Measurement of binding constants for protein-DNA interactions by DNA-cellulose chromatography

Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits

Genetic feedback loops can be used by cells to regulate internal processes or to keep track of time. It is often thought that, for a genetic circuit to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a Hill function, regardless of the actual promoter architecture. Furthermore, genetic circuits do not operate in isolation and often transcription factors are shared between different promoters. In this work we show how mathematical modelling of genetic feedback loops can be facilitated with a mechanistic fold-change function that takes into account the titration effect caused by competing binding sites for transcription factors. The model shows how the titration effect facilitates self-sustained oscillations in a minimal genetic feedback loop: a gene that produces its own repressor directly without cooperative transcription factor binding. The use of delay-differential equations leads to a stability contour that predicts whether a genetic feedback loop will show self-sustained oscillations, even when taking the bursty nature of transcription into account.

What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase

This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.

The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

The Lac system of genes has been an important model system in understanding gene regulation. When the dimer lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The hinge region is disordered when binding to nonoperator sequences. This region of the protein must pay a conformational entropic penalty to order when it is bound to operator DNA. Structural studies show that this region is flexible. Previous simulations showed that this region is disordered when free in solution without the DNA binding domain present. Our simulations corroborate that this region is extremely flexible in solution, but we find that the presence of the DNA binding domain proximal to the hinge helix and salt make the ordered conformation more favorable even without DNA present.

Price of disorder in the lac repressor hinge helix

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.

The forkhead domain hinge-loop plays a pivotal role in DNA binding and transcriptional activity of FOXP2

Forkhead box (FOX) proteins are a ubiquitously expressed family of transcription factors that regulate the development and differentiation of a wide range of tissues in animals. The FOXP subfamily members are the only known FOX proteins capable of forming domain-swapped forkhead domain (FHD) dimers. This is proposed to be due to an evolutionary mutation (P539A) that lies in the FHD hinge loop, a key region thought to fine-tune DNA sequence specificity in the FOX transcription factors. Considering the importance of the hinge loop in both the dimerisation mechanism of the FOXP FHD and its role in tuning DNA binding, a detailed investigation into the implications of mutations within this region could provide important insight into the evolution of the FOX family. Isothermal titration calorimetry and hydrogen exchange mass spectroscopy were used to study the thermodynamic binding signature and changes in backbone dynamics of FOXP2 FHD DNA binding. Dual luciferase reporter assays were performed to study the effect that the hinge-loop mutation has on FOXP2 transcriptional activity in vivo. We demonstrate that the change in dynamics of the hinge-loop region of FOXP2 alters the energetics and mechanism of DNA binding highlighting the critical role of hinge loop mutations in regulating DNA binding characteristics of the FOX proteins.

DNA-cellulose: an economical, fully recyclable and highly effective chiral biomaterial for asymmetric catalysis

We report here the first generation of a DNA-based catalyst bound to a cellulose matrix. The chiral biomaterial is commercially available, trivial to use, highly selective and fully recyclable.

Macromolecular competition titration method accessing thermodynamics of the unmodified macromolecule-ligand interactions through spectroscopic titrations of fluorescent analogs

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand-macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein-nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein-nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein-nucleic acid interactions, it can generally be applied to any ligand-macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined.

DNA-binding properties of T4 UvsY recombination mediator protein: polynucleotide wrapping promotes high-affinity binding to single-stranded DNA

To carry out homologous recombination events in the cell, recombination proteins must be able to recognize and form presynaptic filaments on single-stranded DNA (ssDNA) in the presence of a vast excess of double-stranded DNA (dsDNA). Therefore recombination machineries stringently discriminate between ssDNA and dsDNA lattices. Recent single-molecule studies of bacteriophage T4 recombination proteins revealed that, surprisingly, the UvsY recombination mediator protein binds stronger to stretched dsDNA molecules than to stretched ssDNA. Here, we show that for relaxed DNA lattices, the opposite is true: UvsY exhibits a 1000-fold intrinsic affinity preference for ssDNA over dsDNA at moderate salt concentrations. This finding suggests that UvsY preferentially loads UvsX recombinase onto ssDNA under physiological conditions. The biochemical basis for high-affinity UvsY–ssDNA binding was investigated by hydrodynamic and cross-linking methods. Results show that UvsY forms ring-like hexamers in solution, and that ssDNA binds to multiple subunits within each hexamer, consistent with ssDNA wrapping. The data support a model in which ssDNA wrapping by UvsY protein is important for the selective nucleation of presynaptic filaments on ssDNA versus dsDNA, and for the coordinated transfer of ssDNA from Gp32 (SSB) to UvsY (RMP) to UvsX (recombinase) during filament assembly.

Sequence specific interaction between promoter DNA and Escherichia coli RNA polymerase: comparative thermodynamic analysis with one immobilized partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage DeltaD(III) T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an excellent substrate for Ni(II) ions, while the SPR studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/-12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/-3.6) kcal mol(-1). The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/-2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established.

Isothermal microcalorimetry to investigate non specific interactions in biophysical chemistry

Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.

Concentration and length dependence of DNA looping in transcriptional regulation

In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage), to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein

Upon exposure to alkylating agents, Escherichia coli increases expression of aidB along with three genes (ada, alkA, and alkB) that encode DNA repair proteins. In order to begin to identify the role of AidB in the cell, the protein was purified to homogeneity, shown to possess stoichiometric amounts of flavin adenine dinucleotide (FAD), and confirmed to have low levels of isovaleryl-coenzyme A (CoA) dehydrogenase activity. A homology model of an AidB homodimer was constructed based on the structure of a four-domain acyl-CoA oxidase. The predicted structure revealed a positively charged groove connecting the two active sites and a second canyon of positive charges in the C-terminal domain, both of which could potentially bind DNA. Three approaches were used to confirm that AidB binds to double-stranded DNA. On the basis of its ability to bind DNA and its possession of a redox-active flavin, AidB is predicted to catalyze the direct repair of alkylated DNA.

Physical constraints and functional characteristics of transcription factor-DNA interaction

We study theoretical "design principles" for transcription factor (TF)-DNA interaction in bacteria, focusing particularly on the statistical interaction of the TFs with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of programmability, i.e., the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow range of "optimal" interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TFs, which indicates that TF-DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TFs.

Affinity purification of DNA-binding proteins

The focus of this review is on DNA affinity chromatography, which is the most powerful tool for purification of DNA binding proteins. The use of nonspecific-, sequence specific- and single stranded-DNA affinity columns in purification of various DNA binding proteins is discussed. The purification strategies for transcription factors, restriction enzymes, telomerases, DNA and RNA polymerase and DNA binding antibodies are described. Different applications of DNA affinity chromatography are presented.

Temperature dependence of DNA affinity chromatography of transcription factors

Oligonucleotides bound by the CAAT enhancer binding protein (C/EBP), the lactose repressor, and Gal4 were chemically coupled to cyanogen bromide-activated Sepharose and the temperature dependence of transcription factor chromatography was characterized. Each transcription factor was applied to the appropriate column and eluted using a salt gradient at several temperatures. Each transcription factor showed a unique behavior. As temperature was increases, less salt was required to elute C/EBP, more salt was required to elute lac repressor, while Gal4 showed a biphasic dependency with the amount of salt first decreasing between 4 and 19 degrees C and then increasing above 19 degrees C. This temperature dependence is not due to protein or DNA unfolding but rather is a property of complex formation. By loading a column, washing it at a permissive temperature, and then rapidly changing the column temperature, highly selective elution can be obtained. The thermodynamics of this temperature effect are different for the binding of specific and nonspecific DNA sequences, making chromatography at different temperatures a potentially important way of purifying transcription factors.

Heparin elution of transcription factors from DNA-Sepharose columns

A novel method using heparin for eluting transcription factors from DNA-Sepharose columns was characterized. CAAT enhancer binding protein (C/EBP) or lac repressor fusion proteins were both eluted with heparin from columns containing specific DNA sequences coupled to cyanogen bromide activated Sepharose. The amount of the lac repressor chimera which eluted from the column was shown to increase with increases in the mobile phase heparin concentration. The elution of the protein was also shown to be dependent on the amount of DNA coupled to the column and more protein eluted from columns containing lesser amounts of DNA. These data suggest that heparin and DNA compete for binding to the protein; this competition causes elution. Comparison of heparin- and salt-eluted protein demonstrated the heparin-eluted fraction was significantly purer and comparable to that obtained by elution with isopropyl beta-D-thiogalactopyranoside, a lactose analog. Heparin elution represents an important new tool in the purification of transcription factors and other DNA-binding proteins by DNA affinity chromatography.

A new heat shock protein that binds nucleic acids

We describe the isolation of Hsp15, a new, very abundant heat shock protein that binds to DNA and RNA. Hsp15 is well conserved and related to a number of RNA-binding proteins, including ribosomal protein S4, RNA pseudouridine synthase, and tyrosyl-tRNA synthetase. The region shared between these proteins appears to represent a common, but previously unrecognized, RNA binding motif. Filter binding studies showed that Hsp15 binds to a 17-mer single-stranded RNA with a dissociation constant of 9 microM in 22.5 mM Hepes, pH 7. 0, 5 mM MgCl2. A role of Hsp15 in binding nucleic acids puts this protein into a different functional category from that of many other heat shock proteins that act as molecular chaperones or proteases on protein substrates.

Single-stranded DNA binding properties of the UvsX recombinase of bacteriophage T4: binding parameters and effects of nucleotides

Bacteriophage T4 provides an important model for the biochemistry and genetics of DNA metabolism. Phage-encoded proteins conduct all essential steps of T4 DNA replication, repair, and recombination. Central to these three processes is the T4 UvsX protein, a member of the filamentous, ATP-dependent class of general recombination enzymes typified by the Escherichia coli RecA protein. Like RecA, UvsX forms presynaptic filaments on single-stranded (ss) DNA, which are the obligatory nucleoprotein intermediates in recombination. Aspects of the T4 presynaptic filament are explored by quantitative characterization of the UvsX-ssDNA interaction using an etheno-derivitized single-stranded DNA molecule, epsilonDNA, whose fluorescence is enhanced by UvsX binding. Studies with this model lattice show that UvsX exhibits a moderate level of cooperativity (omega=100) when binding to epsilonDNA with a binding-site size (n) equal to four nucleotide residues. Salt-stability studies of this complex reveal that the non-hydrolyzable ATP analog, ATPgammaS, induces a high-affinity binding mode that is distinguishable from complexes formed with ADP or in the absence of a nucleotide cofactor. With this new information, both functional relationships between the UvsX and RecA recombinases, and implications for UvsX interactions with the other proteins of the T4 presynaptic filament (UvsY and gp32) may be further explored.

Molecular and kinetic basis for the mixed agonist/antagonist activity of estriol

Estriol acts as a weak estrogen when administered in a single dose into immature or ovariectomized laboratory animals, but produces full estrogenic responses upon chronic administration. However, when estriol is injected together with estradiol it acts as an antiestrogen. We studied the dual agonist/antagonist properties of estriol, using recombinant human estrogen receptor (hER) in ligand-binding assay, cell-free transcription assay, electrophoretic mobility shift assay with cVitII estrogen response element (ERE), and ERE-Sepharose chromatography. We show that the weak estrogenic activity of estriol results from impaired hER-ERE interaction. The antiestrogenic activity of estriol was demonstrated in a cell-free transcription assay where it reduced estradiol-dependent transcription in a dose-dependent manner. Estriol interfered with estradiol-induced positive cooperative binding and receptor dimerization, and binding of hER complexes to ERE. These effects of estriol were maximal at a 10-fold molar excess over estradiol; under these conditions estradiol-dependent transcription was decreased by 85%, although [3H]estradiol binding was reduced by only 50%. We propose that when hER, estradiol, and estriol are coequilibrated, several receptor species are formed: unliganded hER monomers and dimers; estradiol-hER monomers and dimers, estriol-hER monomers and dimers; and presumably mixed estradiol-estriol dimers. Since estrogen-hER complexes bind cooperatively to ERE sequences, the concentrations of transcriptionally active complexes (estriol- and estradiol-hER dimers) are reduced to low levels that fail to bind cooperatively with ERE and initiate transcription. We discuss our results in relation to the massive estriol production during pregnancy and to the "Estriol Hypothesis" on the protective role for estriol in opposing carcinogenic effects of estradiol.

Interactions of the bacteriophage T4 gene 59 protein with single-stranded polynucleotides: binding parameters and ion effects

The gene 59 protein (gp59) of bacteriophage T4 is an important accessory protein of the phage-encoded replicative DNA helicase, gp41. The properties of this 26 kDa protein include selective binding to ssDNA, and specific interactions with both gp41 and gp32, the T4-encoded ssDNA- binding protein. gp59 stimulates many of the DNA-dependent activities of the gp41 enzyme by promoting its assembly onto gp32-ssDNA complexes. Direct interactions between gp59 and gp32-ssDNA complexes are essential for helicase assembly, and gp59-gp32 protein-protein interactions have been shown to play a central role. Presumably, the ssDNA-binding activity of gp59 is also important for helicase assembly; however, to date this activity has been poorly characterized. In this study, we present the first detailed biochemical investigation of the interactions of gp59 with single-stranded polynucleotides. Using etheno-DNA fluorescence enhancement and quantitative ssDNA-cellulose methods, we demonstrate the following: (1) gp59 binds to single-stranded polynucleotides with a binding site size of nine to ten nucleotide residues per monomer; (2) gp59 exhibits relative affinities towards four different ssDNA lattices used in this study according to the heirarchy: ssDNA (random sequence) > epsilonDNA (random sequence) > poly(dA) > poly(depsilonA); (3) gp59 exhibits two or more different polynucleotide binding modes distinguished by their cooperativities of binding, and modulated by salt and/or lattice effects; (4) gp59-ssDNA binding is characterized by a large salt effect on the association constant, consistent with multiple ionic contacts between protein and ssDNA phosphate residues and with the displacement of anions from the protein. The implications of our findings for the mechanism of action of gp59 in helicase-ssDNA assembly are discussed.

Escherichia coli lac repressor-lac operator interaction and the influence of allosteric effectors

The wild type E. coli lac operator is embedded in a 35 base-pair DNA sequence containing extensive 2-fold symmetry, suggesting a symmetric repressor operator complex. However, deviations from strict 2-fold symmetry occur at the central base-pair and at three additional base-pairs. Using an operator fragment binding analysis we have determined: (a) a relative contribution each pair provides to the lac repressor-lac operator DNA complex, (b) the operator DNA length necessary for maximum binding to lac repressor; and (c) the contribution of the several non-symmetric base in the wild-type operator to the binding affinity. Since lac repressor-lac operator DNA interaction is reduced upon binding of the gratuitous inducer, isopropyl-beta-D-galactoside (IPTG), the same DNA fragment binding analysis was performed with the low affinity form of lac repressor. In the presence of inducer, the affinity for the left half site of the wild-type lac operator is reduced without significant reduction on the right half of the operator. Conversely, the anti-inducer orthonitrophenylfucoside (ONPF) which stabilizes the lac repressor-lac operator complex increases the binding affinity, particularly to the right half of the operator.

Kinetic analysis of the interaction of human estrogen receptor with an estrogen response element

The kinetics of the interaction between recombinant human estrogen receptor and chicken vitellogenin gene II estrogen response element (ERE) were determined by ERE-Sepharose chromatography. The association constant of the interaction between the ERE and the human estrogen receptor was dependent on receptor concentration, estradiol binding and temperature. The highest association constant (80-100 x 10(6)M-1) was measured for the estradiol-bound receptor prepared at 25 degrees C and at concentrations higher than 7 nM. At high receptor concentrations (>7 nM) the binding mechanism of estradiol to the receptor was positive cooperative, indicating receptor homodimerization. At lower concentrations the binding mechanism was partially cooperative and the association constant of the liganded receptor was significantly lower. The binding mechanism at 4 degrees C was cooperative as well, and the association constants were similarly dependent upon receptor concentration, but were 50% lower than the receptor prepared at 25 degrees C. The association constant of the unliganded receptor was 4- to 5-fold lower than that of the liganded receptor at 25 degrees C. These data suggest that in addition to estradiol-induced conformational changes in the receptor, the receptor dimers are subjected to temperature-dependent changes, which further increase their affinity for an ERE.

Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions

The objective of this study is to quantify the contributions of cations, anions and water to stability and specificity of the interaction of lac repressor (lac R) protein with the strong-binding symmetric lac operator (Osym) DNA site. To this end, binding constants Kobs and their power dependences on univalent salt (MX) concentration (SKobs = d log Kobs/d log[MX]) have been determined for the interactions of lac R with Osym operator and with non-operator DNA using filter binding and DNA cellulose chromatography, respectively. For both specific and non-specific binding of lac R, Kobs at fixed salt concentration [KX] increases when chloride (Cl-) is replaced by the physiological anion glutamate (Glu-). At 0.25 M-KX, the increase in Kobs for Osym is observed to be approximately 40-fold, whereas for non-operator DNA the increase in Kobs is estimated by extrapolation to be approximately 300-fold. For non-operator DNA, SKobsRD is independent of salt concentration within experimental uncertainty, and is similar in KCl (SKobs,RDKCl = -9.8(+/- 1.0) between 0.13 M and 0.18 M-KCl) and KGlu (SKobs,RDKGlu = -9.3(+/- 0.7) between 0.23 M and 0.36 M-KGlu). For Osym DNA, SKobsRO varies significantly with the nature of the anion, and, at least in KGlu appears to decrease in magnitude with increasing [KGlu]. Average magnitudes of SKobsRO are less than SKobsRD, and, for specific binding decrease in the order [SKobsRO,KCl[>[SKobsRO,KAc[>[SKobsRO,KGlu[ . Neither KobsRO nor SKobsRO is affected by the choice of univalent cation M+ (Na+, K+, NH4+, or mixtures thereof, all as the chloride salt), and SKobsRO is independent of [MCl] in the range examined (0.125 to 0.3 M). This behavior of SKobsRO is consistent with that expected for a binding process with a large contribution from the polyelectrolyte effect. However, the lack of an effect of the nature of the cation on the magnitude of KobsRO at a fixed [MX] is somewhat unexpected, in view of the order of preference of cations for the immediate vicinity of DNA (NH4+ > K+ > Na+) observed by 23Na nuclear magnetic resonance. For both specific and non-specific binding, the large stoichiometry of cation release from the DNA polyelectrolyte is the dominant contribution to SKobs. To interpret these data, we propose that Glu- is an inert anion, whereas Ac- and Cl- compete with DNA phosphate groups in binding to lac repressor. A thermodynamic estimate of the minimum stoichiometry of water release from lac repressor and Osym operator (210(+/- 30) H2O) is determined from analysis of the apparently significant reduction in [SKobsRO,KGlu[ with increasing [KGlu] in the range 0.25 to 0.9 M. According to this analysis, SKobs values of specific and non-specific binding in KGlu differ primarily because of the release of water in specific binding. In KAc and KCl, we deduce that anion competition affects Kobs and SKobs to an extent which differs for different anions and for the different binding modes.

A homology domain shared between Drosophila optomotor-blind and mouse Brachyury is involved in DNA binding

The distribution of sequence elements divides the optomotor-blind protein into three regions and is suggestive of a transcriptional regulatory role of this protein. The central region of Omb is homologous to the N-terminal half of the Brachyury protein. The conserved domain of Omb is here shown to possess general DNA binding affinity but has no significant similarity to recognized DNA binding motifs.

Differential DNA binding by calf uterine estrogen and progesterone receptors results from differences in oligomeric states

The studies presented here provided evidence that the calf uterine estrogen and progesterone receptors exhibit different DNA-binding properties in vitro as a result of having different dimerization constants. The affinity of the estrogen and progesterone receptors for DNA was measured by using isocratic elution from DNA-Sepharose. The hormone-free estrogen receptor had a 10-fold higher affinity for DNA than did the hormone-free progesterone receptor when measured at receptor concentrations of 6-12 nM and 180 mM KCl. No effect on DNA binding by binding progesterone to its receptor was detected. This contrasts with the increased affinity for DNA and increased number of ions released upon DNA binding exhibited by the hormone-bound estrogen receptor. Between 2 and 3 ions were released when the progesterone receptor and the diluted estrogen receptor bound DNA. These observations suggested the progesterone receptor was in the monomeric state, whereas the estrogen receptor was in the dimeric state at receptor concentrations of 6-12 nM. When the dimerization constant of the progesterone receptor was measured, the value of approximately 7 nM obtained was 20-fold higher than the value of 0.3 nM reported for the estrogen receptor. This makes it likely the two receptors exist in different forms at the same concentration in vitro. It is also suggested the predominant form of the estrogen and progesterone receptors in vivo could differ.

Affinity and conformation of the estrogen receptor when bound to single-stranded vs. double-stranded nonspecific DNA

The affinity of the hormone-bound estrogen receptor for single-stranded and double-stranded DNA was compared using isocratic elution chromatography. The receptor bound single-stranded DNA with a two-fold higher affinity than double-stranded DNA (17.9 x 10(4) M-1 vs. 9.1 x 10(4) M-1) at 0.2 M KCl. The same number of ions were released when the receptor bound either single-stranded or double-stranded DNA (11.8 vs. 10.6, respectively). These results indicate the hormone-bound estrogen receptor has no strong preference for single-stranded vs. double-stranded nonspecific DNA, and has a similar conformation when bound to either form of DNA at physiological salt concentrations.

Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: spectroscopic approaches to monitor binding

The measurement of equilibrium binding constants for ligand-macromolecule interactions by monitoring a change in some spectral property of the ligand or the macromolecule is a common method used to study these interactions. This is due to the high sensitivity of the spectroscopic methods and general ease in applying these experimental procedures. In addition, binding can be monitored continuously, thus facilitating kinetic measurements. The main problem with these methods results from the fact that the spectroscopic signal is an indirect measure of binding, since the relationship between the change in the spectroscopic signal and the extent of binding is unknown, a priori. A common recourse is to assume a strict proportionality between the signal change and the fractional saturation of the ligand or macromolecule; however, it is often the case that such a direct proportionality does not hold. In this chapter we have reviewed the use of methods to analyze ligand-macromolecule equilibrium titrations that are monitored by indirect spectroscopic techniques. These methods of analysis yield thermodynamically rigorous, model-independent binding isotherms, hence assumptions concerning the relationship between the signal change and the extent of binding are not required. In fact, these methods can also be used to determine quantitatively the relationship between the signal change and the average degree of binding. In addition, the approaches discussed here are general and not limited to spectroscopic signals and therefore can be used with any intensive physicochemical property that reflects binding.

Rapid purification of porcine colostral whey lactoferrin by affinity chromatography on single-stranded DNA-agarose. Characterization, amino acid composition and N-terminal amino acid sequence

We have determined that the major iron-binding and DNA-binding protein in porcine colostral whey is lactoferrin. This lactoferrin was purified to homogeneity in one chromatographic step using immobilized single-stranded DNA-agarose. Although different in chromatographic behavior from human lactoferrin, the porcine lactoferrin purified in this manner was shown to be homogeneous by high-performance ion-exchange chromatography (Mono-S), immobilized metal ion (Cu2+) affinity chromatography, size-exclusion chromatography (TSK-4000SW), and reverse-phase (phenyl) chromatography. Electrophoresis on SDS-polyacrylamide gradient (10-20%) gels under reducing conditions showed the purified lactoferrin to be a single protein (silver-stained) of 78 kDa. Apolactoferrin purified in this manner bound iron and displayed a UV/VIS absorption spectrum indistinguishable from that of human lactoferrin. The molar absorption coefficient of hololactoferrin was 3.86 x 10(3) M-1 at 465 nm and 1.08 x 10(5) M-1 at 280 nm. Affinity elution analyses of the purified lactoferrin on immobilized DNA revealed that the affinity of this protein for DNA was independent of bound iron. Porcine lactoferrin was recognized by antibodies directed against human lactoferrin and bovine lactoferrin. The amino acid composition and N-terminal amino acid sequence analysis (30 residues) revealed a high degree of sequence homology with human, equine and bovine lactoferrin. These results demonstrate the effectiveness of immobilized DNA as a rapid and simple lactoferrin purification procedure and demonstrate the presence of a lactoferrin in porcine colostral whey with a high degree of sequence homology to human lactoferrin.

Differences in nuclear thyroid hormone receptors among species

Hepatic nuclear thyroid hormone receptors from rat, dog, chicken, and rainbow trout were compared. Receptor affinities for 3,5,3'-triiodo-L-thyronine (T3) were similar in preparations from rat, dog, and chicken, using isolated nuclei and nuclear extracts. Rainbow trout nuclear receptor showed a lower affinity for T3. Almost half of the receptors were released into the medium with rat and chicken nuclei, and 79.7 +/- 1.1% of the receptors were released with rainbow trout nuclei, when isolated nuclei were incubated with T3 at 22 degrees for 2 hr. The affinity constant of rat liver receptor for calf thymus DNA-cellulose at 0.17 M KCl, pH 7.4, was 3.98 +/- 1.47 x 10(5) M-1, when determined using DNA-cellulose columns. The number of salt bridges involved in DNA binding of the rat receptor was 5.73 +/- 0.38. When receptor-DNA interactions were compared among species, significant differences were found, but the receptors from dog and rainbow trout liver were similar. Sephacryl S-200 column chromatography showed that chicken receptor had a Stokes radius significantly smaller than that of rat receptor. Partial proteolysis of T3-receptor complex using trypsin alpha-chymotrypsin, elastase, and papain produced distinct T3-binding fragments in different species. Our data provide evidence that nuclear thyroid hormone receptors from different species have significant structural dissimilarities.

High affinity binding of the large T protein of polyoma virus to a genomic mouse DNA sequence

We purified a fragment of mouse DNA to which the large T protein of polyoma virus was bound in chromatin prepared from transformed mouse cells. This sequence, which is not repeated to a measurable extent within the mouse genome, does not show any significant homology to the viral ori region, except in a short region, which comprises a sequence related to the consensus for recognition by large T proteins ((A,T)GPuGGC). This region of pCG4 was confirmed by in vitro binding assays to be essential for T antigen binding.

Measurement of antigen-antibody binding constants by elution of affinity chromatography columns with continuous concentration gradients of dissociating agents

Elution of antibody-Sepharose 4 B columns previously loaded with antigen by a linear concentration gradient of Na I or NaSCN, was used for the calculation of binding constants for the human IgG - anti human IgG system. The values obtained by this method showed good agreement with the values obtained by "stepwise" elution with different NaI concentrations, with the values obtained when the antigen was immobilized, and with the values determined in solution. The method employed appears as a simple and useful possibility for the determination or comparison of K values.

Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: experimental approaches to the determination of thermodynamic parameters

Many biologically important proteins bind nonspecifically, and often cooperatively, to single-or double-stranded nucleic acid lattices in discharging their physiological functions. This binding can generally be described in thermodynamic terms by three parameters: n, the binding site size; K, the intrinsic binding constant; omega, the binding cooperativity parameter. The experimental determination of these parameters often appears to be straightforward but can be fraught with conceptual and methodological difficulties that may not be readily apparent. In this paper we describe and analyze a number of approaches that can be used to measure these protein-nucleic acid interaction parameters and illustrate these methods with experiments on the binding of T4-coded gene 32 (single-stranded DNA binding) protein to various nucleic acid lattices. We consider the following procedures: (i) the titration of a fixed amount of lattice (nucleic acid) with added ligand (protein); (ii) the titration of a fixed amount of ligand with added lattice; (iii) the determination of ligand binding affinities at very low levels of lattice saturation; (iv) the analysis of ligand cluster size distribution on the lattice; (v) the analysis of ligand binding to lattices of finite length. The applicability and limitations of each approach are considered and discussed, and potential pitfalls are explicitly pointed out.

Yeast RNA polymerase III. Chromatographic, catalytic and DNA-binding properties are highly dependent on the type of anion

The chromatographic, catalytic and DNA-binding properties of yeast RNA polymerase III are highly affected by both concentration and type of salt. The type of anion is an especially important modulating factor for the enzymological properties of the enzyme. When acetate or sulfate anions are substituted for chloride anions, RNA polymerase III exhibits a higher affinity for DEAE-Sephadex A25, becomes able to transcribe DNA at relatively high ionic strength and shows a significant increase in the binding strength to DNA. A quantitative analysis of the binding of the enzyme to single-stranded DNA shows that the number of ionic contacts in the complex is not affected by the type of anion, but the nonionic contribution to the binding constant is significantly increased when acetate is substituted for chloride.

Nonspecific binding of lac repressor to DNA. II. A small-angle neutron-scattering study

Complexes between lac repressor and DNA fragments from mononucleosomes have been studied by small-angle neutron scattering. Both the radius of gyration and the molecular weight of the complexes were measured, and the experimental results were interpreted according to a model with two types of complex (M. Charlier and J.-C. Maurizot, Biophys. Chem. 18 (1983) 303), and a statistical distribution of repressor on the DNA fragments. Good agreement between the model calculations and the experimental results was obtained. We concluded that there was an absence of strong cooperativity and of network formation between the complexes. The second type of binding, which does not induce any spectroscopic change, is marked by an increase in molecular weight of the complexes. Kinetic measurements were also made, which allowed the determination of the lifetime of the nonspecific DNA-repressor complexes.

Nonspecific binding of lac repressor to DNA. I. An absorption and circular dichroism study

Nonspecific binding of lac repressor on DNA has been studied by absorption and circular dichroism (CD) spectroscopies. In a first step, the complex formation is accompanied by an absorption difference spectrum and a change of the CD signal of the DNA. The absorption difference spectrum is mainly due to a spectral change of the DNA. The variation of the CD signal has been analyzed according to a model calculation, which takes into account the fact that the excluded site is shorter than the perturbed site. We found that in this first step one repressor can bind every 14 +/- 2 base-pairs, whereas one repressor perturbs 22 +/- 2 base-pairs. In a second step, more repressor can bind on DNA, but without further change in the absorption and CD spectrum, indicating that another binding process occurs. The model calculation developed here is general for all binding processes inducing a perturbation over a length of DNA longer than that of the excluded site.

Measurement of binding constants for divalent antibody-immobilized antigen interaction by antigen-sepharose 4B chromatography

Binding constants for the human IgG-anti human IgG heavy chain were determined from elution profiles obtained by loading human IgG-Sepharose 4B columns with the antibody and eluting it at different NaI concentrations. The agreement between the value obtained at zero NaI concentration and the value determined in solution by equilibrium molecular sieving was good. An application of this column method should be useful for comparison of avidity values of antibody populations of the same specificity.

Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor

It is shown that the amino acid sequence and the DNA gene sequence of the 25 amino-terminal residues of the lac repressor protein of Escherichia coli are homologous with the sequences of five DNA-binding proteins: the cro repressor proteins from phage lambda and phage 434, the cI and cII proteins from phage lambda, and the repressor protein from Salmonella phage P22. The region of homology between lac repressor and the other proteins coincides with the principal DNA-binding region of cro repressor. In particular, residues Tyr-17 through Gln-26 of lac repressor correspond to the alpha-helix Gln-27 through Ala-36 of cro repressor, which we have postulated to bind within the major groove of the DNA and to be primarily responsible for the recognition of the DNA operator region by the protein [Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981) Nature (London) 290, 754--758]. By analogy with cro repressor, we propose that residues 17--26 of lac repressor are alpha-helical and that this helix and a twofold-related alpha-helix in an adjacent subunit bind within successive major grooves of the lac operator, which is in a right-handed Watson--Crick B-DNA conformation. Also, by analogy with cro repressor, we suggest that residues Thr-5 through Ala-13 of lac repressor form a second alpha-helix and contribute, in part, to DNA binding. The proposed structure for the DNA-binding region of lac repressor is consistent with chemical protection data and with genetic experiments identifying the probable locations of a number of the residues of the repressor protein that either do or do not participate in DNA binding.

Salt dependence of the kinetics of the lac repressor-operator interaction: role of nonoperator deoxyribonucleic acid in the association reaction

The kinetics of binding of lac repressor protein and operator deoxyribonucleic acid (DNA) have been studied as a function of monovalent and divalent cation concentration. The salt dependence of the association and dissociation rate constants has been interpreted in light of recent theoretical analyses based on Manning's counterion condensation model. The bell-shaped dependence of the association rate constant on salt concentration evidences a role for nonoperator DNA binding in the repressor's search for the operator site on a large DNA molecule. At intermediate mono- or divalent cation concentrations, the association rate goes through a maximum. At lower cation concentrations, it decreases and becomes dependent on DNA concentration; the high affinity of repressor for nonoperator DNA confines the protein to the DNA. At higher cation concentrations, the association rate decreases and becomes dependent on the weak affinity of repressor for nonoperator DNA. The kinetic data are fit to the theory of Berg and Blomberg [Berg, O. G., & Blomberg, C. (1978) Biophys. Chem. 8, 271] for the salt dependence of association kinetics with coupled diffusion, using published values of the affinity for nonoperator DNA. From this fit, one-dimensional diffusion of repressor along the DNA chain is estimated to be about 4 times faster on MgDNA than on NaDNA. At higher cation concentrations, the salt dependence of the association and dissociation rate constants is consistent with a preequilibrium mechanism for the association reaction [Lohman, T. M., deHaseth, P. L., & Record, M. T., Jr. (1978) Biophys. Chem. 8, 281]. Agreement between literature values (corrected for the presence of Mg2+) and experimental values of the rate constants in the presence of monovalent salt is quite good.

Hydrogen bonding in deoxyribonucleic acid base recognition. 2. Deoxyribonucleic acid binding studies of acridine alkylamides

A series of derivatives of 2-methoxy-6-chloro-9-aminoacridine bearing side chains terminated by various groups, such as carboxamide, N-methylcarboxamide, N,N-dimethylcarboxamide, methyl ester, and methyl were synthesized. The interaction of these intercalating dyes with DNA of various GC content was studied comparatively by using equilibrium dialysis and fluorescence spectroscopy. The results showed that the compounds bearing a chain terminated by a free carboxamide group could interact specifically with GC-rich DNA provided that the length and conformation of the side chain were appropriate. From these results in hand as well as those reported in the preceding paper (NMR studies at the minihelix level) it is thought that the G specificity of these compounds arises from their ability to form hydrogen bonds between the terminal carboxamide group borne by their side chain and the NH2 and N3 of the adjacent guanine located in the small grove.

Site-specific DNA-affinity chromatography of the lac repressor

To test the feasibility of site-specific DNA-affinity chromatography, E. coli lac repressor was bound to an operator-containing DNA column, and in parallel to a non-operator DNA column. Salt gradient elution shows: 1) elution from non-operator DNA was near 250mM KCl or NaCl; interpretation of this result suggests the usefulness of the procedure for studying salt-dependence of DNA-protein affinities; 2) elution from operator-containing DNA was delayed (average elution = 1000mM salt), demonstrating a feasibility of site-specific DNA-affinity chromatography, if one provides a sufficiently favorable ratio of specific to non-specific DNA binding sites; 3) repressor eluted from operator-containing DNA over a very broad salt range, which may represent chromatography-generated repressor heterogeneity.