Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations.
Front Immunol
; 13: 884110, 2022.
Article
em En
| MEDLINE
| ID: mdl-35707541
ABSTRACT
We have carried out a long-timescale simulation study on crystal structures of nine antibody-antigen pairs, in antigen-bound and antibody-only forms, using molecular dynamics with enhanced sampling and an explicit water model to explore interface conformation and hydration. By combining atomic level simulation and replica exchange to enable full protein flexibility, we find significant numbers of bridging water molecules at the antibody-antigen interface. Additionally, a higher proportion of interactions excluding bulk waters and a lower degree of antigen bound CDR conformational sampling are correlated with higher antibody affinity. The CDR sampling supports enthalpically driven antibody binding, as opposed to entropically driven, in that the difference between antigen bound and unbound conformations do not correlate with affinity. We thus propose that interactions with waters and CDR sampling are aspects of the interface that may moderate antibody-antigen binding, and that explicit hydration and CDR flexibility should be considered to improve antibody affinity prediction and computational design workflows.
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Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Simulação de Dinâmica Molecular
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Anticorpos
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Front Immunol
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Reino Unido