Role of supersecondary structural elements in protein G folding

Abstract

Knowledge on the folding of supersecondary structures is very important for a coherent understanding of protein folding mechanisms. Here, the hairpin 1, hairpin 1-helix and helix-hairpin 2 of protein G have each been subject of 50 folding Monte Carlo simulations and 48 ns unfolding molecular dynamics simulations. We find that the helix-hairpin 2 structure can stabilize itself to some extent independent of the rest of protein G but hairpin 1 cannot. Interestingly, an intermediate characterized by a helix-hairpin 2 packed in a non-native arrangement is observed in 50% of all simulations, independently of the temperature, force field, and exact amino acid sequence. This is in line with the framework model which envisages a secondary-tertiary hierarchical process.