Lambda phage cro repressor. DNA sequence-dependent interactions seen by tyrosine fluorescence

Forces Driving the Binding of Homeodomains to DNA†

Homeodomains are helix-turn-helix type DNA-binding domains that exhibit sequence-specific DNA binding by insertion of their "recognition" alpha helices into the major groove and a short N-terminal arm into the adjacent minor groove without inducing substantial distortion of the DNA. The stability and DNA binding of four representatives of this family, MATalpha2, engrailed, Antennapedia, and NK-2, and truncated forms of the last two lacking their N-terminal arms have been studied by a combination of optical and microcalorimetric methods at different temperatures and salt concentrations. It was found that the stability of the free homeodomains in solution is rather low and, surprisingly, is reduced by the presence of the N-terminal arm for the Antennapedia and NK-2 domains. Their stabilities depend significantly upon the presence of salt: strongly for NaCl but less so for NaF, demonstrating specific interactions with chloride ions. The enthalpies of association of the homeodomains with their cognate DNAs are negative, at 20 degrees C varying only between -12 and -26 kJ/mol for the intact homeodomains, and the entropies of association are positive; i.e., DNA binding is both enthalpy- and entropy-driven. Analysis of the salt dependence of the association constants showed that the electrostatic component of the Gibbs energy of association resulting from the entropy of mixing of released ions dominates the binding, being about twice the magnitude of the nonelectrostatic component that results from dehydration of the protein/DNA interface, van der Waals interactions, and hydrogen bonding. A comparison of the effects of NaCl/KCl with NaF showed that homeodomain binding results in a release not only of cations from the DNA phosphates but also of chloride ions specifically associated with the proteins. The binding of the basic N-terminal arms in the minor groove is entirely enthalpic with a negative heat capacity effect, i.e., is due to sequence-specific formation of hydrogen bonds and hydrophobic interactions rather than electrostatic contacts with the DNA phosphates.

Stability and DNA Binding Ability of the DNA Binding Domains of Interferon Regulatory Factors 1 and 3†

The thermodynamic properties and DNA binding ability of the N-terminal DNA binding domains of interferon regulatory factors IRF-1 (DBD1) and IRF-3 (DBD3) were studied using microcalorimetric and optical methods. DBD3 is significantly more stable than DBD1: at 20 degrees C the Gibbs energy of unfolding of DBD3 is -28.6 kJ/mol, which is 2 times larger than that of DBD1, -14.9 kJ/mol. Fluorescence anisotropy titration experiments showed that at this temperature the association constants with the PRDI binding site are 1.1 x 10(6) M(-)(1) for DBD1 and 3.6 x 10(6) M(-)(1) for DBD3, corresponding to Gibbs energies of association of -34 and -37 kJ/mol, respectively. However, the larger binding energy of DBD3 is due to its larger electrostatic component, while its nonelectrostatic component is smaller than that of DBD1. Therefore, DBD1 appears to have more sequence specificity than DBD3. Binding of DBD1 to target DNA is characterized by a substantially larger negative enthalpy than binding of DBD3, implying that the more flexible structure of DBD1 forms tighter contacts with DNA than the more rigid structure of DBD3. Thus, the strength of the DBDs' specific association with DNA is inversely related to the stability of the free DBDs.

Slow Assembly and Disassembly of λ Cro Repressor Dimers

Dimers of Cro are required to recognize operator DNA and repress transcription, but dimerization is weak compared to DNA binding. Fluorophore-conjugated, single-cysteine variants of Cro have been used to investigate the equilibria and kinetics of dimer assembly. Equilibrium distributions of mixed dimers, monitored by fluorescence resonance energy transfer (FRET), confirm that labeled variants have equilibrium dimer dissociation constants in the micromolar concentration range. Subunit exchange experiments yield first order rate constants for dimer dissociation that range from 0.02 s(-1) to 0.04 s(-1). Association rate constants calculated from the ratios of dissociation equilibrium and rate constants range from 0.7x10(4) M(-1) s(-1) to 3x10(4) M(-1) s(-1), depending on the site of the fluorescent label. At nanomolar concentrations of subunits, assembly can be driven by addition of DNA. The bimolecular association rate constants measured under these conditions are not dramatically enhanced, ranging from 7x10(4) M(-1) s(-1) to 9x10(4) M(-1) s(-1). The association rate is second order in protein but independent of DNA concentration between 10 nM and 200 nM. The association of subunits under native conditions is more than four orders of magnitude slower than the fast assembly phase measured previously in refolding experiments, and is unaffected by peptidyl-prolyl isomerases. Stabilization of the folded structure of the protein by residue substitution in Cro F58W or reduced temperature increases the ratio of dimers to monomers and decreases the rate of subunit exchange. These data suggest that native monomers have compact structures with substantial barriers to unfolding and that unfolded or partially folded monomers are the preferred substrates for dimer assembly. Cro binding in vivo may be under kinetic rather than thermodynamic control. The slow assembly of Cro dimers demonstrated here provides a new perspective on the lysis/lysogeny switch of bacteriophage lambda.

Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding I: analysis of cro dimerization from nanomolar to micromolar concentrations

The cro repressor from bacteriophage lambda is an important and classical transcription regulatory protein that binds DNA operator sites as a dimer. Therefore, a complete understanding of gene regulation by cro requires knowledge of the coupled energetics of its protein dimerization and site-specific DNA binding. A method is described by which cro repressor can be labeled in vivo with [(35)S]methionine to a specific activity of 2 x 10(15) cpm/mol. As a prelude to binding studies, the association equilibrium of cro was determined over the range 10(-)(9)-10(-)(3) M using large-zone analytical gel chromatography with radiolabeled repressor. The data are best described by a monomer-dimer stoichiometry with an equilibrium constant of 3.07 (+/-1.08) x 10(6) M(-)(1) total cro monomer. Stokes radii for monomers and dimers were evaluated from the resolved gel partition coefficients. Under the conditions employed in this study (10 mM Bis-Tris, 200 mM KCl, 2.5 mM MgCl(2), 1 mM CaCl(2), 100 microg/mL BSA, pH 7.0, 20 degrees C), self-association of cro to species with assembly states greater than dimers is not observed.

A general method of analysis of ligand binding to competing macromolecules using the spectroscopic signal originating from a reference macromolecule. Application to Escherichia coli replicative helicase DnaB protein nucleic acid interactions

Quantitative and accurate analyses of protein-nucleic acid interactions in solution are greatly facilitated if the formation of the complex is accompanied by a large change of the spectroscopic signal (e.g., fluorescence) originating from the protein or nucleic acid. However, there are many instances when protein-nucleic acid interactions do not induce adequate changes in spectroscopic properties of the interacting macromolecules. We describe the theoretical and experimental aspects of a general method to analyze such protein-nucleic acid interactions. The method is based on quantitative titrations of a reference nucleic acid with the protein in the presence of a competing nucleic acid whose interaction parameters with the protein are to be determined. The Macromolecule Competition Titration (MCT) method allows for the determination of the absolute average binding density and the free protein ligand concentration over a large binding density range, unavailable by other methods, and construction of a model-independent true binding isotherm. Moreover, the determination of the absolute binding density of the ligand on nonfluorescent nucleic acid is independent of a priori knowledge of the binding characteristics of the protein to the reference fluorescent nucleic acid. Although the MCT method is applicable to any type of physicochemical signal that can be used to monitor the binding, we discuss the details of the method as it applies to the analysis monitored by a change in the nucleic acid fluorescence intensity and anisotropy upon binding a ligand. Moreover, the interaction parameters for a given nucleic acid can be determined by using as a reference the long polymer nucleic acid as well as short oligomers. In particular, the analysis is greatly simplified if the short fluorescent nucleic acid fragment, spanning the exact site-size of the complex and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. We have illustrated the MCT method by applying it to the binding of the Escherichia coli DnaB helicase to unmodified, nonfluorescent single-stranded nucleic acids where the interactions are not accompanied by any adequate spectroscopic signal changes. In order to analyze simultaneous binding of a ligand to different competing nucleic acid lattices, we introduced the combined application of the McGhee-von Hippel theory and the Epstein combinatorial approach for the binding of a large ligand to a linear, homogeneous nucleic acid lattice. Our approach allows one to perform a direct fit of the entire experimental isotherm for the protein binding to two competing nucleic acid lattices without resorting to complex numerical calculations.

Spectroscopic studies on lambda cro protein-DNA interactions

Spectroscopic (circular dichroism and fluorescence) and thermodynamic studies were conducted on lambda Cro-DNA interactions. Some base substitutions were introduced to the operator and the effects on the conformation of the complex and thermodynamic parameters for dissociation of the complex were examined. It was found that, (1) in the specific binding of Cro with DNA which has a (pseudo) consensus sequence, DNA is overwound, while in non-specific binding it is unchanged, or rather unwound; (2) substitution of central base-pairs or the introduction of a mismatched base-pair at the center of the operator reduces the extent of DNA conformational change on Cro binding and lessens the stability of the Cro-DNA complex, even though there is apparently no direct interaction between Cro and DNA at these positions; (3) stability of the complex increases with the degree of DNA conformational change of the same type during binding; (4) in some cases of specific binding, there are three states in the dissociation of the complex as observed by salt titration: two conformational states for the complex depending on salt concentration and, in non-specific binding, dissociation is a two-state transition; (5) the number of ions involved in interactions between Cro and 17 base-pair DNA is about 7.7 for NaCl titrations; (6) dissociation free energy prediction of the Cro-DNA complex by simple addition of the dissociation free energy change of a single base-pair substitution agrees with our experimental results when DNA overwinding occurs during binding, i.e. in specific binding.

Detection of protein-DNA complex formation by time-resolved fluorescence depolarization of bound ethidium bromide

We introduce the use of time-resolved fluorescence spectroscopy to probe the interaction between gene regulatory proteins and DNA. Changes in the decay kinetics of fluorescence polarization anisotropy of ethidium bromide bound to DNA segments report changes in hydrodynamic volume and shape which occurs upon complex formation between protein and DNA. We have used the decay of fluorescence polarization anisotropy as a spectroscopic handle on the interaction between several site-specific DNA-binding proteins involved in transcriptional regulation (the cro repressor of coliphage lambda, the lac repressor of Escherichia coli, and the RNA polymerase of coliphage T7) and their target DNA fragments ranging in length from 17 to 36 base pairs. The technique allows one to follow complex formation while varying solution conditions such as temperature, pH, ionic strength, and presence of effector molecules. Macromolecular concentrations ranging from 10(-7) to 10(-4) M can be used, allowing estimates of relative binding affinities. The magnitude of the observed rotational correlation times (phi obs) can be used to infer information about the size and shape of the complexes.

Kinetic studies on Cro repressor-operator DNA interaction

The six operators of phage lambda and their consensus sequence were synthesized as 21 base-pair DNAs and their interactions with Cro repressor were studied using a filter binding assay. The measured equilibrium dissociation constants suggest that Cro has the highest affinity to the consensus operator (KD = 1.2 X 10(-12) M) and then the OR3 operator (KD = 2.0 X 10(-12) M), after that the affinity becomes lower in the following order: OR1, OL1, OL2, OL3, OR2. The competition experiments show that Cro forms the most stable complex with the consensus operator (t1/2 = 150 min), which is followed by the complex with OR3 (t1/2 = 70 min), OR1, OL1, OL2, OL3 and OR2. The association rate constants (ka) were also measured. They are approximately the same (2 X 10(8) to 4 X 10(8) m-1 s-1) for the consensus, OR3, OR2 and OR1 operators. These experiments have thus shown that the sequence difference in the operator affects the dissociation (KD and kd) but not the association (ka) process. The operators' binding strengths relative to OR1 are 14 (for consensus operator), 7.6 (OR3), 0.73 (OL1), 0.42 (OL2), 0.16 (OL3) and 0.1 (OR2). Seven different lengths of OR-containing DNA fragments were prepared. Measurement of kinetic parameters shows that the affinity of Cro to operator DNA (measured by KD) is essentially constant and independent of the DNA length, while the association and dissociation rate constants increase as the DNA length increases. This is consistent with the idea that Cro locates and leaves its operator via a two-step mechanism. It appears that Cro binds first at an arbitrary site on DNA, then is transferred to its operator site by a facilitated mechanism. The process is reversed when Cro dissociates from the operator. Most of our data fit to the theoretical expression formulated by Berg, Winter & von Hippel for the sliding mechanism. We conclude that Cro slides along the DNA to locate and leave the operator.

The absence of non-local conformational changes in OR3 operator DNA on complexing with the cro repressor

The Interaction of the cro protein of lambda phage with a synthetic OR3 operator having 17 base pairs in length and with its 9 bp fragment has been studied using the circular dichroism (CD) method. In both cases, a considerable change in the CD of the samples was found in the region 260-300 nm upon the addition of the cro protein. The stoichiometry obtained by the CD titration was identical for OR3 and its 9 bp fragment: one duplex per dimeric cro. NaCl addition makes the complexes dissociate so that the 9 bp fragment becomes free at [NaCl] greater than 0.2 M while the whole OR3 becomes free at [NaCl] greater than 0.5 M. The CD spectra of both the free duplexes show a typical B-form conservative pattern with a positive CD band (270 nm) and a negative one (250 nm). The specific complexing of both the duplexes results in a substantial CD depression in the positive band. The most pronounced effect occurs at 280 nm. This spectral change is quite distinct from those in the B to A transition and in the non-cooperative winding of the DNA within the B-family of forms. The interaction of the cro protein with the non-operator DNAs, calf thymus DNA and a synthetic 10 bp duplex, reveals no visible CD changes at all. An inference is drawn that the CD change in the specific complexes is mainly due to the induced CD in tyr-26 upon its interaction with a specific base pair in the operator or its fragment, the operator DNA conformation being conserved in a B-like form as a whole.(ABSTRACT TRUNCATED AT 250 WORDS)

Lambda phage cro repressor interaction with its operator DNA: 2'-deoxy-5-fluorouracil OR3 analogues

The experiments here show that chemically synthesized DNA containing fluorine at selected sites can be used to test specific predictions of a model for cro repressor--operator interaction. This is done by observation of the perturbation to the fluorine-19 NMR spectra of analogues of OR3 synthesized with 2'-deoxy-5-fluorouracil at specific positions in the DNA helix. Although the three-dimensional structure of the cro repressor from phage lambda has been determined by Matthews and co-workers [Anderson, W., Ohlendorf, D., Takeda, Y., & Matthews, B. (1981) Nature (London) 290, 754-758], direct structural observations on the complex of the protein with its specific DNA recognition sequence, OR3, are limited. From that structure of the protein, alone, a model of its complex to DNA was built by fitting B-form DNA, with some distortion [Ohlendorf, D., Anderson, W., Fisher, R., Takeda, Y., & Matthews, B. (1982) Nature (London) 298, 718-723]. That model proposes that the cro repressor contacts only one side of this DNA double helix and a number of specific protein--DNA contacts. To test the model, 2'-deoxy-5-fluorouracil was used to place the fluorine-19 nuclear spin-label on the side of the DNA contacting the cro repressor and on the opposite side facing away from the cro repressor. The results presented here are consistent with the prediction that lambda phage cro repressor contacts only one side of the DNA double helix.

Molecular modelling of protein-nucleic acid interactions

Computer modeling techniques to study the interaction of proteins with nucleic acids are presented. The methods utilize information from genetic and chemical modification experiments and macromolecular structural constraints. These techniques, in addition to computer model building procedures and theoretical energy calculations, are illustrated for the study of the lac and cro repressor-operator systems. Our predicted interactions between lac and its operator agree with those recently reported for lac based upon sequence alignment with the cro repressor. Several molecular models of the putative helical segment of cro interacting with its OR3 operator are presented. These models are reflective of intermediate conformations experienced by the repressor in recognition of the operator sequence. The results of our studies are further discussed in terms of the design of short peptides interacting with nucleic acid sequences and the evolutionary requirements in establishing these repressor interactions.

Imino proton assignments in the proton nuclear magnetic resonance spectrum of the lambda phage OR3 deoxyribonucleic acid fragment

The 17 base pair duplex d(TATCACCGCAAGGGATAp) . d(TATCCCTTGCGGTGATAp) corresponding to the OR3 operator site of lambda phage has been synthesized and studied by 1H nuclear magnetic resonance spectroscopy at 470 MHz. The 13 imino proton resonances observed at 20 degrees C have been assigned to specific base pairs at positions 3-15 on the basis of nuclear Overhauser effect measurements and studies of the temperature dependence of peak intensities. Resonances from the A-T base pairs at positions 1, 2, 16, and 17 are assumed to be absent from the spectrum because of terminal fraying. Resonance from many of the base pairs suggested by Ohlendorf et al. [Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y., & Matthews, B. W. (1982) Nature (London) 298, 718-723] to be involved in specific binding of the lambda phage cro repressor are well resolved.