Inducer and anti-inducer interactions with the lac repressor seen by nuclear magnetic resonance changes at tyrosines and tryptophans

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.

Ligand-induced conformational changes in lactose repressor: a fluorescence study of single tryptophan mutants

A key element in the ability of lac repressor protein to control transcription reversibly is the capacity to assume different conformations in response to ligand binding. To investigate regions of the protein involved in these conformational changes, mutant repressor proteins containing single tryptophans were created by mutating each of the two native tryptophan residues to tyrosine and changing the residue of interest to tryptophan. Tryptophans substituted in the following locations were highly accessible to quenchers with no changes in fluorescence or quenching properties in the presence of ligands: in the N-terminal helix-turn-helix for Y7, at the junction between the N-terminus and N-subdomain for L62, in the N-subdomain of the monomer-monomer interface for residue E100 or Q117, or at the C-terminal region for K325. Tryptophan at position F226 in the C-subdomain subunit interface was only moderately exposed to quenchers and unresponsive to ligands. In contrast, the fluorescence and quenching properties of single tryptophans placed in the central region of the protein were affected by ligands. Inducer binding altered the accessibility to quencher for tryptophan at H74 or F293, but no changes were detected upon binding operator. Exposure of tryptophan at the position occupied by Y273 was affected by both inducer and operator, indicating alterations in this region by both ligands. These results suggest that, in the areas of the lac repressor probed by these substitutions, the inducer-bound form differs from the conformation of the unliganded form.

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.

A mutant lactose repressor with altered inducer and operator binding parameters

The lactose repressor protein from the mutant Escherichia coli BG185 contains valine at position 81 instead of alanine. Spectroscopic, chemical and direct binding measurements demonstrate that the BG185 protein exhibits properties similar to the wild-type repressor-inducer complex. Kinetic measurements of inducer binding to BG185 repressor yielded rate constants that were more than two orders of magnitude smaller than those observed for wild-type repressor; these results suggest that the structural transitions required for inducer binding are markedly impaired by the mutation. The fluorescence spectral shift in response to inducer binding was identical for mutant and wild-type proteins. This identity indicates direct effects of inducer binding on the tryptophan(s) near the sugar binding site rather than environmental changes consequent to conformational shifts. Analogy to the bacterial sugar binding proteins suggest that the Ala to Val change at position 81 in BG185 repressor yields a molecule that is fixed in a closed, sugar-binding conformation.

lac operator DNA modification in the presence of proteolytic fragments of the repressor protein

Singly end-labeled DNA fragments containing the lactose operator were methylated in the presence of the lactose repressor and homogeneous preparations of its proteolytic fragments. Binding of core protein produced by mild trypsin digestion yielded a methylation perturbation pattern that differed significantly from that elicited by binding to intact repressor, although similarities in the patterns for these related proteins were noted in the central, asymmetric region of the operator. An NH2-terminal peptide (residues 1 to 56) from lac repressor bound operator fragments in a nitrocellulose filter assay, but failed to perturb DNA methylation significantly relative to the pattern in the absence of peptide. Binding of hybrid tetramers of core and intact repressor monomers produced related but unique methylation patterns for the purines on the operator fragment. The general pattern of perturbation observed suggests preferred binding of a single NH2 terminus to the promoter-distal region of the operator and asymmetric interaction of the core region with the operator sequence. Differences in purine methylation patterns produced by the presence of effector complexes of repressor and core protein suggest the possible nature of changes in protein topology that result in the affinity changes accompanying induction.

Predicted structure of the sugar-binding site of the lac repressor

The lactose repressor protein from Escherichia coli binds sugars, primarily galactosides, which modulate its interactions with operator DNA and thereby affect synthesis of the lac metabolic enzymes. The affinity of the repressor for operator DNA is decreased by binding inducer sugars and increased by binding anti-inducer sugars. Based on regions of the primary structure implicated by genetic methods to be involved in sugar binding, amino acid sequence homology between L-arabinose-binding protein (ABP) and lac repressor has recently been reported. The sugar-binding sites for these two proteins might be expected to have similar structural features, as both bind L-arabinose and D-galactose. The high resolution structure of ABP reported in the accompanying article provides complete definition of amino acids in the sugar-binding site. By identification of homologous residues in the lac repressor, we have now predicted the structure of the portion of the repressor sugar-binding site which accommodates the galactosyl moiety. This prediction provides the first potential view of the inducer/anti-inducer site in the repressor protein.

Sequence-specific resonance assignments in the 1H nuclear-magnetic-resonance spectrum of the lac repressor DNA-binding domain 1-51 from Escherichia coli by two-dimensional spectroscopy

The assignment of the 1H nuclear magnetic resonance (NMR) spectrum of the DNA-binding domain 1-51 of lac repressor from Escherichia coli is described and documented. The assignments are based entirely on the amino acid sequence and on two-dimensional NMR experiments at 360 MHz and 500 MHz. Individual assignments were obtained at 18 degrees C for the backbone protons of 44 out of the total of 51 amino acids residues, the exceptions being Met-1, Lys-2, Tyr-7, Arg-35, Glu-36, Lys-37 and Ile-48. Complete assignments of the non-labile hydrogen atoms of the side chain were obtained for 33 residues, and for Asn-46 and Asn-50 the delta amide protons were also identified. The chemical shifts for the assigned resonances at 18 degrees C are listed for an aqueous solution at pH 4.9 and at pH 6.8.