Wrapped-around models for the lac operon complex.
The protein-DNA complex, involved in the lac operon of enteric bacteria, is paradigmatic in understanding the extent of DNA bending and plasticity due to interactions with protein assemblies acting as DNA regulators. For the lac operon, two classes of structures have been proposed: 1), with the protein tetramer lying away from the DNA loop (wrapped-away model); and 2), with the protein tetramer lying inside the DNA loop (wrapped-around model). A recently developed electrostatic analytical model shows that the size and net charge of the Lac protein tetramer allow the bending of DNA, which is consistent with another wrapped-around model from the literature. Coarse-grained models, designed based on this observation, are extensively investigated and show three kinds of wrapped-around arrangements of DNA and a lower propensity for wrapped-away configurations. Molecular dynamics simulations of an all-atom model, built on the basis of the most tightly collapsed coarse-grained model, show that most of the DNA double-helical architecture is maintained in the region between O3 and O1 DNA operators, that the DNA distortion is concentrated in the chain beyond the O1 operator, and that the protein tetramer can adapt the N-terminal domains to the DNA tension.
La Penna
Giovanni
G
Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo-Metallici, Sesto Fiorentino, Florence, Italy. glapenna@iccom.cnr.it
Perico
Angelo
A
D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D007763:Lac Operon; D056968:Lac Repressors / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D055672:Static Electricity; D013696:Temperature
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D056968:Lac Repressors; C539064:LacI protein, E coli