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MAXTIA: A high-throughput platform for rapid functional epitope mapping by kinetic screening of mutant libraries.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: MAXTIA: A high-throughput platform for rapid functional epitope mapping by kinetic screening of mutant libraries.
Συγγραφείς: Kim K; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan., Matsunaga R; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan., Yokoo T; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan., Nakakido M; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan., Tsumoto K; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.; The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Πηγή: Protein science : a publication of the Protein Society [Protein Sci] 2026 Sep; Vol. 35 (9), pp. e70769.
Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE
Imprint Name(s): Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, N.Y. : Cambridge University Press, c1992-
Ιατρικοί όροι (MeSH): Epitope Mapping*/methods , Epitopes*/chemistry , Epitopes*/genetics , Epitopes*/immunology , High-Throughput Screening Assays*/methods , C-Reactive Protein*/chemistry , C-Reactive Protein*/genetics , C-Reactive Protein*/immunology, Kinetics ; Surface Plasmon Resonance ; Models, Molecular ; Mutation
Περίληψη: Accurate identification of epitope residues is essential for developing biopharmaceuticals and understanding the mechanisms of immune recognition. However, experimental approaches for residue-level epitope mapping remain time-consuming and labor-intensive, while accurate computational prediction of protein-protein interfaces remains challenging. Here, we present MAXTIA, a high-throughput kinetic screening platform that integrates cell-free protein synthesis with high-throughput surface plasmon resonance and demonstrate its application to alanine scanning-based functional epitope mapping. This workflow enables the rapid preparation and kinetic characterization of up to 384 protein variants, allowing the identification of functional epitope residues within 3 days while simultaneously providing binding affinity and kinetic parameters (KD, kon, and koff). We applied MAXTIA to map the epitope of the single-domain antibody (VHH) N1 against the pentraxin domain of neuronal pentraxin-2 (NP2 PTX). Alanine substitutions that cause substantial affinity losses clustered within a localized region on the AlphaFold3-predicted NP2 PTX structure, defining a functional epitope site. These residues closely matched the interface observed in the NP2 PTX-VHH N1 crystal structure, validating the accuracy of MAXTIA. Beyond epitope identification, MAXTIA provides a simple and versatile platform for the quantitative analysis of protein-protein interactions, including high-throughput screening of antibody variants for affinity optimization. This approach should accelerate biopharmaceutical development and facilitate mechanistic studies of molecular recognition.
(© 2026 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)
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Curr Protoc Mol Biol. 2014 Oct 01;108:16.30.1-16.30.11. (PMID: 25271714)
Electrophoresis. 1997 Dec;18(15):2714-23. (PMID: 9504803)
Clin Exp Allergy. 2019 Jan;49(1):17-26. (PMID: 30294841)
Commun Biol. 2024 Jul 3;7(1):805. (PMID: 38961245)
PLoS One. 2022 Jan 25;17(1):e0248666. (PMID: 35077448)
Chem Rev. 2024 Nov 13;124(21):12242-12263. (PMID: 39481095)
J Thromb Haemost. 2013 Dec;11(12):2128-36. (PMID: 24152306)
Glycobiology. 2023 Jun 3;33(5):358-363. (PMID: 36882003)
J Immunol Res. 2015;2015:156241. (PMID: 26526043)
Immunology. 2014 May;142(1):1-23. (PMID: 24219801)
Mol Cell Proteomics. 2024 Nov;23(11):100853. (PMID: 39383946)
PLoS One. 2013 Oct 30;8(10):e78878. (PMID: 24205336)
Protein Sci. 2026 Sep;35(9):e70769. (PMID: 42606277)
Methods Enzymol. 2016;580:21-44. (PMID: 27586327)
Front Anal Sci. 2023;3:. (PMID: 37746528)
J Mol Biol. 1996 Apr 19;257(5):1112-26. (PMID: 8632471)
Protein Sci. 1999 May;8(5):958-68. (PMID: 10338006)
Synth Biol (Oxf). 2019 Oct 29;4(1):ysz025. (PMID: 32995546)
Immunology. 2014 Aug;142(4):526-35. (PMID: 24635566)
Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14652-7. (PMID: 12409616)
Nat Protoc. 2007;2(6):1333-49. (PMID: 17545971)
PLoS One. 2013 Sep 02;8(9):e74320. (PMID: 24023934)
RSC Chem Biol. 2025 Jun 23;6(8):1313-1327. (PMID: 40655043)
J Biol Chem. 2025 Jan;301(1):108072. (PMID: 39674321)
Front Bioeng Biotechnol. 2021 Jul 20;9:715328. (PMID: 34354989)
Cell Mol Immunol. 2021 Aug;18(8):1847-1860. (PMID: 34117370)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
Biochemistry. 2020 Oct 13;59(40):3802-3812. (PMID: 32997500)
Nucleic Acids Res. 2018 Feb 28;46(4):e21. (PMID: 29202193)
ACS Synth Biol. 2023 Jul 21;12(7):1935-1942. (PMID: 37328154)
Protein Sci. 2023 Nov;32(11):e4785. (PMID: 37733481)
Bioinformatics. 2012 Mar 15;28(6):784-91. (PMID: 22210869)
Nat Biotechnol. 2001 Aug;19(8):751-5. (PMID: 11479568)
Commun Biol. 2025 Mar 21;8(1):468. (PMID: 40119113)
PLoS One. 2013 Jul 23;8(7):e68902. (PMID: 23894373)
MAbs. 2023 Jan-Dec;15(1):2285285. (PMID: 38010385)
Front Immunol. 2024 Apr 11;15:1329013. (PMID: 38665908)
J Comput Chem. 2006 Nov 30;27(15):1843-57. (PMID: 16981237)
Immunome Res. 2010 Oct 20;6:6. (PMID: 20961417)
BioDrugs. 2020 Jun;34(3):327-348. (PMID: 32198631)
J Immunol Res. 2016;2016:6760830. (PMID: 28127568)
Immunology. 2014 Sep;143(1):13-20. (PMID: 24854488)
J Biol Chem. 2026 Jan;302(1):110975. (PMID: 41308985)
Biochem Biophys Res Commun. 2005 Mar 4;328(1):98-105. (PMID: 15670756)
Protein Sci. 2024 Jun;33(6):e5029. (PMID: 38801228)
BioDrugs. 2007;21(3):145-56. (PMID: 17516710)
J Mol Biol. 1993 Dec 5;234(3):554-63. (PMID: 7504735)
Front Immunol. 2024 Sep 30;15:1463931. (PMID: 39403389)
Protein Sci. 2025 Mar;34(3):e70065. (PMID: 39981938)
Front Immunol. 2013 Oct 08;4:302. (PMID: 24115948)
J Immunol Methods. 2015 Jan;416:105-23. (PMID: 25445329)
Structure. 2008 Feb;16(2):280-94. (PMID: 18275819)
Microscopy (Oxf). 2016 Feb;65(1):9-22. (PMID: 26611544)
J Mol Biol. 1998 Jul 3;280(1):1-9. (PMID: 9653027)
Commun Biol. 2024 Sep 17;7(1):1159. (PMID: 39289580)
Grant Information: JPMJAX222I Japan Science and Technology Agency; JP223fa627001 Japan Agency for Medical Research and Development; JP223fa727002 Japan Agency for Medical Research and Development; 22K21343 Japan Society for the Promotion of Science London; JPMXP1122714694 Ministry of Education, Culture, Sports, Science and Technology
Contributed Indexing: Keywords: cell‐free protein synthesis; epitope mapping; high‐throughput experimental system; interaction analysis; kinetic screening; protein engineering
Substance Nomenclature: 0 (Epitopes)
9007-41-4 (C-Reactive Protein)
Entry Date(s): Date Created: 20260817 Date Completed: 20260817 Latest Revision: 20260902
Update Code: 20260903
PubMed Central ID: PMC13479966
DOI: 10.1002/pro.70769
PMID: 42606277
Βάση Δεδομένων: MEDLINE
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  Data: MAXTIA: A high-throughput platform for rapid functional epitope mapping by kinetic screening of mutant libraries.
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  Data: <searchLink fieldCode="AU" term="%22Kim+K%22">Kim K</searchLink>; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.<br /><searchLink fieldCode="AU" term="%22Matsunaga+R%22">Matsunaga R</searchLink>; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.<br /><searchLink fieldCode="AU" term="%22Yokoo+T%22">Yokoo T</searchLink>; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.<br /><searchLink fieldCode="AU" term="%22Nakakido+M%22">Nakakido M</searchLink>; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.<br /><searchLink fieldCode="AU" term="%22Tsumoto+K%22">Tsumoto K</searchLink>; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.; The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Cold+Spring+Harbor+Laboratory+Press%22">Cold Spring Harbor Laboratory Press </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>9211750 <i>Publication Model: </i>Print <i>Cited Medium: </i>Internet <i>ISSN: </i>1469-896X (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2209618368%22">09618368 </searchLink><i>NLM ISO Abbreviation: </i>Protein Sci <i>Subsets: </i>MEDLINE
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  Data: Accurate identification of epitope residues is essential for developing biopharmaceuticals and understanding the mechanisms of immune recognition. However, experimental approaches for residue-level epitope mapping remain time-consuming and labor-intensive, while accurate computational prediction of protein-protein interfaces remains challenging. Here, we present MAXTIA, a high-throughput kinetic screening platform that integrates cell-free protein synthesis with high-throughput surface plasmon resonance and demonstrate its application to alanine scanning-based functional epitope mapping. This workflow enables the rapid preparation and kinetic characterization of up to 384 protein variants, allowing the identification of functional epitope residues within 3 days while simultaneously providing binding affinity and kinetic parameters (K<subscript>D</subscript>, k<subscript>on</subscript>, and k<subscript>off</subscript>). We applied MAXTIA to map the epitope of the single-domain antibody (VHH) N1 against the pentraxin domain of neuronal pentraxin-2 (NP2 PTX). Alanine substitutions that cause substantial affinity losses clustered within a localized region on the AlphaFold3-predicted NP2 PTX structure, defining a functional epitope site. These residues closely matched the interface observed in the NP2 PTX-VHH N1 crystal structure, validating the accuracy of MAXTIA. Beyond epitope identification, MAXTIA provides a simple and versatile platform for the quantitative analysis of protein-protein interactions, including high-throughput screening of antibody variants for affinity optimization. This approach should accelerate biopharmaceutical development and facilitate mechanistic studies of molecular recognition.<br /> (© 2026 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)
– Name: Ref
  Label: References
  Group: RefInfo
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(PMID: <searchLink fieldCode="PM" term="%2224152306%22">24152306)</searchLink><br />Glycobiology. 2023 Jun 3;33(5):358-363. (PMID: <searchLink fieldCode="PM" term="%2236882003%22">36882003)</searchLink><br />J Immunol Res. 2015;2015:156241. (PMID: <searchLink fieldCode="PM" term="%2226526043%22">26526043)</searchLink><br />Immunology. 2014 May;142(1):1-23. (PMID: <searchLink fieldCode="PM" term="%2224219801%22">24219801)</searchLink><br />Mol Cell Proteomics. 2024 Nov;23(11):100853. (PMID: <searchLink fieldCode="PM" term="%2239383946%22">39383946)</searchLink><br />PLoS One. 2013 Oct 30;8(10):e78878. (PMID: <searchLink fieldCode="PM" term="%2224205336%22">24205336)</searchLink><br />Protein Sci. 2026 Sep;35(9):e70769. (PMID: <searchLink fieldCode="PM" term="%2242606277%22">42606277)</searchLink><br />Methods Enzymol. 2016;580:21-44. (PMID: <searchLink fieldCode="PM" term="%2227586327%22">27586327)</searchLink><br />Front Anal Sci. 2023;3:. (PMID: <searchLink fieldCode="PM" term="%2237746528%22">37746528)</searchLink><br />J Mol Biol. 1996 Apr 19;257(5):1112-26. (PMID: <searchLink fieldCode="PM" term="%228632471%22">8632471)</searchLink><br />Protein Sci. 1999 May;8(5):958-68. (PMID: <searchLink fieldCode="PM" term="%2210338006%22">10338006)</searchLink><br />Synth Biol (Oxf). 2019 Oct 29;4(1):ysz025. (PMID: <searchLink fieldCode="PM" term="%2232995546%22">32995546)</searchLink><br />Immunology. 2014 Aug;142(4):526-35. (PMID: <searchLink fieldCode="PM" term="%2224635566%22">24635566)</searchLink><br />Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14652-7. (PMID: <searchLink fieldCode="PM" term="%2212409616%22">12409616)</searchLink><br />Nat Protoc. 2007;2(6):1333-49. (PMID: <searchLink fieldCode="PM" term="%2217545971%22">17545971)</searchLink><br />PLoS One. 2013 Sep 02;8(9):e74320. (PMID: <searchLink fieldCode="PM" term="%2224023934%22">24023934)</searchLink><br />RSC Chem Biol. 2025 Jun 23;6(8):1313-1327. (PMID: <searchLink fieldCode="PM" term="%2240655043%22">40655043)</searchLink><br />J Biol Chem. 2025 Jan;301(1):108072. (PMID: <searchLink fieldCode="PM" term="%2239674321%22">39674321)</searchLink><br />Front Bioeng Biotechnol. 2021 Jul 20;9:715328. (PMID: <searchLink fieldCode="PM" term="%2234354989%22">34354989)</searchLink><br />Cell Mol Immunol. 2021 Aug;18(8):1847-1860. (PMID: <searchLink fieldCode="PM" term="%2234117370%22">34117370)</searchLink><br />Nature. 2024 Jun;630(8016):493-500. (PMID: <searchLink fieldCode="PM" term="%2238718835%22">38718835)</searchLink><br />Biochemistry. 2020 Oct 13;59(40):3802-3812. (PMID: <searchLink fieldCode="PM" term="%2232997500%22">32997500)</searchLink><br />Nucleic Acids Res. 2018 Feb 28;46(4):e21. (PMID: <searchLink fieldCode="PM" term="%2229202193%22">29202193)</searchLink><br />ACS Synth Biol. 2023 Jul 21;12(7):1935-1942. (PMID: <searchLink fieldCode="PM" term="%2237328154%22">37328154)</searchLink><br />Protein Sci. 2023 Nov;32(11):e4785. (PMID: <searchLink fieldCode="PM" term="%2237733481%22">37733481)</searchLink><br />Bioinformatics. 2012 Mar 15;28(6):784-91. (PMID: <searchLink fieldCode="PM" term="%2222210869%22">22210869)</searchLink><br />Nat Biotechnol. 2001 Aug;19(8):751-5. (PMID: <searchLink fieldCode="PM" term="%2211479568%22">11479568)</searchLink><br />Commun Biol. 2025 Mar 21;8(1):468. (PMID: <searchLink fieldCode="PM" term="%2240119113%22">40119113)</searchLink><br />PLoS One. 2013 Jul 23;8(7):e68902. (PMID: <searchLink fieldCode="PM" term="%2223894373%22">23894373)</searchLink><br />MAbs. 2023 Jan-Dec;15(1):2285285. (PMID: <searchLink fieldCode="PM" term="%2238010385%22">38010385)</searchLink><br />Front Immunol. 2024 Apr 11;15:1329013. (PMID: <searchLink fieldCode="PM" term="%2238665908%22">38665908)</searchLink><br />J Comput Chem. 2006 Nov 30;27(15):1843-57. (PMID: <searchLink fieldCode="PM" term="%2216981237%22">16981237)</searchLink><br />Immunome Res. 2010 Oct 20;6:6. (PMID: <searchLink fieldCode="PM" term="%2220961417%22">20961417)</searchLink><br />BioDrugs. 2020 Jun;34(3):327-348. (PMID: <searchLink fieldCode="PM" term="%2232198631%22">32198631)</searchLink><br />J Immunol Res. 2016;2016:6760830. (PMID: <searchLink fieldCode="PM" term="%2228127568%22">28127568)</searchLink><br />Immunology. 2014 Sep;143(1):13-20. (PMID: <searchLink fieldCode="PM" term="%2224854488%22">24854488)</searchLink><br />J Biol Chem. 2026 Jan;302(1):110975. (PMID: <searchLink fieldCode="PM" term="%2241308985%22">41308985)</searchLink><br />Biochem Biophys Res Commun. 2005 Mar 4;328(1):98-105. (PMID: <searchLink fieldCode="PM" term="%2215670756%22">15670756)</searchLink><br />Protein Sci. 2024 Jun;33(6):e5029. (PMID: <searchLink fieldCode="PM" term="%2238801228%22">38801228)</searchLink><br />BioDrugs. 2007;21(3):145-56. (PMID: <searchLink fieldCode="PM" term="%2217516710%22">17516710)</searchLink><br />J Mol Biol. 1993 Dec 5;234(3):554-63. (PMID: <searchLink fieldCode="PM" term="%227504735%22">7504735)</searchLink><br />Front Immunol. 2024 Sep 30;15:1463931. (PMID: <searchLink fieldCode="PM" term="%2239403389%22">39403389)</searchLink><br />Protein Sci. 2025 Mar;34(3):e70065. (PMID: <searchLink fieldCode="PM" term="%2239981938%22">39981938)</searchLink><br />Front Immunol. 2013 Oct 08;4:302. (PMID: <searchLink fieldCode="PM" term="%2224115948%22">24115948)</searchLink><br />J Immunol Methods. 2015 Jan;416:105-23. (PMID: <searchLink fieldCode="PM" term="%2225445329%22">25445329)</searchLink><br />Structure. 2008 Feb;16(2):280-94. (PMID: <searchLink fieldCode="PM" term="%2218275819%22">18275819)</searchLink><br />Microscopy (Oxf). 2016 Feb;65(1):9-22. (PMID: <searchLink fieldCode="PM" term="%2226611544%22">26611544)</searchLink><br />J Mol Biol. 1998 Jul 3;280(1):1-9. (PMID: <searchLink fieldCode="PM" term="%229653027%22">9653027)</searchLink><br />Commun Biol. 2024 Sep 17;7(1):1159. (PMID: <searchLink fieldCode="PM" term="%2239289580%22">39289580)</searchLink>
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  Data: JPMJAX222I Japan Science and Technology Agency; JP223fa627001 Japan Agency for Medical Research and Development; JP223fa727002 Japan Agency for Medical Research and Development; 22K21343 Japan Society for the Promotion of Science London; JPMXP1122714694 Ministry of Education, Culture, Sports, Science and Technology
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  Data: <i>Keywords: </i>cell‐free protein synthesis; epitope mapping; high‐throughput experimental system; interaction analysis; kinetic screening; protein engineering
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        StartPage: e70769
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      – SubjectFull: Kinetics
        Type: general
      – SubjectFull: Surface Plasmon Resonance
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      – SubjectFull: Models, Molecular
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      – SubjectFull: Mutation
        Type: general
      – SubjectFull: Epitope Mapping methods
        Type: general
      – SubjectFull: Epitopes chemistry
        Type: general
      – SubjectFull: Epitopes genetics
        Type: general
      – SubjectFull: Epitopes immunology
        Type: general
      – SubjectFull: High-Throughput Screening Assays methods
        Type: general
      – SubjectFull: C-Reactive Protein chemistry
        Type: general
      – SubjectFull: C-Reactive Protein genetics
        Type: general
      – SubjectFull: C-Reactive Protein immunology
        Type: general
    Titles:
      – TitleFull: MAXTIA: A high-throughput platform for rapid functional epitope mapping by kinetic screening of mutant libraries.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Kim K
      – PersonEntity:
          Name:
            NameFull: Matsunaga R
      – PersonEntity:
          Name:
            NameFull: Yokoo T
      – PersonEntity:
          Name:
            NameFull: Nakakido M
      – PersonEntity:
          Name:
            NameFull: Tsumoto K
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 09
              Text: 2026 Sep
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1469-896X
          Numbering:
            – Type: volume
              Value: 35
            – Type: issue
              Value: 9
          Titles:
            – TitleFull: Protein science : a publication of the Protein Society
              Type: main
ResultId 1