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Fernández-Quintero ML, Kroell KB, Heiss MC, Loeffler JR, Quoika PK, Waibl F, Bujotzek A, Moessner E, Georges G, Liedl KR. Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments. Front Mol Biosci 2020; 7:609088. [PMID: 33330636 PMCID: PMC7732698 DOI: 10.3389/fmolb.2020.609088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Fab consist of a heavy and light chain and can be subdivided into a variable (V H and V L ) and a constant region (C H 1 and C L ). The variable region contains the complementarity-determining region (CDR), which is formed by six hypervariable loops, shaping the antigen binding site, the paratope. Apart from the CDR loops, both the elbow angle and the relative interdomain orientations of the V H -V L and the C H 1-C L domains influence the shape of the paratope. Thus, characterization of the interface and elbow angle dynamics is essential to antigen specificity. We studied nine antigen-binding fragments (Fab) to investigate the influence of affinity maturation, antibody humanization, and different light-chain types on the interface and elbow angle dynamics. While the CDR loops reveal conformational transitions in the micro-to-millisecond timescale, both the interface and elbow angle dynamics occur on the low nanosecond timescale. Upon affinity maturation, we observe a substantial rigidification of the V H and V L interdomain and elbow-angle flexibility, reflected in a narrower and more distinct distribution. Antibody humanization describes the process of grafting non-human CDR loops onto a representative human framework. As the antibody framework changes upon humanization, we investigated if both the interface and the elbow angle distributions are changed or shifted. The results clearly showed a substantial shift in the relative V H -V L distributions upon antibody humanization, indicating that different frameworks favor distinct interface orientations. Additionally, the interface and elbow angle dynamics of five antibody fragments with different light-chain types are included, because of their strong differences in elbow angles. For these five examples, we clearly see a high variability and flexibility in both interface and elbow angle dynamics, highlighting the fact that Fab interface orientations and elbow angles interconvert between each other in the low nanosecond timescale. Understanding how the relative interdomain orientations and the elbow angle influence antigen specificity, affinity, and stability has broad implications in the field of antibody modeling and engineering.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Katharina B. Kroell
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Martin C. Heiss
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K. Quoika
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ekkehard Moessner
- Roche Pharma Research and Early Development, Large Molecular Research, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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Meyer S, Evers M, Jansen JHM, Buijs J, Broek B, Reitsma SE, Moerer P, Amini M, Kretschmer A, Ten Broeke T, den Hartog MT, Rijke M, Klein C, Valerius T, Boross P, Leusen JHW. New insights in Type I and II CD20 antibody mechanisms-of-action with a panel of novel CD20 antibodies. Br J Haematol 2018; 180:808-820. [PMID: 29468712 DOI: 10.1111/bjh.15132] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/04/2017] [Indexed: 12/23/2022]
Abstract
Based on their mechanisms-of-action, CD20 monoclonal antibodies (mAbs) are grouped into Type I [complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC)] and Type II [programmed cell death (PCD) and ADCC] mAbs. We generated 17 new hybridomas producing CD20 mAbs of different isotypes and determined unique heavy and light chain sequence pairs for 13 of them. We studied their epitope binding, binding kinetics and structural properties and investigated their predictive value for effector functions, i.e. PCD, CDC and ADCC. Peptide mapping and CD20 mutant screens revealed that 10 out of these 11 new mAbs have an overlapping epitope with the prototypic Type I mAb rituximab, albeit that distinct amino acids of the CD20 molecule contributed differently. Binding kinetics did not correlate with the striking differences in CDC activity among the mIgG2c mAbs. Interestingly, chimerization of mAb m1 resulted in a mAb displaying both Type I and II characteristics. PCD induction was lost upon introduction of a mutation in the framework of the heavy chain affecting the elbow angle, supporting that structural changes within this region can affect functional activities of CD20 mAbs. Together, these new CD20 mAbs provide further insights in the properties dictating the functional efficacy of CD20 mAbs.
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Affiliation(s)
- Saskia Meyer
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Mitchell Evers
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Johannes H M Jansen
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Jos Buijs
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Blanca Broek
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Stephanie E Reitsma
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Petra Moerer
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Mojtaba Amini
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Anna Kretschmer
- Division of Stem Cell Transplantation and Immunotherapy, Department of Internal Medicine II, Christian-Albrechts-University, Kiel, Germany
| | - Toine Ten Broeke
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Christian Klein
- Roche Pharma Research & Early Development, Roche Innovation Center, Zurich, Switzerland
| | - Thomas Valerius
- Division of Stem Cell Transplantation and Immunotherapy, Department of Internal Medicine II, Christian-Albrechts-University, Kiel, Germany
| | - Peter Boross
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Jeanette H W Leusen
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, The Netherlands
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Naschberger A, Fürnrohr BG, Lenac Rovis T, Malic S, Scheffzek K, Dieplinger H, Rupp B. The N14 anti-afamin antibody Fab: a rare V L1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling. Acta Crystallogr D Struct Biol 2016; 72:1267-1280. [PMID: 27917827 PMCID: PMC5137224 DOI: 10.1107/s205979831601723x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/26/2016] [Indexed: 12/31/2022] Open
Abstract
The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.
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Affiliation(s)
- Andreas Naschberger
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Barbara G. Fürnrohr
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Tihana Lenac Rovis
- Center for Proteomics, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
| | - Suzana Malic
- Center for Proteomics, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
| | - Klaus Scheffzek
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Hans Dieplinger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
- Vitateq Biotechnology GmbH, Innrain 66, 6020 Innsbruck, Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
- CVMO, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
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Sampei Z, Igawa T, Soeda T, Funaki M, Yoshihashi K, Kitazawa T, Muto A, Kojima T, Nakamura S, Hattori K. Non-antigen-contacting region of an asymmetric bispecific antibody to factors IXa/X significantly affects factor VIII-mimetic activity. MAbs 2015; 7:120-8. [PMID: 25524207 PMCID: PMC4622617 DOI: 10.4161/19420862.2015.989028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
While antibody engineering improves the properties of therapeutic antibodies, optimization of regions that do not contact antigens has been mainly focused on modifying the effector functions and pharmacokinetics of antibodies. We recently reported an asymmetric anti-FIXa/FX bispecific IgG4 antibody, ACE910, which mimics the cofactor function of FVIII by placing the two factors into spatial proximity for the treatment of hemophilia A. During the optimization process, we found that the activity was significantly affected by IgG subclass and by modifications to the inter-chain disulfide bonds, upper hinge region, elbow hinge region, and Fc glycan, even though these regions were unlikely to come into direct contact with the antigens. Of these non–antigen-contacting regions, the tertiary structure determined by the inter-chain disulfide bonds was found to strongly affect the FVIII-mimetic activity. Interestingly, IgG4-like disulfide bonds between Cys131 in the heavy chain and Cys114 in the light chain, and disulfide bonds between the two heavy chains at the hinge region were indispensable for the high FVIII-mimetic activity. Moreover, proline mutations in the upper hinge region and removal of the Fc glycan enhanced the FVIII-mimetic activity, suggesting that flexibility of the upper hinge region and the Fc portion structure are important for the FVIII-mimetic activity. This study suggests that these non–antigen-contacting regions can be engineered to improve the biological activity of IgG antibodies with functions similar to ACE910, such as placing two antigens into spatial proximity, retargeting effector cells to target cells, or co-ligating two identical or different antigens on the same cell.
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Affiliation(s)
- Zenjiro Sampei
- a Research Division; Chugai Pharmaceutical Co., Ltd ; Tokyo , Japan
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Abstract
This modelling study sought to describe the relationships between elbow joint kinematics and wrist joint linear velocity in cricket fast bowlers, and to assess the sensitivity of wrist velocity to systematic manipulations of empirical joint kinematic profiles. A 12-camera Vicon motion analysis system operating at 250 Hz recorded the bowling actions of 12 high performance fast bowlers. Empirical elbow joint kinematic data were entered into a cricket bowling specific "Forward Kinematic Model" and then subsequently underwent fixed angle, angular offset and angle amplification manipulations. A combination of 20° flexion and 20° abduction at the elbow was shown to maximise wrist velocity within the experimental limits. An increased elbow flexion offset manipulation elicited an increase in wrist velocity. Amplification of elbow joint flexion-extension angular displacement indicated that, contrary to previous research, elbow extension range of motion and angular velocity at the time of ball release were negatively related to wrist velocity. Some relationships between manipulated joint angular waveforms and wrist velocity were non-linear, supporting the use of a model that accounts for the non-linear relationships between execution and outcome variables in assessing the relationships between elbow joint kinematics and wrist joint velocity in cricket fast bowlers.
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Affiliation(s)
- Kane Jytte Middleton
- a School of Sport Science, Exercise and Health , The University of Western Australia , Perth , Australia
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