TCB Publications - Abstract

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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