Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix

We study the designability of all compact 3 x 3 x 3 and 6 x 6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e., sequences that have that structure as their unique lowest-energy state. Previous studies of hydrophobic-polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a two-letter (HP) code in such studies. Here, we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix) and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model-and vice versa-with the associated sequences having enhanced thermodynamic stability.