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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