Binding of lac repressor induces different conformational changes on operator and non-operator DNAs

Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein

Transcription factor (TF) proteins regulate gene expression by binding to specific sites on the genome. In the facilitated diffusion model, an optimized search process is achieved by the TF alternating between 3D diffusion in the bulk and 1D diffusion along DNA. While undergoing 1D diffusion, the protein can switch from a search mode for fast diffusion along nonspecific DNA to a recognition mode for stable binding to specific DNA. It was recently noticed that, for a small TF domain protein, reorientations on DNA happen between the nonspecific and specific DNA binding. We here conducted all-atom molecular dynamics simulations with steering forces to reveal the protein-DNA binding free energetics, confirming that the search and recognition modes are distinguished primarily by protein orientations on the DNA. As the binding free energy difference between the specific and nonspecific DNA system slightly deviates from that being estimated directly from dissociation constants on 15-bp DNA constructs, we hypothesize that the discrepancy can come from DNA sequences flanking the 6-bp central binding sites that impact on the dissociation kinetics measurements. The hypothesis is supported by a simplified spherical protein-DNA model along with stochastic simulations and kinetic modeling.

Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein

We present here the results of a series of small-angle X-ray scattering studies aimed at understanding the role of conformational changes and structural flexibility in DNA binding and allosteric signaling in a bacterial transcription regulator, lactose repressor protein (LacI). Experiments were designed to detect possible conformational changes that occur when LacI binds either DNA or the inducer IPTG, or both. Our studies included the native LacI dimer of homodimers and a dimeric variant (R3), enabling us to probe conformational changes within the homodimers and distinguish them from those involving changes in the homodimer-homodimer relationships. The scattering data indicate that removal of operator DNA (oDNA) from R3 results in an unfolding and extension of the hinge helix that connects the LacI regulatory and DNA-binding domains. In contrast, only very subtle conformational changes occur in the R3 dimer-oDNA complex upon IPTG binding, indicative of small adjustments in the orientations of domains and/or subdomains within the structure. The binding of IPTG to native (tetrameric) LacI-oDNA complexes also appears to facilitate a modest change in the average homodimer-homodimer disposition. Notably, the crystal structure of the native LacI-oDNA complex differs significantly from the average solution conformation. The solution scattering data are best fit by an ensemble of structures that includes (1) approximately 60% of the V-shaped dimer of homodimers observed in the crystal structure and (2) approximately 40% of molecules with more "open" forms, such as those generated when the homodimers move with respect to each other about the tetramerization domain. In gene regulation, such a flexible LacI would be beneficial for the interaction of its two DNA-binding domains, positioned at the tips of the V, with the required two of three LacI operators needed for full repression.

Two HlyIIR dimers bind to a long perfect inverted repeat in the operator of the hemolysin II gene from Bacillus cereus

HlyIIR is a negative transcriptional regulator of hemolysin II gene from B. cereus. It binds to a long DNA perfect inverted repeat (44bp) located upstream the hlyII gene. Here we show that HlyIIR is dimeric in solution and in bacterial cells. No protein-protein interactions between dimers and no significant modification of target DNA conformation upon complex formation were observed. Two HlyIIR dimers were found to bind to native operator independently with Kd level in the nanomolar range. The minimal HlyIIR binding site was identified as a half of the long DNA perfect inverted repeat.

DNA looping

DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulatory proteins have been found. In addition, instances of looped structures have been found in replication and in recombination in both prokaryotes and eukaryotes. DNA loop formation may have different functions in different cellular contexts; in some cases, the loop itself is requisite for regulation, while in others the increase in the effective local concentration of protein may account for the effects observed. The ability of DNA to form loops is affected by the distance between binding sites; by the DNA sequence, which determines deformability and bendability; and by the presence of other proteins that exert an influence on the conformation of a particular sequence. Alteration of the stability of DNA loops and/or protein-DNA binding by extra- or intracellular signals provides responsivity to changing metabolic or environmental conditions. The fundamental property of site-specific protein binding to DNA can be combined with protein-protein and protein-ligand interaction to generate a broad range of physiological states.

Photochemical modification of lac repressor--III. Mutant I12X86 versus wild-type repressor

Photodestruction of the two tryptophan (TRP) residues of the core of the wild-type Escherichia coli lac repressor has already been used as a probe in the study of interactions of the repressor with DNA and effectors. The good correlation between phenomena occurring in the core (photodestruction of TRP residues, effectors binding) and at the headpieces (DNA specific and non-specific binding) can be understood in terms of allosteric behavior of the protein. In the present study, the same approach is applied to a repressor with peculiar binding properties, the I12X86 mutant. The photodestruction of TRP residues of this tight binding repressor, bearing two different amino acids as compared to the wild-type one (Ser 61----Leu, Pro 3----Tyr) indicates a probably subtle (since not detected by classical spectroscopic methods) difference of structure of the entire protein and confirms the similarity between specific and non-specific binding of this mutant repressor to DNA, observed by other methods.

Thermodynamic parameters of the binding of the tight-binding I12X86 lac repressor to operator and non-operator DNA

The thermodynamic parameters delta H and delta S corresponding to the binding of the tight-binding double mutant lac repressor I12X86 with operator and non-operator DNA fragments were determined using the nitrocellulose filter binding assay. In both cases the binding processes are entropically driven and accompanied by an unfavorable enthalpy variation. The differences between these parameters and those previously reported for the wild type lac repressor show that the strategy adopted by the mutant to interact with DNA is highly different from that of the wild type repressor and suggest more hydrophobic contacts between the mutant and DNA.

Photochemical modifications of lac repressor--II. Tryptophan photochemistry as a probe in studying the allosteric behaviour of the protein

Irradiation of lac repressor under aerobic conditions in the near UV region (295-400 nm) decreases the Trp fluorescence of the protein. A total loss of fluorescence corresponds to the destruction of all tryptophanyl residues. Irradiation with light of wavelength between 250 and 400 nm quenches fluorescence completely when only half of the Trp residues ae destroyed. An internal photodynamic effect, in which N-formylkynurenine, a principal photoproduct of Trp, sensitizes further the destruction of the other Trp residues, accounts for our results. Experiments performed in the presence of sodium azide suggest that singlet oxygen is not involved in the destruction of Trp, but may be responsible for histidine degradation. Irradiating the repressor complexed with non-operator E. coli DNA has the same effect on Trp residues as irradiating repressor alone. On the contrary, when repressor is complexed to lac operator, both tryptophanyl residues seem to be destroyed simultaneously. This indicates that binding of specific operator DNA at the DNA site induces changes in the environment of the tryptophanyl residues (mainly tor Trp 220) which cannot further transfer in excitation energy to the photoproduct of the other Trp. A prolonged irradiation destroys the complex, leading to the same result observed for non-specific complex or for repressor alone. These results are discussed in terms of the proximity of Trp from the inducer binding site and the allosteric behaviour of the repressor.

Interaction between the cyclic AMP receptor protein and DNA. Conformational studies

The binding of the cyclic adenosine 3',5' monophosphate receptor protein (CRP or CAP) of Escherichia coli to non-specific DNA and to a specific lac recognition sequence has been investigated by circular dichroism (c.d.) spectroscopy. The effect of cAMP and cGMP on the co-operative non-specific binding was also studied. For the non-specific binding in the absence of cAMP a c.d. change (decrease of the intensity of the positive band with a shift of its maximum to longer wavelength) indicates that the DNA undergoes a conformational change upon CRP binding. This change might reflect the formation of the solenoidal coil previously observed by electron microscopy. The amplitude of the c.d. change increases linearly with the degree of saturation of the DNA and does not depend on the size of the clusters of CRP bound. From the variation of the c.d. effect as a function of the ionic strength, the product K omega (K, the intrinsic binding constant and omega, the co-operativity parameter) could be determined. The number of ion pairs involved in complex formation between CRP and DNA was found to be six to seven. Experiments performed with several DNAs, including the alternating polymers poly[d(A-T)] and poly[d(G-C)], demonstrated that the conformational change does not depend on the DNA sequence. However, in the presence of cAMP the c.d. spectrum of the DNA shows only a small variation upon binding CRP. In contrast, in the presence of cGMP the conformational change of the DNA is similar to that observed when non-liganded CRP binds. For the specific lac operon binding, the c.d. change is different from those observed for non-specific binding in the presence or absence of cAMP. These results emphasize the high variability of the DNA structure upon binding the same protein.

Lac repressor-Lac operator complexes. Solution X-ray scattering and electrophoretic studies

Complexes between the Lac repressor and a small DNA operator fragment (29 base pairs) were investigated using polyacrylamide gel electrophoresis and solution X-ray scattering. Titration of the DNA fragment with the repressor, followed by gel electrophoresis showed that only two types of complexes are formed with repressor/operator ratios of 0.5 and 2. Radii of gyration and forward scattered intensities were obtained from Guinier plots for repressor/operator ratios ranging from 0.3 to 2. They demonstrated that the first complex contains one repressor and two operators, whereas the second one contains four repressors and two operators. Mixing operator and repressor in equimolar concentrations leads to a mixture of both complexes. A possible model for the four repressor/two operator complex is proposed.

NMR studies of the trp repressor from Escherichia coli. Characterisation and assignments of residue types

High-resolution proton nuclear magnetic resonance spectra of the trp repressor of Escherichia coli under various conditions are reported and analysed. The spectrum of the denatured state agrees with that predicted from the amino acid composition, with the exception of the two histidine residues, which have different chemical shifts although they titrate normally. The spectrum of the native protein shows the presence of extensive secondary and tertiary structure. Using information from chemical shifts, numbers of protons, titration behaviour, homonuclear chemical-shift-correlated spectroscopy and nuclear Overhauser enhancement correlated spectroscopy, most of the aromatic protons have been assigned to residue type. Further, about 30% of the aliphatic protons have been assigned to residue type by two-dimensional spectroscopy. Nuclear Overhauser enhancements establish that high-field methyl groups belonging to a valine residue lie directly over an aromatic ring.

TET repressor.tet operator complex formation induces conformational changes in the tet operator DNA

The structural changes of the tet operator DNA upon binding of the TET repressor protein are examined by circular dichroism. For this purpose a 70 bp DNA fragment was prepared which contains both tet operators. About 67% of the base pairs of this DNA are involved in specific interaction with the TET repressor. A rather large change in the CD of the DNA is induced by binding of the TET repressor. The shape of the CD difference spectrum is similar to the respective difference found for the lac operator DNA upon complex formation with the lac repressor. However, the effect induced by the TET repressor on tet operator DNA seems to comprise both the specific and non-specific effect of the lac repressor on the structure of DNA [Culard, F. and Maurizot, J.C. (1981) Nucl. Acids Res. 9, 5157-5184]. Specificity of binding is confirmed by the lack of any effect of the TET repressor on the CD of a 95 bp lac operator containing DNA fragment, by the reduced mobility of TET repressor.tet operator complexes on polyacrylamide gels under CD conditions, and by a titration experiment of tet operator DNA with TET repressor employing the CD change. The latter experiment reveals a stoichiometry of four TET repressors per tet operon control region.