Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems:Relative free energy of binding of trypsin to benzamidine and benzylamine

The relative free energies of binding of trypsin to two amine inhibitors, b enzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI), Comparison of the simulations with the c rystal structures of both complexes, trypsin-BZD and trypsin-BZA, shows tha t NBTI simulations better sample conformational space relative to thermodyn amic integration (TI) simulations. The relative binding free energy calcula ted using NBTI was much closer to the experimentally determined value than that obtained using TI, The error in the TI simulation was found to be prim arily due to incorrect sampling of BZA's conformation in the binding pocket . In contrast, NBTI produces a smooth mutation from BZD to BZA using a surr ogate potential, resulting in a much closer agreement between the inhibitor s' conformations and the omit electron density maps. This superior agreemen t between experiment and simulation, of both relative binding free energy d ifferences and conformational sampling, demonstrates NBTI's usefulness for free energy calculations in macromolecular simulations. Proteins 1999;37:64 1-653. (C) 1999 Wiley-Liss, Inc.