initiated at High Temperature. Curr. Pharm. Biotechnol. 11, 306-308 (2010)
  103. Atsushi Hirano, Kentaro Shiraki, Takako Niikura, Tsutomu Arakawa and Yoshiko Kita. Structure changes of natively disordered Humanin in the presence of lipid. International Journal of Biometrics. (2010)
  104. Kazutoshi Yasui, Masamichi Uegaki, Kentaro Shiraki, and Takeshi Ishimizu. Enhanced solubilization of membrane proteins by alkylamines and polyamines. Protein Science. 19, 486-493 (2010)
  105. Tsutomu Arakawa, Atsushi Hirano, Kentaro Shiraki, Yoshiko Kita and A. Hajime Koyama. Stabilizing and destabilizing effects of arginine on deoxyribonucleic acid. Int. J. Biological Macromolecules. 46, 217-222 (2010)
  106. Kotaro Makino, Atsushi Hirano, Kentaro Shiraki, Yutaka Maeda, Muneaki Hase. Ultrafast vibrational motion of carbon nanotubes in different pH environments. Physical Review B. 80, 245428 (2009)
  107. Sachiko Matsumoto, Mun'delanji Vestergaard, Takafumi Konishi, Shingo Nishikori, Kentaro Shiraki, Naoki Tsuji, Kazumasa Hirata, and Masahiro Takagi. Role of C-terminal cys-rich region of phytochelatin syntase in tolerance to cadmium ion toxicity. J. Plant Biochemistry & Biotechnology 18, 175-180 (2009)
  108. Atsushi Hirano, Yutaka Maeda, Takeshi Akasaka, and Kentaro Shiraki, Synergistically Enhanced Dispersion of Native Protein-Carbon Nanotube Conjugates by Fluoroalcohols in Aqueous Solution. Chem. Eur. J., 15, 9905-9910 (2009)
  109. Tsuneyoshi Matsuoka, Hiroyuki Hamada, Koji Matsumoto, and Kentaro Shiraki. Indispensable Structure of Solution Additives to Prevent Inactivation of Lysozyme during Heating and Refolding. Biotechnol. Prog. 25, 1515-1524 (2009)
  110. Sumon Ganguli, Keitaro Yoshimoto, Shunsuke Tomita, Hiroshi Sakuma, Tsuneyoshi Matsuoka, Kentaro Shiraki, and Yukio Nagasaki. Regulation of Lysozyme Activity Based on Thermotolerant Protein/Smart Polymer Complex Formation. J. Am. Chem. Soc., 131, 6549-6553 (2009)
  111. Hiroyuki Hamada, Tsutomu Arakawa, and Kentaro Shiraki. Effect of additives on protein aggregation. Curr. Pharm. Biotech., 10, 400-407 (2009)
  112. Ataru Kobayashi, Gen-ichi Konishi, and Kentaro Shiraki. Synthesis of Optically Active Polyamines Based on Chiral 1-Cyclohexylethylamine Derivatives, Polymer J. 41, 503-507, (2009)
  113. Naoshige Izumikawa, Shingo Nishikori, Mun'delanji Vestergaard, Tsutomu Hamada, Yoshihisa Hagihara, Noboru Yumoto, Kentaro Shiraki, and Masahiro Takagi. Effect of Phospholipids on conformational structure of bovine pancreatic trypsin inhibitor (BPTI) and its thermolabile mutants. Biopolymers 89, 873-880 (2008)
  114. Akira Nakamura, Yasuaki Takakura, Naohisa Sugimoto, Naoki Takaya, Kentaro Shiraki, and Takayuki Hoshino. Enzymatic analysis of a thermostabilized mutant of an Escherichia colihygromycin B phosphotransferase. Biosci. Biotechnol. Biochem. 28, 2467-2469, (2008)
  115. Len Ito, Toyoaki Kobayashi, Kentaro Shiraki, and Hiroshi Yamaguchi. The effect of additives on protein crystallization. J. Synchro. Rad. 15, 316-318 (2008)
  116. Atsushi Hirano, Tsutomu Arakawa, Kentaro Shiraki. Arginine increases the solubility of coumarin: Comparison with salting-in and salting-out additives. J. Biochem. 144, 363-369 (2008)
  117. Atsushi Hirano, Hiroyuki Hamada, and Kentaro Shiraki. Trans-cyclohexanediamines prevent thermal inactivation of protein: Role of hydrophobic and electrostatic interactions. Protein J. 27, 253-257 (2008)
  118. Hiroyuki Hamada, Ryouta Takahashi, Takumi Noguchi, and Kentaro Shiraki. The differences in the effect of solution additives on heat- and dilution-induced aggregation. Biotechnol. Prog. 24, 436-443 (2008)
  119. Zhemin Zhou, Yoshiteru Hashimoto, Kentaro Shiraki, and Michihiko Kobayashi. Discovery of post-translational maturation by self-subunit swapping. Proc. Natl. Acad. Sci. U.S.A, 105, 14849-54 (2008)

Current Member

Under graduate students are able to join this lab from all majors (as well as Applied Physics) at College of Engineering Science, University of Tsukuba. Graduate students can apply through programs at Graduate School of Pure and Applied Sciences, Univ Tsukuba. The group has links to many academic and industrial scientists, including AIST, RIKEN, Ajinomoto, Terumo, Milbon, Maruha Nichiro, Alliance Protein Lab, and many Universities. More information about current member and alumni.

Member / 2018

  • Kentaro Shiraki, PI
  • Tomoto Ura, M2
  • Suguru Nishinami, M2
  • Keisuke Tsumura, M2
  • Yoshiki Kihara, M1
  • Yoshitaka Nakauchi, M1
  • Yoshitaka Nakauchi, M1
  • Yuto Akahoshi, B4
  • Takayuki Kawamura, B4
  • Akira Nomoto, B4

Special Thanks


  •  Kentaro Shiraki, Division of Applied Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
  •  Rooms 3F-732 (Office), 3G-313 (Lab), 3G-221 (Lab)

More Infomation

You can see more information about the theme, people, and principal investigator, in Japanese. The following illustration was designed by Ms. Hiroko Uchida, a prominent scientific illustrator. Her works have been beloved by many scientists, including Nobel laureates, Prof. Yoshinori Ohsumi and Prof. Osamu Shimomura.