Similarity of Crambin Lattice Protein Homologues in the Semi-flexible H0P Model

The semi-flexible H0P lattice protein model is an extension of the HP model with an extra kind of “neutral” monomer and an energetic term for “bends”. Crambin (a 46 amino acids protein) has been mapped onto the H0P model and studied by replica-exchange Wang-Landau sampling. From the obtained density of states, thermal properties of the lattice protein are extracted at all temperature. With further study by multicanonical sampling, ground state degeneracy as well as the temperature-dependence of structural quantities are measured with high resolution. In this study, we examine five H0P lattice protein homologues of Crambin, i.e. proteins with similar sequences and structures in nature. Our results show that, at low temperature, thermal properties of these H0P-modeled homologues are close to those of Crambin itself, all showing two significant conformational changes. However, results also show that the previous value for the bending energy can lead to high degeneracies for some low excited states of the homologues. Therefore, a slight change has been made to this term, to keep the degeneracies of all tested homologues low and stable.