Accurate calculation of binding and folding free energies by a scaled generalized Born method

Professor Huan-Xiang Zhou
Biophysics, Florida State University


The Poisson-Boltzmann equation is widely used for modeling solvation effects. The computational cost of PB has largely restricted its applications to single-conformation calculations. The generalized Born model provides an approximation at substantially reduced cost. Currently the best GB methods reproduce PB results for electrostatic solvation energies with errors at > 5 to 10 kcal/mol. When two proteins form a complex, the net electrostatic contributions to the binding free energy are typically of the order of 5 to 10 kcal/mol. Similarly, the net contributions of individual residues to protein folding free energy are < 5 kcal/mol. Clearly in these applications the accuracy of current GB methods is insufficient. Here we present a simple scaling scheme that allows our GB method, GBr^6 , to reproduce PB results for binding and folding free energies with high accuracy. From an ensemble of conformations sampled from molecular dynamics simulations, five were judiciously selected for PB calculations. These PB results were used for scaling GBr^6 . Tests on protein binding and folding show that effects of point mutations calculated by scaled GBr^6 are accurate to within 0.5 kcal/mol or less. This method makes it possible to incorporate conformational sampling in electrostatic modeling without loss of accuracy.