Folding Behaviour for Proteins BBL and E3BD with Go-like Models

Folding behaviour of protein BBL and its homologue domain E3BD are studied by using an off-lattice Go-like model. It is found that the folding behaviours of these two proteins are different. Protein BBL folds in a downhill manner, which is consistent with experiments. In contrast, protein E3BD folds cooperatively and has a bimodal distribution of the Q values (the similarity to the native state). By analysing the native structures of the two proteins, it is found that the difference in folding behaviours can be attributed to the different structural features described by the number of nonlocal contacts per residue.