IMPROVING THE ACCURACY OF PROTEIN PK(A) CALCULATIONS - CONFORMATIONALAVERAGING VERSUS THE AVERAGE STRUCTURE

Several methods for including the conformational flexibility of protei ns in the calculation of titration curves are compared. The methods us e the linearized Poisson-Boltzmann equation to calculate the electrost atic free energies of solvation and are applied to bovine pancreatic t rypsin inhibitor (BPTI) and hen egg-white lysozyme (HEWL). An ensemble of conformations is generated by a molecular dynamics simulation of t he proteins with explicit solvent. The average titration curve of the ensemble is calculated in three different ways: an average structure i s used for the pK(a) calculation; the electrostatic interaction free e nergies are averaged and used for the pK(a) calculation; and the titra tion curve for each structure is calculated and the curves are average d. The three averaging methods give very similar results and improve t he pK(a) values to approximately the same degree. This suggests, in co ntrast to implications from other work, that the observed improvement of pK(a) values in the present studies is due not to averaging over an ensemble of structures, but rather to the generation of a single prop erly averaged structure for the pK(a) calculation. (C) 1998 Wiley-Liss , Inc.