Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex

TitleChange of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex
Publication TypeJournal Article
Year of Publication2005
AuthorsCurcio R., Caflisch A., Paci E.
JournalProtein Science
Volume14
Issue10
Pagination2499-2514
Date Published2005 Oct
Type of ArticleResearch Article
ISSN0961-8368
KeywordsAmino Acid Substitution, Antibodies, Monoclonal, Binding Sites, Antibody, Fluorescein-5-isothiocyanate, Haptens, Immunoglobulin Variable Region, Models, Molecular, Point Mutation, Protein Binding
Abstract

We study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single-chain variable-fragment (scFv) anti-fluorescein antibody FITC-E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with metastable intermediates. For the wild type, the rate-limiting step in the unbinding process corresponds to the breaking of the non-native interactions characteristic of a specific intermediate. The H(H58)A mutation disfavors the occurrence of this intermediate. Two events where the hapten partially unbinds in the absence of pulling force are observed in extensive equilibrium simulations of the wild type, and their analysis indicates that forced unbinding and spontaneous unbinding proceed along similar pathways. The different unbinding mechanisms observed in the simulations suggest a possible reason for the difference in the experimental off-rate between the two antibodies. We predict mutations that are expected to modulate the occurrence of the unbinding intermediate. For two such new mutants [H(H58)A and S(H52)A], our predictions are validated in silico by additional simulations. The accompanying paper in this issue by Honegger et al. reports the X-ray structure of FITC-E2 with a derivative of fluorescein, which was used as the starting conformation for the work presented here.

DOI10.1110/ps.041280705
pubindex

0068

Alternate JournalProtein Sci.
PubMed ID16195542
PubMed Central IDPMC2253310
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