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An affibody in complex with a target protein: structure and coupled folding
Elisabet Wahlberg1, Christofer Lendel, Magnus Helgstrand
1Department of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden.
Summary
Engineered affibodies, based on the Z domain scaffold, bind tightly to their targets. The Z(SPA-1) affibody folds upon binding, mimicking natural protein interactions through a large, complementary interface.
Area of Science:
- Protein engineering
- Structural biology
- Biochemistry
Background:
- Affibodies are engineered binding proteins derived from the Z domain scaffold of staphylococcal protein A.
- The Z(SPA-1) affibody was selected for binding to protein A and also binds its parent Z domain.
Purpose of the Study:
- To characterize the Z(SPA-1) affibody and determine the structure of its complex with the Z domain.
- To elucidate the structural basis for Z(SPA-1) binding affinity and specificity.
Main Methods:
- Phage display for affibody selection
- Solution structure determination of the Z:Z(SPA-1) complex
- Protein characterization (uncomplexed and complexed states)
Main Results:
- Uncomplexed Z(SPA-1) is an aggregation-prone molten globule that folds upon binding.
- The Z:Z(SPA-1) complex reveals a fully formed Z domain scaffold with a large interaction interface.
- Binding involves tight steric and polar/nonpolar complementarity, with 10 of 13 mutated residues in Z(SPA-1) participating.
- Z domain exhibits induced fit upon binding Z(SPA-1), similar to Ig Fc binding.
Conclusions:
- The Z(SPA-1) affibody achieves high binding affinity through extensive complementarity and induced folding.
- Z(SPA-1) effectively mimics the natural binding partner of the Z domain, demonstrating adaptable protein scaffold design.