SRYand architectural gene regulation: the kinetic stability of a bent protein-DNA complex can regulate its transcriptional potency.

Protein-directed DNA bending is proposed to regulate assembly of higher-order DNA-multiprotein complexes (enhanceosomes and repressosomes). Because transcriptional initiation is a nonequilibrium process, gene expression may be modulated by the lifetime of such complexes. The human testis-determining factor SRY contains a specific DNA-bending motif, the high-mobility group (HMG) box, and is thus proposed to function as an architectural factor. Here, we test the hypothesis that the kinetic stability of a bent HMG box-DNA complex can in itself modulate transcriptional potency. Our studies employ a cotransfection assay in a mammalian gonadal cell line as a model for SRY-dependent transcriptional activation. Whereas sex-reversal mutations impair SRY-dependent gene expression, an activating substitution is identified that enhances SRY's potency by 4-fold. The substitution (I13F in the HMG box; fortuitously occurring in chimpanzees) affects the motif's cantilever side chain, which inserts between base pairs to disrupt base pairing. An aromatic F13 cantilever prolongs the lifetime of the DNA complex to an extent similar to its enhanced function. By contrast, equilibrium properties (specific DNA affinity, specificity, and bending; thermodynamic stability and cellular expression) are essentially unchanged. This correlation between potency and lifetime suggests a mechanism of kinetic control. We propose that a locked DNA bend enables multiple additional rounds of transcriptional initiation per promoter. This model predicts the occurrence of a novel class of clinical variants: bent but unlocked HMG box-DNA complexes with native affinity and decreased lifetime. Aromatic DNA-intercalating agents exhibit analogous kinetic control of transcriptional elongation whereby chemotherapeutic potencies correlate with drug-DNA dissociation rates.

RNA recognition by a bent alpha-helix regulates transcriptional antitermination in phage lambda.

A novel RNA recognition motif is characterized in an arginine-rich peptide. The motif, derived from lambda transcriptional antitermination protein N, regulates an RNA-directed genetic switch. Its characterization by multidimensional nuclear magnetic resonance (NMR) demonstrates specific RNA-dependent folding of N- and C-terminal recognition helices separated by a central bend. The biological importance of the bent alpha-helix is demonstrated by mutagenesis: binding is blocked by substitutions in the N peptide or its target (the boxB RNA hairpin) associated in vivo with loss of transcriptional antitermination activity. Although arginine side chains are essential, the peptide is also anchored to boxB by specific nonpolar contacts. An alanine in the N-terminal helix docks in the major groove of the RNA stem whereas a tryptophan in the C-terminal helix stacks against a purine in the RNA loop. At these positions all 19 possible amino acid substitutions have been constructed by peptide synthesis; each impairs binding to boxB. The pattern of allowed and disallowed substitutions is in accord with the results of random-cassette mutagenesis in vivo. The helix-bend-helix motif rationalizes genetic analysis of N-dependent transcriptional antitermination and extends the structural repertoire of arginine-rich domains observed among mammalian immunodeficiency viruses.

An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch.

Antitermination protein N regulates the transcriptional program of phage lambda through recognition of RNA enhancer elements. Binding of an arginine-rich peptide to one face of an RNA hairpin organizes the other, which in turn binds to the host antitermination complex. The induced RNA structure mimics a GNRA hairpin, an organizational element of rRNA and ribozymes. The two faces of the RNA, bridged by a sheared GA base pair, exhibit a specific pattern of base stacking and base flipping. This pattern is extended by stacking of an aromatic amino acid side chain with an unpaired adenine at the N-binding surface. Such extended stacking is coupled to induction of a specific internal RNA architecture and is blocked by RNA mutations associated in vivo with loss of transcriptional antitermination activity. Mimicry of a motif of RNA assembly by an RNA-protein complex permits its engagement within the antitermination machinery.

The fibronectin-binding domain of transglutaminase.

Guinea pig liver transglutaminase (EC 2.3.2.13) displays a Ca(2+)-independent binding (Ka = 10(7) M-1) to the same gelatin-binding domain of human plasma fibronectin that is known to form a very tight complex with the human red cell enzyme. The fibronectin-combining site of the liver transglutaminase was investigated by testing fragments obtained from the parent protein by controlled digestion with endoproteinase Lys-C. Overlay assays, probed with anti-fibronectin antibody, revealed that the fibronectin binding ability of the transglutaminase was encoded in a linear sequence in its 28-kDa N-terminal domain. Removal of the first 7 residues by further digestion of the purified 28-kDa material with endoproteinase Glu-C generated a 27-kDa fragment that, however, showed no binding activity. Thus, residues 1-7 in the liver enzyme seem to be of particular importance for influencing its ability to bind to fibronectin.

Association of the A subunits of recombinant placental factor XIII with the native carrier B subunits from human plasma.

Interactions of a recombinant human placental protein (rA2) expressed in yeast and considered to be identical to the catalytic A2 subunits of factor XIII, the fibrin stabilizing factor zymogen, were examined with the native carrier subunits (B2) of the factor isolated from human plasma. Nondenaturing electrophoresis and HPLC gel-filtration experiments showed a tight binding of rA2 to B2 for forming an ensemble similar to that of plasma factor XIII (A2B2). In the presence of excess B2, however, some higher ordered oligomers (rA2Bn, where n > 2) were also seen in electrophoresis. The same technique revealed a microheterogeneity in the rA2 preparation; nevertheless, all isoforms could bind to B2. By employing an ELISA procedure for measuring free B2 in mixtures with rA2, an apparent binding constant of 4 x 10(7) M-1 was derived for the association of rA2 with B2. Fluorescence depolarization was used to monitor the heterologous association of rA2 with fluorescein-labeled B2F as well as the dissociation of the rA2B2F structure. The former was characterized by an increase, and the latter by a decrease, in the fluorescence anisotropy of the system. Binding of rA2 to B2F (pH 7.5, mu = 0.315, 37 degrees C) was not influenced by low concentrations of Ca2+ (< or = 30 mM), and rA2B2F proved to be quite stable under these conditions. Much higher concentrations of Ca2+, as well as higher ionic strengths, were required to dissociate this assembly. By contrast, release of B2F from the thrombin-modified rA2'B2F occurred rapidly in the presence of low concentrations of Ca2+ at low ionic strength.(ABSTRACT TRUNCATED AT 250 WORDS)

Affinity of human erythrocyte transglutaminase for a 42-kDa gelatin-binding fragment of human plasma fibronectin.

Complex formation between the human erythrocyte transglutaminase (protein-glutamine:amine gamma-glutamyltransferase, EC 2.3.2.13) and fibronectin or its fragments was examined by immunoanalytical procedures and by fluorescence polarization. A 42-kDa gelatin-binding structure, obtained from human plasma fibronectin by thermolytic digestion, showed as high an affinity for the cytosolic enzyme as the parent fibronectin chains themselves. A 21-kDa fragment comprising type I modules 8 and 9, the last two modules in the 42-kDa fragment, bound with an affinity 100-fold less than the 42-kDa fragment. Binding was remarkably specific and could be exploited for the affinity purification of transglutaminase directly from the hemoglobin-depleted erythrocyte lysate. In spite of the high affinity, it was possible to elute active enzyme from the 42-kDa fragment column with 0.25% monochloroacetic acid. This solvent might have general applicability in other systems involving separation of tightly bound ligands.

Visualization of purified fibronectin-transglutaminase complexes.

It has been reported previously (Turner, P.M., and Lorand, L. (1989) Biochemistry 28, 628-635) that human erythrocyte transglutaminase forms a noncovalent complex with human plasma fibronectin near its collagen-binding domain. In the present study, we show by nondenaturing electrophoresis that guinea pig liver transglutaminase, similarly to the erythrocyte enzyme, forms a complex with human fibronectin. Studies of anisotropic shifts of fluorescein-labeled liver and erythrocyte transglutaminases, upon addition of fibronectin, indicated that both transglutaminases bind to fibronectin with a stoichiometry of about 2:1. Polymerization of fibrinogen by human erythrocyte transglutaminase was inhibited after complex formation with fibronectin. Complexes of fibronectin with either erythrocyte or liver transglutaminase were isolated by glycerol gradient zone sedimentation and examined by rotary shadowing electron microscopy. The globular transglutaminase could be readily identified binding to the thin fibronectin strand. The binding site for transglutaminase was within 5-10 nm of the N terminus of fibronectin, consistent with its proximity to the collagen-binding domain. Under some experimental conditions, the complex of fibronectin with erythrocyte transglutaminase appeared as a ring-shaped structure in which two transglutaminase molecules had probably dimerized. The molecular weight of the erythrocyte transglutaminase was determined by sedimentation equilibrium to be 71,440 +/- 830.

Conformational properties of streptokinase.

The conformational properties of streptokinase (SK) have been assessed by the techniques of differential scanning calorimetry, circular dichroism (CD), and through a combinational approach employing several algorithms which are predictive of secondary structural characteristics. In low ionic strength buffers, SK undergoes a reversible two-state thermal transition with a temperature of maximum heat capacity (Tm) of 46.1 +/- 0.9, a delta Hcal of 98 +/- 11 kcal/mol and a delta Hcal/delta HvH of approximately 1. In high ionic strength buffers, similar calorimetric properties were obtained with the exception that the delta Hcal/delta HvH values were considerably less than 1, indicating the existence of an additional irreversible thermally induced alteration in the molecule, most likely resulting in its aggregation. The effect of pH on the thermal unfolding properties of SK was determined. The results demonstrated that single two-state thermal transitions were obtained, with progressively decreasing Tm values, as the pH was reduced from 6.4 to 3.4, indicating a destabilization of the entire molecule at reduced pH. In the alkaline region, between pH 8.4 and 9.4, stabilization of a separate region of the molecule was obtained, as evidenced by an increase in the delta Hcal/delta HvH to values approximating 2. CD analysis was performed in order to estimate secondary structural characteristics of SK. The best fit of secondary structural parameters to the experimental CD spectrum provided estimates of 17% helices, 28% beta-sheet, 21% beta-turns, and 34% disordered structures. Both the intensity of the spectral band at 208 nm and the level of antiparallel beta-sheet strongly suggest that SK is an alpha + beta protein.

A differential scanning calorimetric investigation of the domains of recombinant tissue plasminogen activator.

The differential scanning calorimetric (DSC) properties of a series of recombinant tissue plasminogen activators (rt-PA) have been examined. The endotherm obtained for native rt-PA can be deconvoluted into a pair of two-state transitions, which indicates that two separate observable regions of the molecule undergo independent melting. A distinguishing feature of native rt-PA is the dependence of the temperature of the maximum heat capacity of the endothermic transitions (Tm) on the thermal scan rate of the samples, suggesting that a kinetic process, involving conversion of a reversibly denatured to an irreversibly denatured form of the protein, with an energy of activation of approximately 81.5 kcal/mol, characterizes its thermal denaturation. A comparison of the conformational properties of rt-PA preparations which have been produced in different expression systems, as revealed by DSC analysis of their thermal denaturation characteristics, has demonstrated that subtle differences do occur. Similar studies with deletion mutants of rt-PA suggest that the growth factor domain (EGF) plays a role in its overall thermal stability, when the protein also contains the kringle 1 region, and removal of the EGF domain leads to conformational alterations in other areas of the molecule.

Rapid formation of an anion-sensitive active site in stoichiometric complexes of streptokinase and human [Glu1]plasminogen.

We have examined the time-dependent appearance of amidolytic activity in equimolar complexes of streptokinase (SK) and human [Glu1]plasminogen (HPg) under various conditions. When stoichiometric levels of the two proteins are incubated and assayed in hypotonic buffers at 4 degrees C, amidolytic activity toward the chromogenic substrate D-Val-Leu-Lys-p-nitroanilide (S-2251), within the resulting complex, appears with an observed first-order rate constant of 1.03 +/- 0.06/min. On the other hand, when the assay for amidolytic activity is conducted at a C1- concentration of 0.15 M, this same activity develops with an observed first-order rate constant of 0.13 +/- 0.01/min. Under all conditions of assay of importance to the mechanism proposed, the only molecular components present are SK and HPg. The rate of appearance of an enzyme species displaying amidolytic activity is dependent on the anion in its assay; a much slower rate constant is obtained with C1- than with AcO-. These observations are consistent with the formation, within the complex, of an early anion-sensitive active site (SK-HPg) that is converted to a form (SK-HPg') that is much less sensitive to the presence of anions. During the time period of this process, no conversion of plasminogen to plasmin occurs within the complex. Steadystate kinetic properties of SK-HPg and SK-HPg' have been measured toward the substrate S-2251. Consistent with the mechanism suggested above, the amidolytic activity of SK-HPg is inhibited by C1- to a much greater extent than is that of SK-HPg'.