Affinity Maturation for Antibody Engineering: The Critical Role of Residues on CDR Loops of Antibodies in Antigen Binding.

Authors: Yoshida, Mutsumi¹ (AUTHOR), Oda, Masayuki¹ (AUTHOR) oda@kpu.ac.jp

Source: Molecules. Feb2025, Vol. 30 Issue 3, p532. 12p.

Subject Terms: *ISOTHERMAL titration calorimetry, *IMMUNOTECHNOLOGY, *STRUCTURAL dynamics, *CRYSTAL structure, *THERMAL stability

Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity

Authors: Numoto, Nobutaka, Kondo, Fumiya, Bekker, Gert-Jan, Liao, Zengwei, Yamashita, Mitsuaki, Iida, Akira, Ito, Nobutoshi, Kamiya, Narutoshi, Oda, Masayuki

Source: In International Journal of Biological Macromolecules November 2024 281 Part 4

Construction of a Tm-value prediction model and molecular dynamics study of AmNA-containing gapmer antisense oligonucleotide

Authors: Kuroda, Masataka, Kasahara, Yuuya, Hirose, Masako, Yamaguma, Harumi, Oda, Masayuki, Nagao, Chioko, Mizuguchi, Kenji

Source: In Molecular Therapy - Nucleic Acids 10 September 2024 35(3)

Affinity-matured antibody with a disulfide bond in H-CDR3 loop

Authors: Yoshida, Mutsumi, Hanazono, Yuya, Numoto, Nobutaka, Nagao, Satoshi, Yabuno, Saaya, Kitagawa, Yumi, Sekiguchi, Hiroshi, Ito, Nobutoshi, Azuma, Takachika, Oda, Masayuki

Source: In Archives of Biochemistry and Biophysics August 2024 758

Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states

Authors: Hosoe, Yuhi, Miyanoiri, Yohei, Re, Suyong, Ochi, Saki, Asahina, Yuya, Kawakami, Toru, Kuroda, Masataka, Mizuguchi, Kenji, Oda, Masayuki

Source: FEBS journal. 290(9):2366-2378

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195605107.0x000001&indx=1&recIds=ETOCvdc_100195605107.0x000001

Metal-binding and folding thermodynamics of Escherichia coli ribonuclease HI related to its catalytic function

Authors: Kitagawa, Yumi, Liao, Zengwei, Morikawa, Kosuke, Oda, Masayuki

Source: In Biophysical Chemistry April 2023 295

Role of Cys residues of C-terminal SH2 domain of phosphoinositide 3-kinase in its conformational stability and CD28-binding ability

Authors: Iiyama, Momoka, Hantani, Yoshiji, Wink, Rene H., Kuroda, Masataka, Oda, Masayuki

Source: In Chemical Thermodynamics and Thermal Analysis December 2022 8

Evaluation of multi-specificity of antibody G2 using its single-chain Fv and its covalently linked antigen peptides

Authors: Hayashi, Takahiro, Kamatari, Yuji O., Oda, Masayuki

Source: In Biophysical Chemistry November 2022 290

Monoclonal antibodies against jellyfish collagen.

Authors: Momma, Keiko, Shimizu, Takeyuki, Hayashi, Takahiro, Hirakawa, Yuki, Kuroda, Masataka, Oda, Masayuki

Source: Journal of Biomaterials Applications; Feb2025, Vol. 39 Issue 7, p807-815, 9p

Subject Terms: SURFACE plasmon resonance, AMINO acid sequence, CYTOSKELETAL proteins, SCALES (Fishes), JELLYFISHES

Interdomain interactions in Grb2 revealed by the conformational stability and CD28 binding analysis

Authors: Ochi, Saki, Iiyama, Momoka, Oda, Masayuki

Source: In Biophysical Chemistry May 2022 284

Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking

Authors: Hosoe, Yuhi, Sekiguchi, Hiroshi, Sasaki, Yuji C., Oda, Masayuki

Source: In Biophysical Chemistry November 2021 278

Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding

Authors: Tanaka, Masahiro, Kato, Tatsuhisa, Oda, Masayuki

Source: In Biophysical Chemistry October 2021 277

Single-chain Fv antibody covalently linked to antigen peptides and its structural evaluation

Authors: Hayashi, Takahiro, Kawasaki, Maki, Kamatari, Yuji O., Oda, Masayuki

Source: In Analytical Biochemistry 15 September 2021 629

Effects of chain length, temperature, and ionic strength on association and dissociation thermodynamics of DNA

Authors: Kawasaki, Maki, Oda, Masayuki

Source: In Chemical Thermodynamics and Thermal Analysis September 2021 3-4

Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains

Authors: Iiyama, Momoka, Numoto, Nobutaka, Ogawa, Shuhei, Kuroda, Masataka, Morii, Hisayuki, Abe, Ryo, Ito, Nobutoshi, Oda, Masayuki ^*

Source: In Molecular Immunology March 2021 131:51-59

Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking.

Authors: Oda, Masayuki¹ (AUTHOR) oda@kpu.ac.jp

Source: International Journal of Molecular Sciences. Sep2023, Vol. 24 Issue 18, p13717. 11p.

Subject Terms: *CYTOSKELETAL proteins, *STRUCTURAL dynamics, *DNA-binding proteins, *ISOTHERMAL titration calorimetry, *LIGAND binding (Biochemistry), *X-ray scattering

Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridisAHK190 with high activity and thermal stability

Authors: Emori, Miho, Numoto, Nobutaka, Senga, Akane, Bekker, Gert‐Jan, Kamiya, Narutoshi, Kobayashi, Yuma, Ito, Nobutoshi, Kawai, Fusako, Oda, Masayuki

Source: Proteins. 89(5):502-511

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100119370979.0x000001&indx=1&recIds=ETOCvdc_100119370979.0x000001

A synergy of activity, stability, and inhibitor‐interaction of HIV‐1 protease mutants evolved under drug‐pressure

Authors: Khan, Shahid N., Persons, John D., Guerrero, Michel, Ilina, Tatiana V., Oda, Masayuki, Ishima, Rieko

Source: Protein science. 30(3):571-582

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100115469303.0x000001&indx=1&recIds=ETOCvdc_100115469303.0x000001

Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02

Authors: Bekker, Gert‐Jan, Numoto, Nobutaka, Kawasaki, Maki, Hayashi, Takahiro, Yabuno, Saaya, Kozono, Yuko, Shimizu, Takeyuki, Kozono, Haruo, Ito, Nobutoshi, Oda, Masayuki, Kamiya, Narutoshi

Source: Protein science. 32(10)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195918293.0x000001&indx=1&recIds=ETOCvdc_100195918293.0x000001

Naïve balance between structural stability and DNA-binding ability of c-Myb R2R3 under physiological ionic conditions

Authors: Kawasaki, Maki, Hosoe, Yuhi, Kamatari, Yuji O., Oda, Masayuki

Source: In Biophysical Chemistry March 2020 258