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Journal of Biological ChemistryVolume 279, Issue 18, 30 April 2004, Pages 18870-18877

Directed in Vitro Evolution and Crystallographic Analysis of a Peptide-binding Single Chain Antibody Fragment (scFv) with Low Picomolar Affinity(Article)

  • aBiochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
  • bArch. et Fonction Macromolec. Biol., CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France

Abstract

We generated a single chain Fv fragment of an antibody (scFv) with a binding affinity of about 5 pM to a short peptide by applying rigorous directed evolution. Starting from a high affinity peptide binder, originally obtained by ribosome display from a murine library, we generated libraries of mutants with error-prone PCR and DNA shuffling and applied off-rate selection by using ribosome display. Crystallographic analysis of the scFv in its antigen-bound and free state showed that only few mutations, which do not make direct contact to the antigen, lead to a 500-fold affinity improvement over its potential germ line precursor. These results suggest that the affinity optimization of very high affinity binders is achieved by modulating existing interactions via subtle changes in the framework rather than by introducing new contacts. Off-rate selection in combination with ribosome display can evolve binders to the low picomolar affinity range even for peptide targets.

Indexed keywords

Engineering controlled terms:AntibodiesAntigensBindersDNAOptimization
Engineering uncontrolled terms:Binding affinityPeptide binders
Engineering main heading:Biochemistry
EMTREE drug terms:antibodyantigenpeptide
EMTREE medical terms:articlebinding affinitycontrolled studycrystallographyDNA shufflingevolutionin vitro studymolecular interactionnonhumanpolymerase chain reactionpriority journalribosome
MeSH:Amino Acid SubstitutionAnimalsBinding SitesCrystallography, X-RayDirected Molecular EvolutionElectrostaticsImmunoglobulin Variable RegionMiceModels, MolecularMutationPeptide LibraryPeptidesProtein Binding
Species Index:Murinae

Chemicals and CAS Registry Numbers:

Immunoglobulin Variable Region; Peptide Library; Peptides

  • ISSN: 00219258
  • CODEN: JBCHA
  • Source Type: Journal
  • Original language: English
  • DOI: 10.1074/jbc.M309169200
  • PubMed ID: 14754898
  • Document Type: Article

  Plückthun, A.; Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, Switzerland;
© Copyright 2008 Elsevier B.V., All rights reserved. © MEDLINE® is the source for the MeSH terms of this document.

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