Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.
Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR-DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50-180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure.
Swigon
David
D
Departments of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA. swigon@pitt.edu
Coleman
Bernard D
BD
Olson
Wilma K
WK
D001426:Bacterial Proteins / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D003850:Deoxyribonuclease I / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry*; D015964:Gene Expression Regulation, Bacterial; D056968:Lac Repressors; D017895:Manganese Compounds / Q000737:chemistry; D008854:Microscopy, Electron; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D010087:Oxides / Q000737:chemistry; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D023302:Protein Footprinting; D012097:Repressor Proteins / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D004278:DNA, Superhelical; D029968:Escherichia coli Proteins; D056968:Lac Repressors; D017895:Manganese Compounds; D010087:Oxides; D012097:Repressor Proteins; C048856:permanganic acid; D003850:Deoxyribonuclease I