We present a multiresolution approach to modeling complexes between protein and
DNA that contain looped or coiled DNA. The approach combines a coarse-grained model of the DNA
loop, based on the classical theory of elasticity, with an atom level model of proteins and proteinDNA interfaces based on molecular dynamics. The coarse-grained DNA description is controlled
through the atom level protein description and vice versa. The feasibility of the resulting multiscale
modeling approach is demonstrated for a protein-DNA complex in which a protein called the E. coli
lac repressor forces DNA into a 76 base pair loop. The required simulation involves 230,000 atoms,
a number that would triple if both protein and DNA loops were described at the atomic level.