Consensus protein design

Abstract

A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering.

Keywords: consensus design; multiple sequence alignment; protein stability; semi-rational design; statistical sequence analysis; thermostability.

Fig. 1

Sequence alignment of 12 WW domains across several species and parent proteins. In the consensus, a ‘−’ is a gap, whilst a ‘+’ is an ambiguous position with no consensus. The most conserved residues are highlighted.

Fig. 2

Smoothing of five hypothetical energy landscapes by consensus design. Five protein homologues exhibit differences in their energy landscapes, with three containing kinetic traps that present a propensity for misfolding. As the kinetic traps are not conserved across all five homologues, consensus design is capable of smoothing out the energy landscape to eliminate non-conserved features.