- faculty profiles
- IKEGUCHI Masamichi
|Specialized field||Living organism molecular science
|Classes||Bioinformatics Seminar 3
Bioinformatics Seminar 4
General Topics in Science and Engineering
Advanced Topics in Science and Engineering
Case Study 1
Case Study 2
Current Topics in Biofunctional Engineering
Advanced Study of Biofunctional Engineering
Advanced Biopolymer Science
Advanced Course of Bioengineering
Advanced Laboratory Course of Bioengineering
Laboratory in Bioinformatics 1
Laboratory in Bioinformatics 2
|Research theme||Elucidation of Protein Folding Mechanism|
Bioinformatics of Graduate school of engineering
Major field Biochemistry, Biophysics, Protein Science, Protein Engineering Research Theme The aim of our research is to understand how proteins acquire their unique three-dimensional structures and how they assemble to form supramolecular structures. Understanding of the protein folding and assembly mechanism is also essential for a rational design of artificial proteins. Current research projects (1) understanding of folding mechanism on the basis of physicochemical principle. The folding reactions of various proteins are followed by various spectroscopic methods and several folding intermediates are detected. The three-dimensional structures of the intermediates are characterized by NMR. Effect of amino acid substitution on the folding reaction is addressed.
(2) elucidation of assembly mechanism of ferritin. The assembly reactions of ferritin and related proteins are investigated by time-resolved small-angle X-ray scattering and other physicochemical techniques. Key residues for assembly are investigated by site-directed mutagenesis.
Publications "A physicochemical and mutational analysis of intersubunit interactions of Escherichia coli ferritin A"
Ohtomo, H., Ohtomo, M., Daisuke, S., Kurobe, A., Sunato, A., Matsumura, Y., Kihara, H., Fujiwara, K. & Ikeguchi, M.
Biochemistry (2015) 54, 6243-6251
"The origin of β-strand bending in globular proteins"
Fujiwara, K., Ebisawa, S., Watanabe, Y., Fujiwara, H. & Ikeguchi, M.
BMC Struct Biol. (2015) 15, 21
"Effect of non-native helix destabilization on the folding of equine β-lactoglobulin"
Okabe, T., Miyajima, T., Nakagawa, K., Tsukamoto, S., Fujiwara, K. & Ikeguchi, M.
J. Biochem. (2014) 156, 291-297
"Local sequence of protein β-strands influences twist and bend angles"
Fujiwara, K., Ebisawa, S., Watanabe, Y., Toda, H. & Ikeguchi, M.
Proteins: Struct. Funct. Bioinfo. (2014) 82, 1484-1493
"α-Helix formation rate of oligopeptides at subzero temperatures"
Qin, Z. J., Shimizu, A., Li, J., Ikeguchi, M., Shinjo, M. & Kihara, H.
Biophysics (2014) 10, 9-13
"Relationship between chain collapse and secondary structure formation in a partially folded protein"
Nakagawa, K., Yamada, Y., Matsumura, Y., Tsukamoto, S., Yamamoto-Ohtomo, M., Ohtomo, H., Okabe, T., Fujiwara, K. & Ikeguchi, M.
Biopolymers (2014) 101, 651-658
"Delineation of solution burst-phase protein folding events by encapsulating the proteins in silica gels"
Okabe, T., Tsukamoto, S., Fujiwara, K., Shibayama N. & Ikeguchi, M.
Biochemistry (2014) 53, 3858-3866
"Transient Non-Native Helix Formation during the Folding of β-Lactoglobulin"
Biomolecules (2014) 4, 202-216
"Dependence of alpha-helical and beta-sheet amino acid propensities on the overall protein fold type"
Fujiwara, K., Toda, H. & Ikeguchi, M.
BMC Struct. Biol. (2012) 12, 18
"Importance of polypeptide chain length for the correct local folding of a β-sheet protein"
Yamamoto, M., Nakagawa, K. & Ikeguchi, M.
Biophys. Chem. (2012) 168-169, 40-47
"Important role of methionine 145 in dimerization of bovine β-lactoglobulin"
Ohtomo, H., Fujiwara, K. & Ikeguchi, M.
J. Biochem. (2012) 151, 329-334
"A Native Disulfide Stabilizes Non-Native Helical Structures in Partially Folded States of Equine β-Lactoglobulin"
Yamamoto, M., Nakagawa, K., Fujiwara, K., Shimizu, A., Ikeguchi, M. & Ikeguchi, M.
Biochemistry (2011) 50, 10590-10597
"Structure and stability of Gyuba, a β-lactoglobulin chimera"
Ohtomo, H., Konuma, T., Utsunomiya, H., Tsuge, H. & Ikeguchi, M.
Protein Sci. (2011) 20, 1867-1875
"Fatty acids bound to recombinant tear lipocalin and their role in structural stabilization"
Tsukamoto, S., Fujiwara, K. & Ikeguchi, M
J. Biochem. (2009) 146, 343-350
"Non-native alpha-helix formation is not necessary for folding of lipocalin: comparison of burst-phase folding between tear lipocalin and beta-lactoglobulin"
Tsukamoto S, Yamashita T, Yamada Y, Fujiwara K, Maki K, Kuwajima K, Matsumura Y, Kihara H, Tsuge H, Ikeguchi M.
Proteins. (2009) 76, 226-236
"OLIGAMI: OLIGomer Architecture and Molecular Interface"
Fujiwara K & Ikeguchi M.
Open Bioinfo. J. (2008) 2, 50-53
"Helix-Rich Transient and Equilibrium Intermediates of Equine β-Lactoglobulin in Alkaline Buffer"
Matsumura Y, Li J, Ikeguchi M & Kihara H
Biophys. Chem. (2008) 134, 84-92
"Chloride-ion Concentration Dependence of Molecular Dimension in the Acid-Denatured State of Equine β-Lactoglobulin"
Yamada Y, Yajima T, Tsukamoto S, Nakagawa K, Fujiwara K, Kihara H & Ikeguchi M
J. Appl. Crystallogr. (2007) 40, s213-s216
"An Alpha-Helical Burst in the src SH3 Folding Pathway"
Li J, Shinjo M, Matsumura Y, Morita M, Baker D, Ikeguchi M & Kihara H
Biochemistry (2007) 46, 5072-5082
"Interactions responsible for secondary structure formation during folding of equine β-lactoglobulin"
Nakagawa K, Yamada Y, Fujiwara K & Ikeguchi M
J. Mol. Biol. (2007) 367, 1205-1214
"Proline Scanning Mutagenesis Reveals Non-Native Fold in the Molten Globule State of Equine β-Lactoglobulin"
Nakagawa, K., Tokushima, A., Fujiwara, K. & Ikeguchi, M.
Biochemistry (2006) 45, 15468 - 15473
"Structural and Thermodynamic Consequences of Removal of a Conserved Disulfide Bond from Equine beta-Lactoglobulin"
Yamada, Y., Nakagawa, K., Yajima, T., Saito, K., Tokushima, A., Fujiwara, K. & Ikeguchi, M.
Proteins: Struct Funct Bioinfo (2006) 63, 595-602
"Helical and Expanded Conformation of Equine beta-Lactoglobulin in the Cold-denatured State"
Yamada Y., Yajima T., Fujiwara K., Arai M., Ito K., Shimizu A., Kihara H., Kuwajima K., Amemiya Y. & Ikeguchi M.
J Mol Biol (2005) 350, 338-348