2B88

Structural basis for molecular recognition in an affibody:affibody complex

Summary for 2B88

• Entry DOI: 10.2210/pdb2b88/pdb
• Related: 2B87 2B89
• NMR Information: BMRB: 6804
• Descriptor: ZTaq affibody (1 entity in total)
• Functional Keywords: protein-protein interactions, protein engineering, molecular recognition, nmr spectroscopy, induced fit, affibody, protein binding
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 1
• Total formula weight: 6491.26

Authors

Lendel, C.,Dogan, J.,Hard, T. (deposition date: 2005-10-06, release date: 2006-05-23, Last modification date: 2024-05-15)

Primary citation

Lendel, C.,Dogan, J.,Hard, T.
Structural basis for molecular recognition in an affibody:affibody complex.
J.Mol.Biol., 359:1293-1304, 2006

PubMed Abstract: Affibody molecules constitute a class of engineered binding proteins based on the 58-residue three-helix bundle Z domain derived from staphylococcal protein A (SPA). Affibody proteins are selected as binders to target proteins by phage display of combinatorial libraries in which typically 13 side-chains on the surface of helices 1 and 2 in the Z domain have been randomized. The Z(Taq):anti-Z(Taq) affibody-affibody complex, consisting of Z(Taq), originally selected as a binder to Taq DNA polymerase, and anti-Z(Taq), selected as binder to Z(Taq), is formed with a dissociation constant K(d) approximately 100 nM. We have determined high-precision solution structures of free Z(Taq) and anti-Z(Taq), and the Z(Taq):anti-Z(Taq) complex under identical experimental conditions (25 degrees C in 50 mM NaCl with 20 mM potassium phosphate buffer at pH 6.4). The complex is formed with helices 1 and 2 of anti-Z(Taq) in perpendicular contact with helices 1 and 2 of Z(Taq). The interaction surface is large ( approximately 1670 A(2)) and unusually non-polar (70 %) compared to other protein-protein complexes. It involves all varied residues on anti-Z(Taq), most corresponding (Taq DNA polymerase binding) side-chains on Z(Taq), and several additional side-chain and backbone contacts. Other notable features include a substantial rearrangement (induced fit) of aromatic side-chains in Z(Taq) upon binding, a close contact between glycine residues in the two subunits that might involve aliphatic glycine Halpha to backbone carbonyl hydrogen bonds, and four hydrogen bonds made by the two guanidinium N(eta)H(2) groups of an arginine side-chain. Comparisons of the present structure with other data for affibody proteins and the Z domain suggest that intrinsic binding properties of the originating SPA surface might be inherited by the affibody binders. A thermodynamic characterization of Z(Taq) and anti-Z(Taq) is presented in an accompanying paper.

PubMed: 16750222
DOI: 10.1016/j.jmb.2006.04.043

Experimental method

SOLUTION NMR