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Yoshida M, Hanazono Y, Numoto N, Nagao S, Yabuno S, Kitagawa Y, Sekiguchi H, Ito N, Azuma T, Oda M. Affinity-matured antibody with a disulfide bond in H-CDR3 loop. Arch Biochem Biophys 2024; 758:110068. [PMID: 38909835 DOI: 10.1016/j.abb.2024.110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Affinity maturation increases antigen-binding affinity and specificity of antibodies by somatic hypermutation. Various monoclonal antibodies against (4-hydroxy-3-nitrophenyl)acetyl (NP) were obtained during affinity maturation. Among them, highly matured anti-NP antibodies, such as E11 and E3, possess Cys96H and Cys100H in the complementarity-determining region 3 of the heavy chain, which would form a disulfide bond. In this study, we evaluated the effects of disulfide bonds on antigen binding by generating single-chain Fv (scFv) antibodies of E11 and its mutants, E11_C96KH/C100EH and E11_C96KH/C100QH, and determined their antigen-binding thermodynamics and kinetics. The binding affinities of the Cys mutants were lower than that of E11 scFv, indicating that the disulfide bond contributed to antigen binding, especially for stable complex formation. This was also supported by the decreased affinity of E11 scFv in the presence of a reducing agent. The crystal structures of NP-free and NP-bound E11 scFvs were determined at high resolution, showing the existence of a disulfide bond between Cys96H and Cys100H, and the antigen recognition mechanism, which could be compared with those of other anti-NP antibodies, such as germline-type N1G9 and matured-type C6, as reported previously. These structures could explain the molecular basis of changes in antigen-binding affinity and thermal stability in the absence or presence of antigens. Small-angle X-ray scattering further showed a local conformational change in E11 scFv upon antigen binding in solution.
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Affiliation(s)
- Mutsumi Yoshida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Yuya Hanazono
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Satoshi Nagao
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Saaya Yabuno
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Yumi Kitagawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Takachika Azuma
- Antibody Technology Research Center, Inc., 2361-1Yamazaki, Noda, Chiba, 278-0022, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan.
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Sasaki YC. Diffracted X-ray Tracking for Observing the Internal Motions of Individual Protein Molecules and Its Extended Methodologies. Int J Mol Sci 2023; 24:14829. [PMID: 37834277 PMCID: PMC10573657 DOI: 10.3390/ijms241914829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
In 1998, the diffracted X-ray tracking (DXT) method pioneered the attainment of molecular dynamics measurements within individual molecules. This breakthrough revolutionized the field by enabling unprecedented insights into the complex workings of molecular systems. Similar to the single-molecule fluorescence labeling technique used in the visible range, DXT uses a labeling method and a pink beam to closely track the diffraction pattern emitted from the labeled gold nanocrystals. Moreover, by utilizing X-rays with extremely short wavelengths, DXT has achieved unparalleled accuracy and sensitivity, exceeding initial expectations. As a result, this remarkable advance has facilitated the search for internal dynamics within many protein molecules. DXT has recently achieved remarkable success in elucidating the internal dynamics of membrane proteins in living cell membranes. This breakthrough has not only expanded our knowledge of these important biomolecules but also has immense potential to advance our understanding of cellular processes in their native environment.
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Affiliation(s)
- Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Chiba 277-8561, Japan;
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 6-2-3 Kashiwanoha, Chiba 277-0882, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho 679-5198, Japan
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Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023; 24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Although many protein structures have been determined at atomic resolution, the majority of them are static and represent only the most stable or averaged structures in solution. When a protein binds to its ligand, it usually undergoes fluctuation and changes its conformation. One attractive method for obtaining an accurate view of proteins in solution, which is required for applications such as the rational design of proteins and structure-based drug design, is diffracted X-ray tracking (DXT). DXT can detect the protein structural dynamics on a timeline via gold nanocrystals attached to the protein. Here, the structure dynamics of single-chain Fv antibodies, helix bundle-forming de novo designed proteins, and DNA-binding proteins in both ligand-unbound and ligand-bound states were analyzed using the DXT method. The resultant mean square angular displacements (MSD) curves in both the tilting and twisting directions clearly demonstrated that structural fluctuations were suppressed upon ligand binding, and the binding energies determined using the angular diffusion coefficients from the MSD agreed well with the binding thermodynamics determined using isothermal titration calorimetry. In addition, the size of gold nanocrystals is discussed, which is one of the technical concerns of DXT.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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Oda M. Structural, functional, and physiological properties of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during the course of affinity maturation. Biophys Rev 2022; 14:1521-1526. [PMID: 36659986 PMCID: PMC9842813 DOI: 10.1007/s12551-022-01008-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 01/22/2023] Open
Abstract
Structural and functional analyses of antibodies in the affinity maturation pathway can help us understand the molecular mechanisms of protein recognition. Using one of the haptens, (4-hydroxy-3-nitrophenyl)acetyl (NP), various monoclonal antibodies have been obtained, either at the early or late stage of immunization. The variable regions of monoclonal antibodies and their site-directed mutants can also be obtained as single-chain Fv (scFv) antibodies. The change in antigen-binding affinity and avidity of matured-type antibodies from germline-type antibodies could be evaluated based on binding kinetics and thermodynamics, proposing the antigen recognition mode. Crystal structures of a germline-type antibody, N1G9, and a matured-type antibody, C6, in complex with NP were determined, revealing different antigen-binding mode at atomic resolution. Notably, the Tyr to Gly mutation at the 95th residue of the heavy chain is critical for changing the configuration of complementarity determining region 3, which is involved in antigen binding. Furthermore, thermal stability analyses of scFv antibodies have revealed trade-off between antigen-binding affinity and thermal stability in the antigen-unbound state. To increase affinity, the stability of the variable region may be decreased, possibly due to protein architecture. The high stability of germline-type antibodies and the low stability of matured-type antibodies, which increase upon antigen binding, can be explained by the stability of antibodies required at the respective stages of immunization.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522 Japan
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A Trade-off Between Thermostability and Binding Affinity of Anti-(4-hydroxy-3-nitrophenyl)Acetyl Antibodies During the Course of Affinity Maturation. Protein J 2022; 41:293-303. [DOI: 10.1007/s10930-022-10053-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
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Hosoe Y, Sekiguchi H, Sasaki YC, Oda M. Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking. Biophys Chem 2021; 278:106669. [PMID: 34416518 DOI: 10.1016/j.bpc.2021.106669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Diffracted X-ray tracking (DXT) is one of methods for the real-time evaluation of protein structural dynamics by detecting the movement of a gold-nanocrystal attached to a target protein. However, one of the technical concerns is the size of the gold-nanocrystals, which are larger than the protein. In our previous results of mean square angular displacement curves in DXT analysis, dynamical movements of the DNA-binding protein, c-Myb R2R3, were observed in only one population in either DNA-unbound or -bound state, and was found to decrease upon DNA binding. In this study, c-Myb R2R3 dynamical movements were re-evaluated with a low density of the protein immobilized on the DXT substrate, to decrease the possibility that the gold-nanocrystals attached to more than one R2R3 molecule. We observed two dynamical moving populations in the DNA-bound state, which could be classified due to electrostatic attraction and repulsion between the DNA-protein complexes, and determined the apparent angular diffusion constant, which was similar to the value calculated in our previous study. We showed more real movement of the protein could be observed by lowering the immobilization density of the protein.
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Affiliation(s)
- Yuhi Hosoe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yuji C Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan.
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Hayashi T, Kawasaki M, Kamatari YO, Oda M. Single-chain Fv antibody covalently linked to antigen peptides and its structural evaluation. Anal Biochem 2021; 629:114312. [PMID: 34302799 DOI: 10.1016/j.ab.2021.114312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 11/17/2022]
Abstract
The monoclonal antibody G2 specifically recognizes different peptides. The single-chain Fv (scFv) antibodies of G2 covalently linked to antigen peptides, Pep18mer and Pep395, via a flexible linker were expressed in Escherichia coli in the insoluble fraction, and were solubilized using guanidine HCl, followed by refolding. We analyzed the folding thermodynamics of the refolded proteins, purified as monomers using size-exclusion chromatography (SEC). The results of the differential scanning calorimetry (DSC) showed that the thermal stabilities of antigen peptide-linked G2 scFvs were higher than those of antigen-free G2 scFv in the absence or presence of antigen peptides. The folding thermodynamics further indicated how the antigen-antibody affinity affect the intramolecular interactions. The combination of SEC and DSC experiments could confirm the folding correctness of antigen peptide-linked G2 scFvs and could be applied for "structural screening" of refolded proteins in the case that the "functional screening" like antigen binding is difficult to apply. The present method to covalently link the peptide would contribute to the stable complex structure, and would be widely applied to other antibodies recognizing peptide antigens.
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Affiliation(s)
- Takahiro Hayashi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Maki Kawasaki
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan.
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Kawasaki M, Hosoe Y, Kamatari YO, Oda M. Naïve balance between structural stability and DNA-binding ability of c-Myb R2R3 under physiological ionic conditions. Biophys Chem 2020; 258:106319. [DOI: 10.1016/j.bpc.2019.106319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/26/2019] [Accepted: 12/31/2019] [Indexed: 01/22/2023]
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Yamaoka T, Kamatari YO, Maruno T, Kobayashi Y, Oda M. Structural and functional evaluation of single-chain Fv antibody HyC1 recognizing the residual native structure of hen egg lysozyme. Biosci Biotechnol Biochem 2020; 84:358-364. [DOI: 10.1080/09168451.2019.1683441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABSTRACT
Evaluation of the molecular mechanisms by which an antibody recognizes a specific antigen could help in better understanding of the protein recognition mechanisms. We previously showed that anti-hen egg lysozyme (HEL) monoclonal antibody, HyC1, recognized the structural and hydrodynamic change in HEL. Here, we generated HyC1 single-chain Fv (scFv), and characterized it using different structural and biophysical methods. Similar to HyC1 monoclonal antibody, HyC1 scFv could recognize native HEL from carboxymethylated Cys6 and Cys127 HEL (CM6,127-HEL). Comparison of the binding thermodynamics of HyC1 scFv between HEL and CM6,127-HEL showed that the binding enthalpy change was different, while the binding entropy was remained unchanged. The results indicated that the fluctuation of the residual native structure in both HEL and CM6,127-HEL was similar. The NMR experiments for 15N-labeled HyC1 scFv indicated that the flexibility of HyC1 scFv decreased upon the binding to HEL.
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Affiliation(s)
- Takanori Yamaoka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | | | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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Nishiguchi A, Numoto N, Ito N, Azuma T, Oda M. Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Mol Immunol 2019; 114:545-552. [DOI: 10.1016/j.molimm.2019.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Accepted: 09/02/2019] [Indexed: 10/26/2022]
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Hosoe Y, Inaba S, Sekiguchi H, Sasaki YC, Oda M. DNA-binding induced conformational change of c-Myb R2R3 analyzed using diffracted X-ray tracking. Biochem Biophys Res Commun 2018; 503:338-343. [DOI: 10.1016/j.bbrc.2018.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 11/29/2022]
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Usui D, Inaba S, Kamatari YO, Ishiguro N, Oda M. Light-chain residue 95 is critical for antigen binding and multispecificity of monoclonal antibody G2. Biochem Biophys Res Commun 2017; 490:1205-1209. [DOI: 10.1016/j.bbrc.2017.06.183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/29/2017] [Indexed: 11/28/2022]
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Usui D, Inaba S, Sekiguchi H, Sasaki YC, Tanaka T, Oda M. First observation of metal ion-induced structural fluctuations of α-helical peptides by using diffracted X-ray tracking. Biophys Chem 2017; 228:81-86. [DOI: 10.1016/j.bpc.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
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Sato Y, Inaba S, Fukada H, Azuma T, Oda M. Pronounced effect of hapten binding on thermal stability of an anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Mol Immunol 2017; 85:130-136. [DOI: 10.1016/j.molimm.2017.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/13/2017] [Accepted: 02/18/2017] [Indexed: 10/20/2022]
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Miki A, Inaba S, Maruno T, Kobayashi Y, Oda M. Tryptophan introduction can change β-glucan binding ability of the carbohydrate-binding module of endo-1,3-β-glucanase. Biosci Biotechnol Biochem 2017; 81:951-957. [PMID: 28388361 DOI: 10.1080/09168451.2017.1285687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/13/2017] [Indexed: 10/20/2022]
Abstract
Endo-1,3-β-glucanase from Cellulosimicrobium cellulans DK-1 has a carbohydrate-binding module (CBM-DK) at the C-terminal side of a catalytic domain. Out of the imperfect tandem α-, β-, and γ-repeats in CBM-DK, the α-repeat primarily contributes to β-glucan binding. This unique feature is derived from Trp273 in α-repeat, whose corresponding residues in β- and γ-repeats are Asp314 and Gly358, respectively. In this study, we generated Trp-switched mutants, W273A/D314W, D270A/W273A/D314W, W273A/G358W, and D270A/W273A/G358W, and analyzed their binding abilities toward laminarioligosaccharides and laminarin. While the binding affinities of D270A/W273A and W273A mutants were either lost or much lower than that of the wild-type, those of Trp-switched mutants recovered, indicating that a Trp introduction in β- or γ-repeat can substitute the α-repeat by primarily contributing to β-glucan binding. Thus, we have successfully engineered a CBM-DK that binds to laminarin by a mechanism different from that of the wild-type, but with similar affinity.
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Affiliation(s)
- Ayako Miki
- a Graduate School of Life and Environmental Sciences, Kyoto Prefectural University , Kyoto , Japan
| | - Satomi Inaba
- a Graduate School of Life and Environmental Sciences, Kyoto Prefectural University , Kyoto , Japan
| | - Takahiro Maruno
- b Graduate School of Engineering, Osaka University , Suita , Japan
| | - Yuji Kobayashi
- b Graduate School of Engineering, Osaka University , Suita , Japan
| | - Masayuki Oda
- a Graduate School of Life and Environmental Sciences, Kyoto Prefectural University , Kyoto , Japan
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