Three dimensional modelling of two monoclonal antibodies specific to the same antigen
Three dimensional modelling of two monoclonal antibodies specific to the same antigen
We have studied the recognition of a pair of different monoclonal antibodies (DB 19/1 and DB 19/25) which specifically bind to the same tetrapeptide sequence. Although their primary structure and binding affinities for a range of peptide antigens have been determined, three dimensional representations of the antigen-antibody complexes are a prerequisite for further investigations. Previous attempts to determine the structure of both Fab fragments by X-ray crystallography have failed, and therefore computer modelling methods were employed to obtain preliminary models of the peptide-binding sites. The well precedented CONGEN systematic search algorithm was used to construct the three-dimensional protein models with a series of modifications to allow small changes in the packing of framework residues close to the hypervariable loops, The two peptide-binding site models obtained were strikingly different with few similarities evident in either the position or properties of exposed antibody residues. Further optimisation of the model structures was performed using energy minimisation and molecular dynamics on the combining site region of the variable domains. While molecular dynamics with a continuum solvent potential was particularly effective at relaxing regions of high strain in the structures of the peptide-binding loops, the degree of loop mobility suggested that substantial changes in position of combining site amino acid sidechains was possible. However, even in the molecular simulations, the architecture of the two structural models remained dissimilar. In preliminary work aimed at modelling the two peptide/Fv complexes, we analysed the changes in free energy determined from measured binding affinities of DB 19/1 and DB 19//25 with a series of peptide antigens in order to assess the importance of different residues. Although binding to almost identical regions of a nonapeptide antigen, DB 19/1 exhibited a narrower specificity compared to DB 19/25. These changes in affinity, together with conformations of the nonapeptide obtained from a dynamics search, were used to construct a model of the peptide complex with DB 19/1. Since binding differences could not be explained solely by changes in enthalpic contributions, we propose that the binding affinity of flexible ligands may be related to the populations of particular conformations of the unbound antigen.
University of Southampton
Chamberlin, Stephen Gareth
1991
Chamberlin, Stephen Gareth
Chamberlin, Stephen Gareth
(1991)
Three dimensional modelling of two monoclonal antibodies specific to the same antigen.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
We have studied the recognition of a pair of different monoclonal antibodies (DB 19/1 and DB 19/25) which specifically bind to the same tetrapeptide sequence. Although their primary structure and binding affinities for a range of peptide antigens have been determined, three dimensional representations of the antigen-antibody complexes are a prerequisite for further investigations. Previous attempts to determine the structure of both Fab fragments by X-ray crystallography have failed, and therefore computer modelling methods were employed to obtain preliminary models of the peptide-binding sites. The well precedented CONGEN systematic search algorithm was used to construct the three-dimensional protein models with a series of modifications to allow small changes in the packing of framework residues close to the hypervariable loops, The two peptide-binding site models obtained were strikingly different with few similarities evident in either the position or properties of exposed antibody residues. Further optimisation of the model structures was performed using energy minimisation and molecular dynamics on the combining site region of the variable domains. While molecular dynamics with a continuum solvent potential was particularly effective at relaxing regions of high strain in the structures of the peptide-binding loops, the degree of loop mobility suggested that substantial changes in position of combining site amino acid sidechains was possible. However, even in the molecular simulations, the architecture of the two structural models remained dissimilar. In preliminary work aimed at modelling the two peptide/Fv complexes, we analysed the changes in free energy determined from measured binding affinities of DB 19/1 and DB 19//25 with a series of peptide antigens in order to assess the importance of different residues. Although binding to almost identical regions of a nonapeptide antigen, DB 19/1 exhibited a narrower specificity compared to DB 19/25. These changes in affinity, together with conformations of the nonapeptide obtained from a dynamics search, were used to construct a model of the peptide complex with DB 19/1. Since binding differences could not be explained solely by changes in enthalpic contributions, we propose that the binding affinity of flexible ligands may be related to the populations of particular conformations of the unbound antigen.
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Published date: 1991
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Local EPrints ID: 461247
URI: http://eprints.soton.ac.uk/id/eprint/461247
PURE UUID: 1cbc0da2-5627-44dd-8738-5ea4bc8d809f
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Date deposited: 04 Jul 2022 18:41
Last modified: 04 Jul 2022 18:41
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Author:
Stephen Gareth Chamberlin
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