Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B

Molecular dynamics simulations of the activation domain of porcine procarbo xypeptidase B (ADBp) were performed in order to examine the effects of the inclusion of a reaction field (RF) term into the calculation of electrostat ics forces for highly charged proteins, Two simulations were performed with the GROMOS96 package, studying the influence of counterions on the final r esults, Comparison with previous results without the inclusion of the RF te rm (Marti-Renom,M.A., Mas,J,M,, Oliva,B,, Querol,E. and Aviles,F.X., Protei n Engng, 1998, 11, 101-110) shows that the structure is well maintained whe n the RF term is included. Moreover, the analysis of the trajectories shows that simulations of solvated highly-charged proteins are sensitive to the presence of counterions, the secondary structures being more stable when th eir charges are neutralized.