MOLECULAR-DYNAMICS FREE-ENERGY STUDY OF A PROTEIN IN SOLUTION WITH ALL DEGREES OF FREEDOM AND LONG-RANGE COULOMB INTERACTIONS

Free energy perturbation calculations based on molecular dynamics (MD) simulations were carried out for a charge-creating phenomenon in a protein, i.e., a large pK(a) shift of Asp(10) in ribonuclease HI (RNase HI). The MD simulations were performed in solution with all degrees of freedom and long-range Coulomb interactions included, which were efficiently calculated by a recently developed method [PPPC method; Mel. Simul. 8,321 (1992)] without any truncations. A deprotonation free energy was evaluated for both Asp10 in RNase HI and a free aspartic acid in solution by the acceptance ratio method (ARM) from MD trajectories in which force-field parameters were gradually changed. The pK, shift obtained from the difference between these deprotonation free energies was 2.1 +/- 0.6 and in good agreement with the experimental value (2.3 +/- 0.1). The equilibrium structure of the deprotonated state in solution was close to the initial X-ray structure. The root mean square fluctuation around the equilibrium structure was strongly correlated with the fluctuation deduced from the X-ray B-factor. Additional MD/free energy calculations were also carried out for the same systems using the conventional 10 Angstrom cutoff method for comparison. The value obtained (-15.2) was significantly different from both the experimental result (2.3) and the no cutoff result (2.1). The present study demonstrated that the free energy perturbation methodology can be applicable to charge-changing phenomena in proteins by explicitly including long-range Coulomb interactions.