About: Potential Aggregation-Prone Regions in Complementarity-Determining Regions of Antibodies and Their Contribution Towards Antigen Recognition: A Computational Analysis

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About: Potential Aggregation-Prone Regions in Complementarity-Determining Regions of Antibodies and Their Contribution Towards Antigen Recognition: A Computational Analysis Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Potential Aggregation-Prone Regions in Complementarity-Determining Regions of Antibodies and Their Contribution Towards Antigen Recognition: A Computational Analysis
Creator	Kumar, Sandeep Singh, Satish Wang, Xiaoling
Source	Medline; PMC
abstract	PURPOSE: To analyze contribution of short aggregation-prone regions (APRs), which may self-associate via cross-β motif and were earlier identified in therapeutic mAbs, towards antigen recognition via structural analyses of antibody-antigen complexes. METHODS: A dataset of 29 publically available high-resolution crystal structures of Fab-antigen complexes was collected. Contribution of APRs towards the surface areas of the Fabs buried by the cognate antigens was computed. Propensities of amino acids to occur in APRs and to be involved in antigen binding were compared. Coincidence between APRs and individual CDR loops was examined. RESULTS: All Fabs in the dataset contain at least one APR in CDR loops and adjacent framework β-strands. The average contribution of APRs towards buried surface area of Fabs is 16.0 ± 10.7%. Aggregation and antigen recognition may be coupled via aromatic residues (Tyr, Trp), which occur with high propensities in both APRs and antigen binding sites. APRs are infrequent in the heavy chain CDR 3 (H3) loops (7%), but are frequent in H2 loops (45%). CONCLUSIONS: Co-incidence of APRs with antigen recognition sites can potentially lead to the loss of function upon aggregation. Rational structure-based design or selection strategies are suggested for biotherapeutics with improved druggability while maintaining potency. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11095-010-0143-5) contains supplementary material, which is available to authorized users.
has issue date	2010-04-27(xsd:dateTime)
bibo:doi	10.1007/s11095-010-0143-5
bibo:pmid	20422267
has license	no-cc
sha1sum (hex)	e3a8e110eae3c5b739f9bead4574adbda49e1603
schema:url	https://doi.org/10.1007/s11095-010-0143-5
resource representing a document's title	Potential Aggregation-Prone Regions in Complementarity-Determining Regions of Antibodies and Their Contribution Towards Antigen Recognition: A Computational Analysis
has PubMed Central identifier	PMC7088613
has PubMed identifier	20422267
schema:publication	Pharm Res
resource representing a document's body	covid:e3a8e110eae3c5b739f9bead4574adbda49e1603#body_text
is schema:about of	named entity 'APRs' named entity 'CONTRIBUTION' named entity 'COMPLEMENTARITY' named entity 'CROSS' named entity 'SHORT' named entity 'PURPOSE' named entity 'ANTIBODY' named entity 'MOTIF' named entity 'PRONE' named entity 'COMPLEXES' named entity 'PRONE' named entity 'THEIR' named entity 'POTENTIAL' named entity 'ANTIGEN RECOGNITION' named entity 'REGIONS' named entity 'STRUCTURAL' named entity 'ANTIGEN RECOGNITION' named entity 'ANTIBODIES' named entity 'COMPUTATIONAL ANALYSIS' named entity 'EARLIER' named entity 'THERAPEUTIC' named entity 'SELF' named entity 'IDENTIFIED' named entity 'ASSOCIATE' named entity 'REGIONS' named entity 'AGGREGATION' named entity 'CONTRIBUTION' named entity 'ANTIGEN' named entity 'AGGREGATION' named entity 'therapeutic' named entity 'antibody-antigen complexes' named entity 'APRs' named entity 'Complementarity' named entity 'Maas' named entity 'solvent-accessible surface area' named entity 'amyloid' named entity 'thermodynamic' named entity 'immunoglobulin light chain' named entity 'Fab' named entity 'mAb' named entity 'Neuropilin-1' named entity 'antigen' named entity 'Fab' named entity 'APRs' named entity 'antibody' named entity 'light chains' named entity 'antigen' named entity 'binding sites' named entity 'Polar and nonpolar' named entity 'CDR loops' named entity 'polysaccharides' named entity 'asymmetric unit' named entity 'surface area' named entity 'ion pairs' named entity 'potency' named entity 'peptide' named entity 'amino acid' named entity 'light chain' named entity 'Thioflavin' named entity 'potency' named entity 'binding sites' named entity 'Fab' named entity 'antigen' named entity 'antibody' named entity 'experimental validation' named entity 'Fab' named entity 'APRs' named entity 'APRs' named entity 'antibody-antigen complexes' named entity 'potency' named entity 'type 2' named entity 'conformationally' named entity 'Hydrophobic residues' named entity 'solvent' named entity 'APRs' named entity 'β-strands' named entity 'Fab' named entity 'sequence variation' named entity 'antigen'

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