Journal of Chemical Physics, Vol.113, No.11, 4794-4798, 2000
Correspondence of potentials of mean force in proteins and in liquids
The concept of potential of mean force (PMF) is now widely used in predicting protein structures. Proteins notably differ from liquids by their inhomogeneity and chain connectivity. Does meaningful correspondence exist between PMFs in proteins and PMFs in liquids? This question was addressed in this article. We constructed "proteins" each with 90 residues selected from a system of 500 hard spheres. The residues were of two types, N and P. They interact among themselves (with energies E-NN, E-PP, E-NP) and the 410 "solvent" spheres (with energies E-NS and E-PS). Out of the 500 hard spheres, we first identified all chains consisting of 90 residues that have appropriate distances between nearest neighbors. The conformation of a protein was selected as the one having the lowest total energy among the 3.7 million chains. A corresponding liquid system was constructed without imposing distance constraints among solute spheres. The PMFs obtained from the proteins and the liquid system show remarkable similarities. For eleven sets of the energy parameters, the first minima of the PMFs in the proteins agree with their counterparts in the liquid state to within a constant.