PMID:14725772

Citation	Balaeff, A, Mahadevan, L and Schulten, K (2004) Structural basis for cooperative DNA binding by CAP and lac repressor. Structure 12:123-32
Abstract	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 loop. Here we present a multiscale 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. We predict that the loop is underwound in the binary complex with the LR, whereas in the ternary complex with the LR and CAP, the loop is overwound and extended due to an upstream relocation of a DNA binding hand of LR. The computed relocation distance matches the experimental observations and the energy balance of the system explains the cooperativity effect. Using the multiscale approach, we build an all-atom model of the ternary complex that suggests a series of further experimental investigations.
Links	PubMed
Keywords	Binding, Competitive; Cyclic AMP Receptor Protein/genetics; Cyclic AMP Receptor Protein/metabolism; DNA, Bacterial/genetics; DNA, Bacterial/metabolism; Escherichia coli/genetics; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Models, Molecular; Nucleic Acid Conformation; Promoter Regions, Genetic; Repressor Proteins/genetics; Repressor Proteins/metabolism
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