Effect of sequence and intermolecular interactions on the number and nature of low-energy states for simple model proteins

Publisher Website
Google Scholar
Abstract
We have studied the thermodynamically significant low-energy conformations of 200 random 24-residue model proteins on a square lattice with the Rosenbluth and Rosenbluth (1955) chain growth algorithm combined with multilink additions and Boltzmann weighting. We use a model proposed by Dill (1985) that represents the protein as a connected sequence of hydrophobic and hydrophilic beads on the lattice with nearest-neighbor interactions between the constituent beads. Two interaction sets were investigated—attraction between just the hydrophobic beads and attraction between hydrophobic residues and also between hydrophilic residues. The distribution of energies found with attraction only between hydrophobic beads is broad and consistent with the previous results of Lau and Dill (1989). However, the low-energy states are highly degenerate and noncompact. When attraction between hydrophilic beads is included with the attraction between hydrophobic beads, the energy distribution is sharp. Also, the low-energy configurations are reasonably nondegenerate and compact. This indicates that even with this simple model, important characteristics of the low-energy states of the model proteins are sensitive to the details of the interaction set used.