Lab. Biophysical Chemistry, Dept. Biomolecular Chemistry (April, 2008 ～)
Molecular Recognition Mechanisms by Proteins
－Protein Structure, Flexibility, and Function－

（Japanese version）

Masayuki Oda, Ph.D.


Graduate School of Life and Environmental Sciences
Kyoto Prefectural University
1-5, Hangi-cho, Shimogamo, Sakyo-ku,
Kyoto 606-8522, Japan
TEL＆FAX: +81-75-703-5673
E-mail: oda＠kpu.ac.jp



1. Graduate and Undergraduate Students;

Yoichi Tanabe (D1)
Nobutaka Komichi (M2)
Yuichiro Takagi (M2)
Kuniomi Nakamura (M2)
Asami Maruoka (M1)
Tomoki Sano (B4)
Tomoyuki Sunahashi (B4)
Tomonari Tamashiro (B4)
Kotaro Hara (B4)
Satomi Inaba (B3)
Yukiko Kajiwara (B3)
Yusuke Tanaka (B3)


Alumni;
Yasutomo Inui, Hidekazu Kaminaka, Keiko Watanabe


2. Research;

My research interests are all related to understanding the correlation of protein structure
and function. We especially focus on the protein flexibility, which is difficult to be determined
but is critical for fully understanding protein structure and function. To achieve our projects,
we purify proteins, and analyze their molecular interactions using biophysical methods, such as
isothermal titration calorimetry and surface plasmon resonance biosensor. We also analyze
three dimensional structures of proteins at atomic resolution using X-ray crystallography,
nuclear magnetic resonance, and electron microscopy. The present targets for protein
interactions are as follows.

2-1. Antigen-Antibody Interaction
Antibodies can assume a wide range of conformations as a consequence of domain mobility
and segmental flexibility, which contribute to their antigen recognition and subsequent signaling.
We focus on the dynamic structure of antibodies and the conformational changes induced by
antigen binding.

2-2. Interaction between Intracellular Regions of CD28 Family Molecules and Adapter Proteins
To activate T cells, costimulatory signals via CD28 family molecules are required, together with
antigen-specific signals triggered by the binding of the TCR to the peptide–MHC complex. We
analyze the molecular interactions between CD28 families, CD28, ICOS, and CTLA-4, and adaptor
proteins, Grb2, Gads, and PI3K. We also analyze the three dimensional structures of these complexes.

2-3. 3α-Hydroxysteroid Dehydrogenase
The NAD(P)+-dependent enzyme, 3α-hydroxysteroid dehydrogenase (3α-HSD) catalyzes the
reversible interconversion of hydroxy and oxo groups at position 3 of the steroid nucleus. Because
the types of nucleotide cofactors can modulate the catalytic function of this enzyme, we analyze
the mechanism of cofactor recognistion by 3α-HSD, and its correlation with catalytic function.

2-4. Endo-1,3-β-Glucanase
We analyze the three dimensional structure of endo-1,3-β-glucanase, and its catalytic function.
In addition, because we found that a fraction of β-glucan oligomer from the hydrolytic product
of laminarin exhibited immunostimulating activity, we analyze the struture-activity relationship of
this β-glucan.


3. Recent Publications;

Oda, M., Kitai, A., Murakami, A., Nishimura, M., Ohkuri, T., Abe, Y., Ueda, T.,
Nakamura, H., and Azuma, T. (2010) Evaluation of the conformational equilibrium of
reduced hen egg lysozyme by antibodies to the native form. Arch. Biochem. Biophys., 494 (2), 145-150.

Oda, M.*, Uchiyama, S.*, Noda, M., Nishi, Y., Koga, M., Mayanagi, K.,
Robinson, C.V., Fukui, K., Kobayashi, Y., Morikawa, K., and Azuma, T. (2009)
Effects of antibody affinity and antigen valence on the molecular form of
immune complexes. Mol. Immunol., 47 (2-3), 357-364. (*equal contributors)

Shiga, D., Nakano, D., Inomata, T., Masuda, H., Oda, M., Noda, M., Uchiyama, S.,
Fukui, K., Takano, Y., Nakamura, H., Mizuno, T., and Tanaka, T. (2009)
The effect of the side chain length of Asp and Glu on coordination structure of
Cu2+ in a de novo designed protein. Biopolymers, 91 (11), 907-916.

Mizuno, T., Suzuki, K., Imai, T., Kitade, Y., Furutani, Y., Kudou, M.,
Oda, M., Kandori, H., Tsumoto, K., and Tanaka, T. (2009)
Manipulation of the protein-complex function by using an engineered
heterotrimeric coiled-coil switch. Org. Biomol. Chem., 7, 3102-3111.

Oda, M., Saito, M., Tsumuraya, T, and Fujii, I. (2009).
Contribution of the trifluoroacetyl group in the thermodynamics of antigen-antibody binding.
J. Mol. Recognit., in press.

Mizuno, T., Hasegawa, C., Tanabe, Y., Hamajima, K., Muto, T., Nishi, Y., Oda, M., Kobayashi, Y., and Tanaka, T. (2009).
Organic ligand binding by hydrophobic cavity in a designed tetrameric coiled-coil protein.
Chem. Eur. J., 15 (6), 1491-1498.

Tanabe, Y., Pang, Z., and Oda, M. (2008).
Cloning and sequencing of endo-1,3-β-glucanase from Cellulosimicrobium cellulans.
J. Biol. Macromol., 8 (3), 60-63. [PDF]

Thielges, M.C., Zimmermann, J., Yu, W., Oda, M., and Romesberg, F.E. (2008).
Exploring the energy landscape of antibody-antigen complexes:
Protein dynamics, flexibility, and molecular recognition.
Biochemistry, 47 (27), 7237-7247.

Shimizu, T., Osaka, Y., Banri-Koike, C., Yoshida, M., Endo, K., Furukawa, K., Oda, M.,
Murakami, A., Ogawa, S., Abe, R., and Azuma, T. (2007).
T cells specific to hapten-carrier but not to carrier alone assist in the production of
anti-hapten and anti-carrier antibodies.
Int. Immunol., 19 (10), 1157-1164.

Mizuno, T., Murao, K., Tanabe, Y., Oda, M., and Tanaka, T. (2007).
Metal-ion-dependent GFP emission in vivo by combining a circularly permutated GFP with
an engineered metal ion binding coiled-coil.
J. Am. Chem. Soc., 129 (37), 11378-11383.

Oda, M., Ito, N., Tsumuraya, T., Suzuki, K., Sakakura, M., and Fujii, I. (2007).
Thermodynamics and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis.
J. Mol. Biol., 369 (1), 198-209.

Oda, M., Kanaori, K., and Akasaka, K. (2007).
Increased thermodynamic stability by hydrophilic amino acid substitutions on the surface of
Streptomyces subtilisin inhibitor.
J. Biol. Macromol., 7 (1), 3-8. [PDF]

Nakamura, S., Oda, M., Kataoka, S., Ueda, S., Uchiyama, S., Yoshida, T., Kobayashi, Y., and Ohkubo, T. (2006).
Apo- and holo-structures of 3α-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831:
Loop-helix transition induced by coenzyme binding.
J. Biol. Chem., 281 (42), 31876-31884.

Kataoka, S., Nakamura, S., Ohkubo, T., Ueda, S., Uchiyama, S., Kobayashi, Y., and Oda, M. (2006).
Crystallization and preliminary X-ray analysis of the complex of NADH and 3α-hydroxysteroid
dehydrogenase from Pseudomonas sp. B-0831.
Acta Crystallogr., F62, 569-571.

Oda, M., Uchiyama, S., Robinson, C.V., Fukui, K., Kobayashi, Y., and Azuma, T. (2006).
Regional and segmental flexibility of antibodies in the interaction with antigens of different size.
FEBS J., 273 (7), 1476-1487.

Izutani, Y., Kanaori, K., Imoto, T., and Oda, M. (2005).
Interaction of gymnemic acid with cyclodextrins analyzed by isothermal titration calorimetry,
NMR, and dynamic light scattering.
FEBS J., 272 (23), 6154-6160.

Izutani, Y., Murai, T., Imoto, T., Ohnishi, M., Oda, M., and Ishijima, S. (2005).
Gymnemic acids inhibit rabbit glyceraldehyde-3-phosphate dehydrogenase and induce
a smearing of its electrophoretic band and dephosphorylation.
FEBS Lett., 579 (20), 4333-4336.

Pang, Z., Otaka, K., Maoka, T., Hidaka, K., Ishijima, S., Oda, M., and Ohnishi, M. (2005).
Structure of β-glucan oligomer from laminarin and its effect on human monocytes
to inhibit the proliferation of U937 cells.
Biosci. Biotechnol. Biochem., 69 (3), 553-558. [PDF]

Saito, M., Okazaki, I., Oda, M., and Fujii, I. (2005).
A free energy calculation study of the effect of H→F substitution on binding affinity in ligand-antibody interactions.
J. Comp. Chem., 26 (3), 272-282.

Pang, Z., Kang, Y.-N., Ban, M., Oda, M., Kobayashi, R., Ohnishi, M., and Mikami, B. (2005).
Crystallization and preliminary crystallographic analysis of endo-1,3-β-glucanase from Arthrobacter sp.
Acta Crystallog. F61, 68-70.

Sagawa, T., Oda, M., Morii, H., Takizawa, H., Kozono, H., and Azuma, T. (2005).
Conformational changes in the antibody constant domains upon hapten binding.
Mol. Immunol., 42 (1), 9-18.

Saito, K.*, Oda, M.*, Sarai, A., Azuma, T, and Kozono, H. (2004).
Bound peptide-dependent thermal stability of major histocompatibility complex class II molecule I-Ek.
Biochemistry, 43 (31), 10186-10191. (*equal contributors)

Oda, M., Sato-Nakamura, N., and Azuma, T. (2004).
Molecular characterization of monovalent and multivalent hapten-protein conjugates
for analysis of the antigen-antibody interaction.
Anal. Biochem., 333 (2), 365-371.

Ueda, S., Oda, M., Imamura, S., and Ohnishi, M. (2004).
Kinetic study of the enzymatic cycling reaction conducted with 3α-hydroxysteroid
dehydrogenase in the presence of excessive thio-NAD+ and NADH.
Anal. Biochem., 332 (1), 84-89.

Ueda, S., Oda, M., Imamura, S., and Ohnishi, M. (2004).
Transient-phase kinetic studies on the nucleotide binding to 3α-hydroxysteroid
dehydrogenase from Pseudomonas sp. B-0831 using fluorescence stopped-flow procedures.
Eur. J. Biochem., 271 (9), 1774-1780.

Shimizu, T.*, Kozono, Y.*, Kozono, H., Oda, M., and Azuma, T. (2004).
Affinity maturation of secreted IgM pentamers on B cells.
Int. Immunol., 16 (5), 675-684. (*equal contributors) [PDF]

Saito, K., Oda, M., Sarai, A., Azuma, T, and Kozono, H. (2004).
Contribution of a single hydrogen bond between βHis81 of MHC class II I-Ek
and the bound peptide to the pH-dependent thermal stability.
Micro. Immunol., 48 (1), 53-57. [PDF]

Sugiyama, S., Kohyama, M., Oda, M., Azuma, T., Wither, J. E., and Hozumi, N. (2004).
Molecular basis of antigen recognition by insulin specific T cell receptor.
Immunol. Lett., 91 (2-3), 133-139.

Tobita, T.*, Oda, M.*, and Azuma, T. (2004).
Segmental flexibility and avidity of IgM in the interaction of polyvalent antigens.
Mol. Immunol., 40 (11), 803-811. (*equal contributors)

Saito, K., Sarai, A., Oda, M., Azuma, T, and Kozono, H. (2003).
Thermodynamic analysis of the increased stability of major histocompatibility complex class II
molecule I-Ek complexed with peptide at acidic pH.
J. Biol. Chem., 278 (17), 14732-14738. [PDF]

Shimizu, T., Oda, M., and Azuma, T. (2003).
Estimation of the relative affinity of B cell receptor by flow cytometry.
J. Immunol. Methods, 276 (1-2), 33-44.

Oda, M., Kozono, H., Morii, H., and Azuma, T. (2003).
Evidence of allosteric conformational changes in the antibody constant region upon antigen binding.
Int. Immunol., 15 (3), 417-426. [PDF]

Sagawa, T., Oda, M., Ishimura, M., Furukawa, K., and Azuma, T. (2003).
Thermodynamic and kinetic aspects of antigen evolution during the immune response to hapten.
Mol. Immunol., 39 (13), 801-808.

Tobita, T., Oda, M., Morii, H., Kuroda, M., Yoshino, A., Azuma, T., and Kozono, H. (2003).
A role for the P1 anchor residue in the thermal stability of MHC class II molecule I-Ab.
Immunol. Lett., 85 (1), 47-52.

Oda, M., Tamura, A., Kanaori, K., Kojima, S., Miura, K., Momma, K., Tonomura, B., and Akasaka, K. (2002).
Functional tolerance of Streptomyces subtilisin inhibitor toward conformational and stability changes
caused by single-point mutations in the hydrophobic core.
J. Biochem., 132 (6), 991-995.

Oda, M., and Azuma, T. (2000).
Reevaluation of stoichiometry and affinity/avidity in interactions between anti-hapten antibodies
and mono- or multi-valent antigens.
Mol. Immunol., 37 (18), 1111-1122.

Oda, M., Furukawa, K., Sarai, A., and Nakamura, H. (1999).
Construction of an artificial tandem protein of the c-Myb DNA-binding domain and analysis of its DNA binding specificity.
Biochem. Biophys. Res. Commun., 262 (1), 94-97.

Oda, M., Furukawa, K., Sarai, A., and Nakamura, H. (1999).
Kinetic analysis of DNA binding by the c-Myb DNA-binding domain using surface plasmon resonance.
FEBS Lett., 454 (3), 288-292.

Oda, M., Shiraishi, A., and Hasegawa, M. (1998).
Analysis of the ternary complex formation of human urokinase with the separated two domains of its receptor.
Eur. J. Biochem., 256 (2), 411-418. [PDF]

Oda, M., Furukawa, K., Ogata, K., Sarai, A., and Nakamura, H. (1998).
Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain.
J. Mol. Biol., 276 (3), 571-590.

Oda, M., Furukawa, K., Ogata, K., Sarai, A., Ishii, S., Nishimura, Y., and Nakamura, H. (1997).
Identification of indispensable residues for specific DNA-binding in the imperfect tandem repeats of c-Myb R2R3.
Protein Eng., 10 (12), 1407-1414.（Cover Illustration）[PDF]

Oda, M., Furukawa, K., Ogata, K., Sarai, A., Ishii, S., Nishimura, Y., and Nakamura, H. (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
J. Biol. Chem., 272 (29), 17966-17971. [PDF]

Last updated； February 2, 2010