Molecular Dynamics Simulations of DNA and Protein—DNA Complexes Including Solvent

Abstract

The results of three new molecular dynamics (MD) trajectories for the d(CGCGAATTCGCG) double helix in water, including one of 1 nanosecond (ns) duration, and an MD study of the lambda repressor-operator complex are described. The DNA simulations form the basis for a detailed analysis of the progress of the trajectory over time and the dynamics of axis bending. The results indicate that the ns dynamical trajectory progresses through a series of three substates of B form DNA, with lifetimes of the order of hundreds of picoseconds (ps). Evidence for an incipient dynamical structure is presented. To validate the simulation, the calculated axis bending is compared with that observed in corresponding crystal structure data. The results indicate that, for this system at least, significant new dynamical behavior is introduced in the ns regime, that previously reported calculations at the ps level did not reveal. Simulation of the protein-DNA complex and the independent components thereof have been carried out for 100-320 ps to date. Some preliminary results from the protein-DNA complex and indications of the extent of structural reorganization on complex formation are presented.