Strong Enrichment of Aromatic Residues in Binding Sites From a Charge-neutralized Hyperthermostable Sso7d Scaffold Library

J Biol Chem. 2016 Oct 21;291(43):22496-22508. doi: 10.1074/jbc.M116.741314. Epub 2016 Aug 30.

Abstract

The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation.

Keywords: aromatic amino acids; directed evolution; epidermal growth factor receptor (EGFR); molecular evolution; protein charge; protein stability; scaffold protein; yeast display.

MeSH terms

  • Amino Acids, Aromatic / chemistry
  • Amino Acids, Aromatic / genetics
  • Animals
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Binding Sites
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • HEK293 Cells
  • Hot Temperature*
  • Humans
  • Mice
  • Protein Stability
  • Sulfolobus solfataricus / chemistry*
  • Sulfolobus solfataricus / genetics

Substances

  • Amino Acids, Aromatic
  • Archaeal Proteins
  • DNA-Binding Proteins
  • Sso7d protein, Sulfolobus

Associated data

  • PDB/1SSO