Thermodynamic analysis of protein sequence-structure relationships in monomer and dimer forms

Two-dimensional lattice model is employed to analyze the sequence–structure relationships between HP and YhHX protein sequences and compact structures in monomer and homodimer forms. Our results show that most structures are encoded by normal and prion protein sequences, and about one-third of the protein sequences are potentially able to refold from its native monomer conformation to alternative ones upon dimerization thermodynamically. Such findings partially reflect the existences of the dimer and oligomer protein structures in living organism and the occurrence of pathologic dimerization or aggregation of monomer proteins. It is observed that protein sequences differ drastically in the number of strains. Statistically, the number of protein sequences decreases exponentially with the number of strains. Calculations using various energy parameters show that the expected value of maximum number of strains for a 16-residue sequence is about its length.