1H0T

An affibody in complex with a target protein: structure and coupled folding

Summary for 1H0T

• Entry DOI: 10.2210/pdb1h0t/pdb
• Related: 1DEE
• Descriptor: IMMUNOGLOBULIN G BINDING PROTEIN A, ZSPA-1 AFFIBODY (2 entities in total)
• Functional Keywords: immune system, protein-protein interactions, protein engineering, molecular recognition, nmr spectroscopy, molten globule, induced fit, coupled protein folding, affibody, igg binding protein a
• Biological source: STAPHYLOCOCCUS AUREUS; More
• Cellular location: Secreted, cell wall ; Peptidoglycan-anchor : P02976
• Total number of polymer chains: 2
• Total formula weight: 13095.58

Authors

Wahlberg, E.,Lendel, C.,Helgstrand, M.,Allard, P.,Dincbas-Renqvist, V.,Hedqvist, A.,Berglund, H.,Nygren, P.-A.,Hard, T. (deposition date: 2002-06-27, release date: 2003-02-27, Last modification date: 2024-05-15)

Primary citation

Wahlberg, E.,Lendel, C.,Helgstrand, M.,Allard, P.,Dincbas-Renqvist, V.,Hedqvist, A.,Berglund, H.,Nygren, P.-A.,Hard, T.
An Affibody in Complex with a Target Protein: Structure and Coupled Folding
Proc.Natl.Acad.Sci.USA, 100:3185-3190, 2003

PubMed Abstract: Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z(SPA-1) affibody has been selected from a phage-displayed library as a binder to protein A. Z(SPA-1) also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z(SPA-1) affibody in its uncomplexed state and determined the solution structure of a Z:Z(SPA-1) protein-protein complex. Uncomplexed Z(SPA-1) behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z(SPA-1). We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z(SPA-1) and Ig Fc, respectively, suggesting that the Z(SPA-1) affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.

PubMed: 12594333
DOI: 10.1073/PNAS.0436086100

Experimental method

SOLUTION NMR