Computational modelling of cyclic peptides incorporating reverse turn peptidomimetics
Computational modelling of cyclic peptides incorporating reverse turn peptidomimetics
As part of an effort to develop a model system for peptide recognition by proteins, two monoclonal antibodies (DB19/1 and DB19/25) were raised which recognised the pentapeptide Ac.PYPYDV which had been observed to adopt a type II turn in aqueous solution. As beta turns are commonly found in biologically active peptides and have been postulated to be the recognition element of several linear peptides, there has been considerable interest in the development of peptidomimetic analogues which stabilise beta turn conformation. Although such peptide analogues may exhibit increased potency and selectivity in their biological properties, any failure of the analogue to bind to its receptor may be due to the inability of the binding site to accommodate chemical modification of the peptide ligand rather than the analogue mimicking an inactive conformation.
Our strategy in the elucidation of the bound conformation of Ac.YPYDV was to form a cyclic peptide incorporating the YPYD epitope. In this case, the cyclisation of the YPYD sequence to a rigid template was proposed. The chimeric analogue so formed would limit the conformation of the attached loop by fixing the geometry of the ends of the YPYD loop. It was noted that the use of a beta turn mimetic as the template group should induce a complementary beta turn across the tetrapeptide sequence. In contrast to traditional structure-function studies employing conformationally well-defined amino acid analogues such an "external" restraint would not affect the chemical structure of the peptide.
In this case molecular modelling techniques were employed in the prediction of conformation as a preliminary study prior to any synthesis of chimeric mimetics. We therefore undertook an investigation of the conformation of the unconstrained peptides by the molecular modelling of the peptides using a Monte Carlo (MC) conformational search procedure. In order to effectively model this system a working understanding of the factors underlying adoption of secondary structure in solution as related to the sequence of peptide was required. Consequently, a limited nuclear magnetic resonance (NMR) analysis of the conformation of peptides related to the pentapeptide Ac.YPYDV was carried out. The computational results were then evaluated and interpreted on the basis of experimental NMR measurements.
University of Southampton
1996
Porter, Craig Thomas
(1996)
Computational modelling of cyclic peptides incorporating reverse turn peptidomimetics.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
As part of an effort to develop a model system for peptide recognition by proteins, two monoclonal antibodies (DB19/1 and DB19/25) were raised which recognised the pentapeptide Ac.PYPYDV which had been observed to adopt a type II turn in aqueous solution. As beta turns are commonly found in biologically active peptides and have been postulated to be the recognition element of several linear peptides, there has been considerable interest in the development of peptidomimetic analogues which stabilise beta turn conformation. Although such peptide analogues may exhibit increased potency and selectivity in their biological properties, any failure of the analogue to bind to its receptor may be due to the inability of the binding site to accommodate chemical modification of the peptide ligand rather than the analogue mimicking an inactive conformation.
Our strategy in the elucidation of the bound conformation of Ac.YPYDV was to form a cyclic peptide incorporating the YPYD epitope. In this case, the cyclisation of the YPYD sequence to a rigid template was proposed. The chimeric analogue so formed would limit the conformation of the attached loop by fixing the geometry of the ends of the YPYD loop. It was noted that the use of a beta turn mimetic as the template group should induce a complementary beta turn across the tetrapeptide sequence. In contrast to traditional structure-function studies employing conformationally well-defined amino acid analogues such an "external" restraint would not affect the chemical structure of the peptide.
In this case molecular modelling techniques were employed in the prediction of conformation as a preliminary study prior to any synthesis of chimeric mimetics. We therefore undertook an investigation of the conformation of the unconstrained peptides by the molecular modelling of the peptides using a Monte Carlo (MC) conformational search procedure. In order to effectively model this system a working understanding of the factors underlying adoption of secondary structure in solution as related to the sequence of peptide was required. Consequently, a limited nuclear magnetic resonance (NMR) analysis of the conformation of peptides related to the pentapeptide Ac.YPYDV was carried out. The computational results were then evaluated and interpreted on the basis of experimental NMR measurements.
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Published date: 1996
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Local EPrints ID: 459385
URI: http://eprints.soton.ac.uk/id/eprint/459385
PURE UUID: b2f73e8a-b594-4873-b5a3-a70e6f72f6b6
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Date deposited: 04 Jul 2022 17:09
Last modified: 04 Jul 2022 17:09
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Author:
Craig Thomas Porter
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