We have performed three molecular dynamics simulations using the CHARMM molecular modeling program to study the repressor protein from bacteriophage 434 complexed with DNA operators of two different sequences. Two approaches to the modeling of the solvent were used. In the first method, applied to the R1-69/OR1 truncated complex, water molecules were included explicitly in conjunction with a stochastic boundary force to solvate the complex. In the second approach, used for simulations of the R1-69/OR1 and the R1-69/OR3 complexes, the solvent was omitted and implicitly represented by using a distance-dependent dielectric constant and it scaling of the charges on the exposed residues. The simulation with the model which explicitly includes the solvent serves as a validation of the simulations using a simpler solvent representation. In our discussion of the results we focus upon the important interactions between the DNA binding motif of the 434 repressor (motif helix turn helix) and the operators and how the structures of the complexes change with time.
