Molecular dynamics simulations in pre-polymerization mixtures for peptide recognition.
Interaction energies
Molecular dynamics (MD)
Molecularly imprinted polymers (MIPs)
Peptide recognition
Plastic antibodies
Journal
Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569
Informations de publication
Date de publication:
15 Jul 2024
15 Jul 2024
Historique:
received:
25
01
2024
accepted:
08
07
2024
medline:
15
7
2024
pubmed:
15
7
2024
entrez:
15
7
2024
Statut:
epublish
Résumé
Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin. Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å
Identifiants
pubmed: 39007951
doi: 10.1007/s00894-024-06069-x
pii: 10.1007/s00894-024-06069-x
doi:
Substances chimiques
Peptides
0
Melitten
20449-79-0
Molecularly Imprinted Polymers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
266Subventions
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : Beca de Doctorado Nacional 21231161
Organisme : Agencia Nacional de Investigación y Desarrollo
ID : EXPLORACION 13220020
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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