Surface Area Included in Energy Refinement of Proteins: A Comparative Study on Atomic Solvation Parameters

Abstract

With the program FANTOM, we study the effect of a solvation energy term modelled by four atomic solvation parameter sets on energy refinement of proteins. Two parameter sets had previously been derived from measured free energies of transfer of hydrocarbons and amino acid side-chain analogues. Alternatively, the other two parameter sets correspond to the total or apolar accessible surface area of the protein. Twenty-five conformations of BPTI and the α-amylase inhibitor tendamistat were refined with respect to emprical energy terms (ECEPP/2) plus a solvation energy term modelled by one of the four atomic solvation parameter sets. These minimizations were compared to minimizations of the ECEPP/2 energy alone with regard to violations of upper distance limits obtained from NMR experiments as well as to root mean square deviations to NMR structures. We find that minimizations of the ECEPP/2 energy plus the total or apolar accessible surface area are superior to minimizations of the ECEPP/2 energy alone. In contrast, minimizations of the ECEPP/2 energy plus a solvation energy term based on free energies of transfer perform poorly.