STUDIES ON PROTEIN FOLDING, UNFOLDING AND FLUCTUATIONS BY COMPUTER SIMULATION IV. Hydrophobic Interactions

摘要: The theoretical model of proteins on the two-dimensional square lattice, introduced previously, is extended to include hydrophobic interactions. Two proteins, whose native conformations have different folded patterns, are studied. Units in protein chains classified into polar units and nonpolar units. If there a vacant lattice point next unit, it interpreted as being occupied by solvent water entropy system assumed decrease certain amount. Besides these free energies, specific long-range interactions studied previous papers be operative chain. Equilibrium properties folding unfolding transitions two found similar, even though one them was predicted, based globule transitions, unfold through significant intermediate state (or at least show tendency toward such behavior), when strongly weighted. failure this prediction led development more refined transitions; non-interacting local structure model. here character non-specific Because effect decelerating kinetics. deceleration less pronounced conformation stabilized many pairs medium-range It therefore inferred that power cope with