Tangle Analysis of Protein-DNA Complexes

Monday, September 17, 2007 - 1:30pm - 2:30pm
EE/CS 3-180
Isabel Darcy (The University of Iowa)
Protein-DNA complexes have been modeled using tangles. A tangle consists of arcs properly embedded in a 3-dimensional ball. The protein is modeled
by the 3D ball while the segments of DNA bound by the protein can be
thought of as arcs embedded within the protein ball. This is a very simple
model of protein-DNA binding, but from this simple model, much information
can be gained. The main idea is that when modeling protein-DNA reactions,
one would like to know how to draw the DNA. For example, are there any
crossings trapped by the protein complex? How do the DNA strands exit the
complex? Is there significant bending? Tangle analysis cannot determine
the exact geometry of the protein-bound DNA, but it can determine the
overall entanglement of this DNA, after which other techniques may be used
to more precisely determine the geometry. The latest mathematics and software for solving tangle equations will be discussed.