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Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.


ABSTRACT: Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.

SUBMITTER: Clark LA 

PROVIDER: S-EPMC2242497 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature

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Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design.

Clark Louis A LA   Boriack-Sjodin P Ann PA   Eldredge John J   Fitch Christopher C   Friedman Bethany B   Hanf Karl J M KJ   Jarpe Matthew M   Liparoto Stefano F SF   Li You Y   Lugovskoy Alexey A   Miller Stephan S   Rushe Mia M   Sherman Woody W   Simon Kenneth K   Van Vlijmen Herman H  

Protein science : a publication of the Protein Society 20060405 5


Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was incre  ...[more]

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