Circular dichroism studies of the binding of o-nitrophenyl-beta-D-fucoside and o-nitrophenyl-beta-D-galactoside to lac repressor

Ligand interactions with lactose repressor protein and the repressor-operator complex: the effects of ionization and oligomerization on binding

Specific interactions between proteins and ligands that modify their functions are crucial in biology. Here, we examine sugars that bind the lactose repressor protein (LacI) and modify repressor affinity for operator DNA using isothermal titration calorimetry and equilibrium DNA binding experiments. High affinity binding of the commonly-used inducer isopropyl-beta,D-thiogalactoside is strongly driven by enthalpic forces, whereas inducer 2-phenylethyl-beta,D-galactoside has weaker affinity with low enthalpic contributions. Perturbing the dimer interface with either pH or oligomeric state shows that weak inducer binding is sensitive to changes in this distant region. Effects of the neutral compound o-nitrophenyl-beta,D-galactoside are sensitive to oligomerization, and at elevated pH this compound converts to an anti-inducer ligand with slightly enhanced enthalpic contributions to the binding energy. Anti-inducer o-nitrophenyl-beta,D-fucoside exhibits slightly enhanced affinity and increased enthalpic contributions at elevated pH. Collectively, these results both demonstrate the range of energetic consequences that occur with LacI binding to structurally-similar ligands and expand our insight into the link between effector binding and structural changes at the subunit interface.

Lactose repressor protein: functional properties and structure

The lactose repressor protein (LacI), the prototype for genetic regulatory proteins, controls expression of lactose metabolic genes by binding to its cognate operator sequences in E. coli DNA. Inducer binding elicits a conformational change that diminishes affinity for operator sequences with no effect on nonspecific binding. The release of operator is followed by synthesis of mRNA encoding the enzymes for lactose utilization. Genetic, chemical and physical studies provided detailed insight into the function of this protein prior to the recent completion of X-ray crystallographic structures. The structural information can now be correlated with the phenotypic data for numerous mutants. These structures also provide the opportunity for physical and chemical studies on mutants designed to examine various aspects of lac repressor structure and function. In addition to providing insight into protein structure-function correlations, LacI has been utilized in a wide variety of applications both in prokaryotic gene expression and in eukaryotic gene regulation and studies of mutagenesis.

Unfolding of lac repressor and its proteolytic fragment by urea: headpieces stabilize the core within lac repressor

Circular dichroism measurements were used to compared the urea-induced unfolding transition of the lac repressor with those of its separated tryptic fragments, the tetrameric core, and the N-terminal headpiece. The presence of the headpieces covalently linked to the core in the intact repressor leads to a stabilization against urea denaturation as compared to that for the isolated core. This results in a shift of the midpoint of the transition by about 0.5 M urea. When the inducer isopropyl beta-D-thiogalactoside is bound, the core is stabilized more than the entire repressor. The isolated headpiece is considerably more stable against urea denaturation than the tryptic core or the lac repressor. The reversible denaturation process of the headpiece was quantitatively analyzed, and the free energy of unfolding in the absence of urea was found to be 2.4 or 2.9 kcal/mol, depending on the method of calculation used. Comparison between the circular dichroism spectra of the lac repressor, the tryptic core of the lac repressor, and the headpiece supply further evidence that there are no major conformational differences between the structural domains (core and headpieces) before and after proteolytic cleavage of the lac repressor. These results are discussed with respect to the contacts between the different domains of the protein. It is concluded that relatively weak interdomain contacts are probably responsible for the stabilization of the core by the covalently linked headpieces and that these contacts might be weakened upon binding of the inducer.

Genetic assignment of resonances in the NMR spectrum of a protein: lac repressor

By using a systematic genetic approach, the resonances in the 19F NMR spectrum of 3-fluorotyrosine-substituted lac repressor protein have been assigned. The NMR data indicate that each monomer of the repressor consists of two distinct and independent domains. One domain, the NH2-terminal sixth of the primary sequence, which has been shown to be very important for DNA binding, is very mobile. The remaining COOH-terminal sequence is more rigid. Ligands of the repressor, which affect its DNA binding capability, lead to conformational changes in the COOH-terminal domain. The approach to the assignment of spectral features taken here can be extended to other systems.