TCB Publications - Abstract

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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: PDF (524.0KB), Journal