Medium effects on the selection of sequences folding into stable proteins in a simple model

Abstract

We study the medium effects on the selection of sequences in protein folding by taking account of the surface potential in HP-model. Our analysis on the proportion of H and P monomers in the sequences gives a direct interpretation that the lowly designable structures possess small average gap. The numerical calculation by means of our model exhibits that the surface potential enhances the average gap of highly designable structures. It also shows that a most stable structure may be no longer the most stable one if the medium parameters changed.