Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Structural basis for cooperative DNA binding by CAP and
Lac repressor.
Structure, 12:123-132, 2004.
BALA2004
Catabolite gene activator protein (CAP) and lac repressor (LR)
are
celebrated transcription-regulating proteins that bind to DNA
cooperatively forming a ternary complex with the promoter DNA
loop.
Here we present a multi-scale model of the ternary complex
derived
from crystal structures of the proteins and a continuous structure of
the DNA loop built using the theory of elasticity. The structure of
the CAP binding site, observed in the CAP-DNA crystal, is
embedded
within the loop by means of accordingly adjusted curvature and
twist
terms. We predict that the loop is underwound in the binary
complex
with the LR, whereas in the ternary complex the loop is
overwound and
extended due to an upstream movement of a DNA-binding hand
of LR. The
estimated energy difference between the two states of the loop
explains the cooperativity effect. All-atom model of the whole
ternary complex is built on the basis of the multi-scale model.
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