Elizabeth Villa, Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Multi-scale method for simulating protein-DNA complexes. Multiscale Modeling and Simulation, 2:527-553, 2004.

VILL2004 We present a multi-resolution 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 protein-DNA 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 multi-scale 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 loop would be described at the atomic level.

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