An approximate treatment of long-range interactions in proteins

An approximate method, valid beyond a critical distance, is presented for evaluating the long-range interaction energies between the residues of a protein. This approximation results in large reductions in the computer time required to evaluate the energies, compared to the usual procedure of summing the interactions over all pairs of atoms in the interacting residues. Beyond a critical distance between convenient reference atoms in each residue, the long-range nonbonded (attractive) energy may be approximated by -B_ij/(R_ij)⁶, where R_ij is the distance between the above-mentioned reference atoms, and the long-range electrostatic energy may be evaluated as the Coulombic interaction energy between the centers of positive and negative charge on each residue. In this approximate procedure, the interactions between residues are computed in terms of properties of the residues instead of those of the individual atoms of each residue.