2B2X

VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab

Summary for 2B2X

• Entry DOI: 10.2210/pdb2b2x/pdb
• Related: 1MHP
• Descriptor: Integrin alpha-1, Antibody AQC2 Fab, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: computational design, antibody-antigen complex, immune system
• Biological source: Rattus norvegicus (Norway rat); More
• Cellular location: Membrane; Single-pass type I membrane protein: P18614
• Total number of polymer chains: 6
• Total formula weight: 145643.02

Authors

Clark, L.A.,Boriack-Sjodin, P.A.,Eldredge, J.,Fitch, C.,Friedman, B.,Hanf, K.J.,Jarpe, M.,Liparoto, S.F.,Li, Y.,Lugovskoy, A. (deposition date: 2005-09-19, release date: 2006-04-18, Last modification date: 2023-08-23)

Primary citation

Clark, L.A.,Boriack-Sjodin, P.A.,Eldredge, J.,Fitch, C.,Friedman, B.,Hanf, K.J.,Jarpe, M.,Liparoto, S.F.,Li, Y.,Lugovskoy, A.,Miller, S.,Rushe, M.,Sherman, W.,Simon, K.,Van Vlijmen, H.
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design
Protein Sci., 15:949-960, 2006

PubMed 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.

PubMed: 16597831
DOI: 10.1110/ps.052030506

Experimental method

X-RAY DIFFRACTION (2.2 Å)