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Structure and dynamics of the anti-AMCV scFv(F8): Effects of selected mutations on the antigen combining site

TitleStructure and dynamics of the anti-AMCV scFv(F8): Effects of selected mutations on the antigen combining site
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication2008
AuthorsArcangeli, Caterina, Cantale Cristina, Galeffi Patrizia, and Rosato V.
JournalJournal of Structural Biology
Volume164
Pagination119-133
ISSN10478477
KeywordsAntibody, antibody combining site, antigen binding, antigen specificity, antigen structure, artichoke mottled crinkle virus, article, Binding Sites, Computer simulation, immunoglobulin variable region, in vitro study, Models, Molecular, molecular dynamics, molecular interaction, Molecular recognition, molecular stability, mutagenicity, Plant Viruses, priority journal, Protein Conformation, protein engineering, protein stability, single chain fragment variable antibody, structural homology, substitution reaction, wild type
Abstract

The recombinant antibody fragment scFv(F8), which recognizes the coat protein of the plant virus AMCV, is characterized by peculiar high in vitro stability and functional folding even in reducing environments, making it fit for designing stable antibodies with desired properties. Mutagenesis and functional analysis evidenced two residues, at positions 47 and 58 of the VH chain, playing a crucial role in the antigen binding recognition. Here, we used a computational procedure to assess the effects of these mutations on the stability, structure and dynamics of the antigen-binding site. Structural models of the wild type scFv(F8) and of its H47 and H58 mutants were built by homology modelling and assessed by multiple 15.5 ns of molecular dynamics simulations. Computational results indicate that the 47H substitution strongly affects the CDR-H2 conformation, destabilizes the VH/VL interface and confers high conformational flexibility to the antigen-binding site, leading the mutant to functional loss. The mutation at position H58 strenghtens the binding site, bestowing a high antigen specificity on the mutant. The essential dynamics and the analysis of the protein-solvent interface further corroborate the correspondence between the extent of the structurally-determined flexibility of the binding site with the different functional behaviours proved by the wild-type and its mutants. These results may have useful implications for structure-based design of antibody combining site. © 2008 Elsevier Inc. All rights reserved.

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URLhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-51749110001&doi=10.1016%2fj.jsb.2008.06.013&partnerID=40&md5=e3a64f27f985af6e8f9fc4680a8475b8
DOI10.1016/j.jsb.2008.06.013
Citation KeyArcangeli2008119