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Ling WL, Su CTT, Lua WH, Yeo JY, Poh JJ, Ng YL, Wipat A, Gan SKE. Variable-heavy (VH) families influencing IgA1&2 engagement to the antigen, FcαRI and superantigen proteins G, A, and L. Sci Rep 2022; 12:6510. [PMID: 35444201 PMCID: PMC9020155 DOI: 10.1038/s41598-022-10388-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/07/2022] [Indexed: 12/18/2022] Open
Abstract
Interest in IgA as an alternative antibody format has increased over the years with much remaining to be investigated in relation to interactions with immune cells. Considering the recent whole antibody investigations showing significant distal effects between the variable (V) and constant (C)- regions that can be mitigated by the hinge regions of both human IgA subtypes A1 and A2, we performed an in-depth mechanistic investigation using a panel of 28 IgA1s and A2s of both Trastuzumab and Pertuzumab models. FcαRI binding were found to be mitigated by the differing glycosylation patterns in IgA1 and 2 with contributions from the CDRs. On their interactions with antigen-Her2 and superantigens PpL, SpG and SpA, PpL was found to sterically hinder Her2 antigen binding with unexpected findings of IgAs binding SpG at the CH2-3 region alongside SpA interacting with IgAs at the CH1. Although the VH3 framework (FWR) is commonly used in CDR grafting, we found the VH1 framework (FWR) to be a possible alternative when grafting IgA1 and 2 owing to its stronger binding to antigen Her2 and weaker interactions to superantigen Protein L and A. These findings lay the foundation to understanding the interactions between IgAs and microbial superantigens, and also guide the engineering of IgAs for future antibody applications and targeting of superantigen-producing microbes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Newcastle University Singapore, Singapore, Singapore
| | - Chinh Tran-To Su
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yuen-Ling Ng
- Newcastle University Singapore, Singapore, Singapore
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Experimental Drug Development Centre, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,James Cook University, Singapore, Singapore. .,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China. .,Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.
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Thean RKR, Ong DXY, Heng ZSL, Gan SKE, Yeo JY. To Plate or to Simply Unfreeze, That Is the Question for Optimal Plasmid Extraction. J Biomol Tech 2021; 32:57-62. [PMID: 34121935 PMCID: PMC8174125 DOI: 10.7171/jbt.20-3203-001] [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] [Indexed: 11/20/2022]
Abstract
Many molecular biology applications require fast plasmid DNA extraction, spurring multiple studies on how to speed up the process. It is regularly instructed in standard laboratory protocols to plate out frozen glycerol bacterial stocks prior to bacteria incubation in liquid media and subsequent plasmid extraction, although the rationale for this is often unexplained (other than for the isolation of single colonies). Given the commonality and importance of this laboratory operation, such a practice is time-consuming and laborious. To study the impact of this practice and the alternative direct culturing method, we investigated the association between bacterial cell mass and its potential influence on plasmid yields from the 2 methods. Our results showed no difference with preplating for 7 out of 8 plasmid constructs used in the study, suggesting that direct glycerol recovery would not lead to poorer plasmid yields. The findings support the rationale for direct glycerol recovery for plasmid extraction, without the need of an intermediate preplating step.
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Affiliation(s)
| | | | | | - Samuel Ken-En Gan
- Antibody & Product Development Lab, A*STAR, Singapore 138671, Singapore
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore; and
- p53 Laboratory, A*STAR, Singapore 138648, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, A*STAR, Singapore 138671, Singapore
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore; and
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Phua SX, Chan KF, Su CTT, Poh JJ, Gan SKE. Perspective: The promises of a holistic view of proteins-impact on antibody engineering and drug discovery. Biosci Rep 2019; 39:BSR20181958. [PMID: 30630879 PMCID: PMC6398899 DOI: 10.1042/bsr20181958] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/27/2018] [Accepted: 01/09/2019] [Indexed: 12/23/2022] Open
Abstract
The reductionist approach is prevalent in biomedical science. However, increasing evidence now shows that biological systems cannot be simply considered as the sum of its parts. With experimental, technological, and computational advances, we can now do more than view parts in isolation, thus we propose that an increasing holistic view (where a protein is investigated as much as a whole as possible) is now timely. To further advocate this, we review and discuss several studies and applications involving allostery, where distant protein regions can cross-talk to influence functionality. Therefore, we believe that an increasing big picture approach holds great promise, particularly in the areas of antibody engineering and drug discovery in rational drug design.
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Affiliation(s)
- Ser-Xian Phua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kwok-Fong Chan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- APD SKEG Pte Ltd, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- APD SKEG Pte Ltd, Singapore
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
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Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding. Antibodies (Basel) 2018; 7:antib7020020. [PMID: 31544872 PMCID: PMC6698812 DOI: 10.3390/antib7020020] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/02/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022] Open
Abstract
Therapeutic antibodies have shifted the paradigm of disease treatments from small molecules to biologics, especially in cancer therapy. Despite the increasing number of antibody candidates, much remains unknown about the antibody and how its various regions interact. Recent findings showed that the antibody constant region can govern localization effects that are useful in reducing side effects due to systemic circulation by the commonly used IgG isotypes. Given their localized mucosal effects, IgA antibodies are increasingly promising therapeutic biologics. While the antibody Fc effector cell activity has been a focus point, recent research showed that the Fc could also influence antigen binding, challenging the conventional idea of region-specific antibody functions. To investigate this, we analysed the IgA antibody constant region and its distal effects on the antigen binding regions using recombinant Pertuzumab IgA1 and IgA2 variants. We found that mutations in the C-region reduced Her2 binding experimentally, and computational structural analysis showed that allosteric communications were highly dependent on the antibody hinge, providing strong evidence that we should consider antibodies as whole proteins rather than a sum of functional regions.
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