[3P-66] The Relationship between Designability of Protein and Preference of Local Structures: A lattice model study
Designability of protein structure is the number of sequences that can design the structure, that is the number of sequences which determines the structure as the unique ground state. What features determine the designability of structures? Here, we hypothesize that local rules of real protein determine designability. In order to verify this hypothesis, we use the HP model to investigate whether local rules are determinants of designability or not. Corresponding to the local rules of protein, we impose a penalty that increase the energy of structures on a local structure of the HP model. After imposing a penalty on a local structure, we identified all the non-degenerate pairs of sequences and structures. We found that the relationship between sequences and structures of HP model is consistent with that of observed in the database of real proteins: The local structure with penalty does not appear in highly designable structures, and it appears in some of the poorly designable structures. These results suggest that local rules of protein are the determinant of the designability of protein structures.