Molecular basis of a million-fold affinity maturation process in a protein-protein interaction

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology

Publication Date


Document Type



Bacterial Proteins; Crystallography, X-Ray; Models, Molecular; Mutagenesis; Mutant Proteins; Protein Binding; Protein Engineering; *Protein Interaction Mapping; Protein Structure, Quaternary; Receptors, Antigen, T-Cell


Bioinformatics | Computational Biology | Molecular Biology | Systems Biology


Protein engineering is becoming increasingly important for pharmaceutical applications where controlling the specificity and affinity of engineered proteins is required to create targeted protein therapeutics. Affinity increases of several thousand-fold are now routine for a variety of protein engineering approaches, and the structural and energetic bases of affinity maturation have been investigated in a number of such cases. Previously, a 3-million-fold affinity maturation process was achieved in a protein-protein interaction composed of a variant T-cell receptor fragment and a bacterial superantigen. Here, we present the molecular basis of this affinity increase. Using X-ray crystallography, shotgun reversion/replacement scanning mutagenesis, and computational analysis, we describe, in molecular detail, a process by which extrainterfacial regions of a protein complex can be rationally manipulated to significantly improve protein engineering outcomes.

DOI of Published Version



J Mol Biol. 2011 Aug 12;411(2):321-8. doi: 10.1016/j.jmb.2011.06.009. Link to article on publisher's site

Journal/Book/Conference Title

Journal of molecular biology

Related Resources

Link to Article in PubMed

PubMed ID