2M5A

Protein A binding by an engineered Affibody molecule


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule.

Lindborg, M.Dubnovitsky, A.Olesen, K.Bjorkman, T.Abrahmsen, L.Feldwisch, J.Hard, T.

(2013) Protein Eng.Des.Sel. 26: 635-644

  • DOI: 10.1093/protein/gzt038

  • PubMed Abstract: 
  • Affibody molecules are engineered binding proteins, in which the three-helix bundle motif of the Z domain derived from protein A is used as a scaffold for sequence variation. We used phage display to select Affibody binders to staphylococcal protein ...

    Affibody molecules are engineered binding proteins, in which the three-helix bundle motif of the Z domain derived from protein A is used as a scaffold for sequence variation. We used phage display to select Affibody binders to staphylococcal protein A itself. The best binder, called ZpA963, binds with similar affinity and kinetics to the five homologous E, D, A, B and C domains of protein A, and to a five-domain protein A construct with an average dissociation constant, K(D), of ~20 nM. The structure of ZpA963 in complex with the Z domain shows that it interacts with a surface on Z that is identical in the five protein A domains, which explains the multi-domain affinity. This property allows for high-affinity binding by dimeric Affibody molecules that simultaneously engage two protein A domains in a complex. We studied two ZpA963 dimers in which the subunits were linked by a C-terminal disulfide in a symmetric dimer or head-to-tail in a fusion protein, respectively. The dimers both bind protein A with high affinity, very slow off-rates and with saturation-dependent kinetics that can be understood in terms of dimer binding to multiple sites. The head-to-tail (ZpA963)2htt dimer binds with an off-rate of k(off) ≤ 5 × 10(-6) s(-1) and an estimated K(D) ≤ 16 pM. The results illustrate how dimers of selected monomer binding proteins can provide an efficient route for engineering of high-affinity binders to targets that contain multiple homologous domains or repeated structural units.


    Organizational Affiliation

    Affibody AB, Gunnar Asplunds Allé 24, SE-171 63 Solna, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein A
A
58Staphylococcus aureusMutation(s): 0 
Gene Names: spa
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ZpA963
B
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-19 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Hard, T.

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references