Large-scale bending
Using the DNA-segment method only, initial attempts at docking the DBDs
onto I1 or I2 were not satisfactory. A second type of DNA
conformation change was applied to conduct large-scale bending of DNA
using Web 3DNA 2.0, a web-based server23 designed to
manipulate DNA conformations. The software generates rigid-body values
(three translations and three rotations) of a single base pair (bp) and
six step parameters for neighboring bps. It allows modification of the
bp and step parameters to build customized DNA structures.
To calculate the bp step parameters to bend DNA within a plane, we
followed the recommendations in Calladine et
al .24 DNA roll angles were modified gradually at each
bp step in the relevant region in which the roll angle
Rn at step n is given by , where a
larger A results in a greater total bend angle and b introduces a phase
angle to position the maximum roll angle at the desired location along
the DNA. This formula makes the approximation that a full helical twist
of B‑DNA contains 10 bp/turn and that the roll angle has the same period
of 10 steps (also see Discussion). Values for A and b were selected
empirically by presenting HDOCK with a variety of bent DNA structures
and choosing the docked structure with the best surface complementarity.