Tài liệu Báo cáo khoa học: A differential scanning calorimetry study of tetracycline repressor pptx

A differential scanning calorimetry study of tetracycline repressor Sylwia Ke ˛ dracka-Krok and Zygmunt Wasylewski Department of Physical Biochemistry, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland Tetracycline repressor (TetR), which constitutes the most common mechanism of bacterial resistance to an antibiotic, is a homodimeric protein composed of two identical sub- units, each of which contains a domain possessing a helix– turn–helix motif and a domain responsible for binding tetra- cycline. Binding of tetracycline in the protein pocket is accompanied by conformational changes in TetR, which abolish the specific interaction between the protein and DNA. Differential scanning calorimetry (DSC) and CD measurements, performed at pH 8.0, were used to observe the thermal denaturation of TetR in the absence and pres- ence of tetracycline. The DSC results show that, in the absence of tetracycline, the thermally induced transitions of TetR can be described as an irreversible process, strongly dependent on scan rate and indicating that the protein denaturation is under kinetic control described by the simple kinetic scheme: N 2 À! k D 2 ,wherek is a first-order kinetic constant, N is the native state, and D is the denatured state. On the other hand, analysis of the scan rate effect on the transitions of TetR in the presence of tetracycline shows that thermal unfolding of the protein can be described by the two-state model: N 2 ! U 2 À! D. In the proposed model, TetR in the presence of tetracycline undergoes co-operative unfolding, characterized by an enthalpy change (DH cal ¼ 1067 kJÆmol )1 ) and an entropy change (DS ¼ 3.1 kJÆmol )1 ). Keywords: circular dichroism; differential scanning calori- metry; tetracycline repressor; tetracycline; thermal denatur- ation. Resistance to tetracycline (Tc), which is the most common form of antibiotic resistance in Gram-negative bacteria, is based on the activation of the drug efflux through the cytoplasmic membrane mediated by the antiporter protein TetA. Expression of the tetA gene is strictly regulated by the Tc repressor (TetR) protein. TetR occurs as a homodimer in which two identical helix–turn–helix (HTH) motifs bind in the absence of [Mg–Tc] + to two adjacent major grooves of DNA, thus, preventing transcription of the tetR gene that encodes TetR itself and of the tetA gene that encodes the resistance protein TetA. If Tc enters a resistant bacterial cell, it binds with high affinity to TetR [1]. This binding is accompanied by conformational changes in TetR, which abolish the specific interaction with DNA, reduces the binding affinity for operator DNA by 6–8 orders of magnitude [2] and finally induces the release of the TetR– [Mg–Tc] + ternary complex, thereby initiating expression of TetA [3,4]. Regulation of TetR by binding of [Mg–Tc] + takes place in the core of the repressor, which is formed by helices a5toa10 of both subunits. Study of the crystal structure of the TetR homodimer in complex with its palindromic DNA operator shows that after [Mg–Tc] + insertion into the binding tunnel in the repressor core, Tc is anchored by hydrogen bonds between its functional groups and the C-terminal side chains of helix a4, and helices a5 and a6. This initiates conformational changes starting with C-terminal unwinding and shifting of the short helix a6in each monomer. Subsequently, it forces a pendulum-like motion of helix a4, which increases the separation of the attached DNA-binding domains by 3 A ˚ [5]. As TetR–tetO is the most efficient inducible system of transcriptional regulation known so far, it is often used as a tool for selective target gene regulation in eukaryotes [6,7]. From the studies of Backes et al. [8], it is known that urea-induced unfolding of TetR is a reversible reaction described by a two-state model. There was no evidence for the existence of unfolding intermediates, so the conclusion was drawn that the TetR dimer dissociates and unfolds in coincident reaction and that the folded monomers are unstable. Thermal denaturation studies, using temperature gradient gel electrophoresis, indicate that the free TetR and its complex with Tc exhibit monophasic transition upon denaturation [9]. The main aim of this study is to show how binding of Tc influences the stability of TetR. Differential scanning calorimetry (DSC) was applied as the most direct experi- mental technique to elucidate the energetics of conforma- tional transitions of biological macromolecules [10–12]. Materials and methods Materials Acrylamide, phenylmethanesulfonyl fluoride, Tc and Tris were purchased from Sigma. Dithiothreitol, MgCl 2 .6H 2 O and NaCl were from Fluka. The Fractogel EMD Correspondence to Z. Wasylewski, Department of Physical Biochemistry, Faculty of Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland. Fax: + 48 12 25 26 902, Tel.: + 48 12 25 26 122, E-mail: wasylewski@mol.uj.edu.pl Abbreviations: TetR, tetracycline repressor; DSC, differential scanning calorimetry; DLS, dynamic light scattering; CRP, cAMP receptor protein. (Received 26 June 2003, revised 15 September 2003, accepted 29 September 2003) Eur. J. Biochem. 270, 4564–4573 (2003) Ó FEBS 2003 doi:10.1046/j.1432-1033.2003.03856.x SO À 3 650 (M) was from Merck, and Q Sepharose Fast Flow and Sephacryl S-200 HR were from Amsterdam Pharmacia Biotech. The nutrients for bacterial growth were from Life Technologies. All other chemicals were products of analyt- ical grade from Polish Chemical Reagents (Gliwice, Poland). Buffers in water purified by the Millipore system were used throughout this work. Protein purification The wild-type Tet repressor was overproduced in Escheri- chia coli strain RB 791 (a gift from W. Hillen, Universitat Erlangen-Nurnberg, Germany). Protein purification in general followed the scheme described by Ettner et al. [13] with a few modifications [14]. After the purification procedure, the protein was highly pure (> 97%) as judged by SDS/PAGE and Coomassie Brilliant Blue staining. The dimer repressor concentration was determined spectrophotometrically using an excitation coefficient e 280nm ¼ 30 · 10 3 M )1 Æcm )1 [15]. The activity of the proteins was checked using the Tc titration method. The concentration of Tc was determined in 0.1 M HCl using an excitation coefficient e 355nm ¼ 13320 M )1 Æcm )1 [16]. All measurements for unliganded protein were performed in buffer A (10 mM Tris/HCl, 150 mM NaCl, 2 m M dithiothreitol, pH 8.0), but for the complex of protein with Tc, buffer B, which also contained 10 mM MgCl 2 ,was used. The Tris/HCl buffer was chosen because the [TetR–Tc] complex is stable at high pH up to 12. Below pH 8.0, the complex stability decreases, and the binding of Tc is completely inhibited at pH 5.0 [17]. It is known that Tris buffer exhibits a pronounced dpK/dT dependence. However, the results were not significantly affected by pH change with increasing temperature. A comparison of calorimetric enthalpy and denaturation temperature for the protein in the absence of Tc, in buffer with and without Mg, does not show any differences in these values. Differential scanning calorimetry DSC experiments were performed on a Calorimetry Sciences Corporation (CSC) 6100 Nano II differential scanning calorimeter with a cell volume of 0.3228 mL, interfaced with a personal computer (IBM-compatible). Different concen- trations of the protein samples within the 0.4–4.0 mgÆmL )1 range and different scan rates of 0.1–2.0 KÆmin )1 were used. Before the measurements, the protein samples were exhaust- ively dialyzed against buffer A, and the samples with Tc against buffer B. The samples and reference solutions were degassed for at least 5 min at room temperature and carefully loaded into the cells to avoid bubble formation. Cells were carefully cleaned before each experiment. A constant pressure of 304 kPa was maintained to prevent possible degassing of the samples on heating. A background scan recorded with the buffer in both cells was subtracted from each test scan. The reversibility of thermal transitions was checked by examining the reproducibility of the calorimetric trace in the second heating of the sample immediately after fast cooling from the first scan. The excess molar heat capacity was calculated using the molecular mass of the Tet repressor of 46 708 Da and the partial specific volume of the protein equal to 0.73 mLÆg )1 , which has been calculated from the amino-acid sequence as described by Perkins [18]. To obtain the C exc p ,the ORIGIN software package (Microcal) was used for baseline subtrac- tion and determination of total enthalpy change. The pre- transition and post-transition parts of the DSC profiles were extrapolated by nth order polynomial in the Origin, although 4th order polynomial (in SIGMA PLOT )wasalso checked. The differences in mean calorimetric enthalpy and denaturation temperature obtained with these two methods did not exceed 5% and 0.2 °C, respectively. The shape of the pre-transition and post-transition baselines changed from scan to scan, but these differences were not significant. The transition curves were integrated numerically. Molar transition enthalpies DH cal referring to the molecular mass of the protein and the van’t Hoff enthalpies (DH vH )were calculated from the equation: DH vH ¼ ART 2 max C exc;max p DH cal ð1Þ where C exc,max p is the excess of molar specific heat capacity over the baseline value at maximum transition, T max is the denaturation temperature in Kelvin, DH cal is the total molar enthalpy change during the denaturation process, R is the gas constant, and A is equal to 4.0 for monomer or for nondissociated dimer [19]. Circular dichroism CD measurements were performed on a Jasco-710 spectro- polarimeter equipped with water-jacketed cell holder and a Julabo F25 circulator bath with programmable temperature controller. The actual temperature inside the quartz cell (with path length of 1 mm) was measured with Digi-sense thermocouple thermometer. Protein thermal denaturation was monitored by following the changes in ellipticity at 222nm with a scan rate of 1KÆmin )1 . Spectra were collected in the temperature range 25–80 °C. The data were analysed and the midpoint melting temperature (T m )values were determined by noise reduction and differentiation of curves using the Standard Analysis program provided with the instrument. Dynamic light scattering (DLS) DLS measurements were made using a DynaPro-MS800 instrument from Protein Solution Inc. (Charlottesville, VA, USA). All samples were filtered through a 0.02-lmmem- brane (Whatman; Anodisc 13) into a 45-lL(3mmpath length) quartz cuvette. The measurements were performed at 20 ± 0.1 °C. DLS data were analyzed by the auto- correlation method to calculate the translational diffusion coefficient (D T ) of the TetR protein and its complex with Tc. The results were analyzed by applying monomodal and bimodal models. The hydrodynamic radius (R H )isderived from D T using the Stokes–Einstein equation: R H ¼ k B T=6pgD T ð2Þ where k B is the Boltzman constant, T is temperature in Kelvin, and g is the solvent viscosity. The theoretical hydrodynamic radius (R theo H ) can be obtained from the following formula: Ó FEBS 2003 DSC study of tetracycline repressor (Eur. J. Biochem. 270) 4565 R theo H ¼½ð3Mðm þ hÞÞ=ð4pN A Þ 1=3 where N A is the Avogadro constant, m is the partial specific volume, h is the hydration, and M is the molar mass of the protein. The ratio R H =R theo H provides informa- tion about the shape of a molecule in the solution. Results DSC measurements Wild-type TetR and its complex with Tc underwent irreversible denaturation under all adopted conditions, even if the sample was cooled immediately after the peak absorption was completed and then it was scanned again, or when heating was stopped near maximum point and then the sample was cooled and reheated. Aggregation was evident in samples extracted from the calorimetric cell. There were substantial instrumental distortions that resulted in uncertainties and baseline variability. In addition, an exothermic peak was present for higher protein concentra- tions on the high temperature side of the DSC endotherm. The calorimetric effect for the sample (without Tc) at protein concentrations lower than 0.4 mgÆmL )1 was at the level of the instrumental noise, which was approximately ±0.4 lW. The concentration effect Thermograms for TetR were measured in buffer A as a function of protein concentration from 0.4 to 4.0 mgÆmL )1 at a scan rate of 1.0 KÆmin )1 . Denaturation scans for samples with Tc were carried out in buffer B at a molar ratio of 5 mol Tc per mol of the protein dimer, with a similar concentration range and the same scan rate as for samples without the ligand. The typical denaturation curves for TetR and its complex with Tc are presented in Fig. 1. Fig. 2 shows the dependence of T max on the concentration of the protein. In the case of TetR, the T max obtained decreases with increasing protein concentration, which indicates that TetR unfolds without dissociation. Indeed, if multimeric proteins undergo unfolding with simultaneous dissociation into monomers, T max should increase with the total protein concentration [20,21]. The DSC profiles obtained for TetR alone are highly asymmetrical, and the ratio DH cal /DH vH is much below unity, i.e. between 0.55 and 0.76 (Table 1), which indicates some oligomerization, which is independent of protein concentration over the range used in these studies. The calorimetric enthalpy, DH cal , although determined with some inaccuracy because of the existence of an exothermic peak, increases a little with a rise in TetR concentration (Table 1). The enthalpic effect that accompanies the aggregation of TetR is pronounced above a concentration of 0.4 mgÆmL )1 , and cannot be ignored. Furthermore, the minimum of the negative peak shifts towards the low temperature, and the exotherm intensity decreases as the concentration increases. It is evident that the concentration influences the two thermal phenomena in the same direction, namely both peaks shift towards the low temperature side when concentration increases. However, this effect is greater for the exothermic peak than for the endothermic one. As a consequence, at the high protein concentration (% 4.0 mgÆmL )1 ) the two peaks almost overlap. The dependence of T max on the concentration of Tc bound to TetR is more complex (Fig. 2). The very small changes in the T max of the [TetR–Tc] complex observed on increasing the temperature, together with the observation that the transitions do not change their symmetrical shape with increasing temperature, lead us to conclude that the Fig. 1. Typical thermograms of TetR (broken line) and complex of TetR with Tc (solid line). Measurements were made in buffer A (10 m M Tris/ HCl buffer, pH 8.0, containing 150 mM NaCl and 2 m M dithiothrei- tol) at a scan rate of 1 KÆmin )1 and buffer B (10 m M Tris/HCl buffer, pH 8.0, containing 150 m M NaCl, 2 m M dithiothreitol and 10 m M MgCl 2 )atascanrateof1KÆmin )1 , for TetR alone and for the com- plex of TetR with Tc, respectively. Protein concentration in both cases was 0.4 mgÆmL )1 . The ratio of concentrations was 5 mol Tc/mol TetR dimer. Fig. 2. Effect of concentration on transition temperature (T max ). The circles correspond to T max for TetR obtained from DSC measurements (d) and CD experiments (s). The triangles correspond to T max for the complex of Tet repressor with Tc (5 mol excess of Tc over 1 mol of the dimer was applied); (m) data obtained from DSC; (n)datafromCD measurements. 4566 S. Ke˛dracka-Krok and Z. Wasylewski (Eur. J. Biochem. 270) Ó FEBS 2003 liganded TetR unfolds without simultaneous dissociation into monomers. For TetR alone, at a concentration of 0.4 mgÆmL )1 and scan rate of 1 KÆmin )1 , T max is 60.4 °C. The denaturation temperature, T max , of the complex of TetR with Tc is 70.4 °C, measured at a protein concentration of 0.4 mgÆmL )1 and scan rate of 1 KÆmin )1 (Figs 1 and 2). Therefore, under these experimental conditions, binding of Tc causes an increase in the T max of the protein of % 10.0 °C. The ligand binding leads to a doubling of the denaturation enthalpy value (Table 1). Effect of the scan rate Thermal denaturation of TetR was carried out at a protein concentration of 0.6 mgÆmL )1 andscanrate(v)of 0.1–2.0 KÆmin )1 . Measurements of liganded protein were performed in buffer B, at a protein concentration of 0.4 mgÆmL )1 and at fivefold molar excess of Tc per mol of the dimer. The denaturation enthalpy values of the proteins (in the absence and presence of ligand) as a function of scan rate are shown in Table 2. A small decrease in denaturation enthalpy was observed on a rise in scan rate for the repressor in the absence of Tc, whereas for the ligated protein, a slight increase was noted. The T max is the increasing linear function of the scan rate of TetR (Fig. 3). These results indicate that denaturation of TetR protein occurs as a kinetically controlled process, which cannot be described by equilibrium thermodynamics [21–23]. This kind of denaturation process is assumed to be a first-order reaction with a rate constant, k, that changes with temperature, according to the Arrhenius equation: k ¼ Aexp À E a RT  ¼ exp E a R  1 T à À 1 T  where E a is the activation energy and T* is the temperature at which k ¼ 1min )1 (the frequency factor is equal to exp(E/RT*)). The rate of transition between these states is limited by the energy of activation, which is determined by the conformation of the transition state. In this case, the excess heat capacity C exc p is given by the equation [24]: C exc p ¼ 1 m DHexp E a R 1 T à À 1 T  ÂÀ 1 m Z T T 0 exp E a R 1 T à À 1 T  dT 8 < : 9 = ; ð3Þ Table 1. Apparent thermodynamic transition parameters for TetR and complex of TetR with Tc at various concentrations. The buffer for TetR was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, pH 8.0. The buffer for TetR + Tc was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, 10 mM MgCl 2 ,pH8.0. TetR TetR + Tc c (mgÆmL )1 ) DH cal (kJÆmol )1 ) DH cal /DH vH c (mgÆmL )1 ) DH cal (kJÆmol )1 ) DH cal /DH vH 0.40 397.84 0.59 0.30 954.40 0.89 0.60 411.54 0.55 0.40 1058.14 0.92 0.90 502.76 0.68 0.50 1230.56 1.08 1.50 517.59 0.71 1.00 1031.91 0.88 2.00 520.23 0.76 2.00 1134.11 1.03 3.00 515.79 0.57 2.80 1025.80 0.91 4.00 527.98 0.58 3.40 1080.94 0.89 – – 4.00 976.98 1.03 – – – 4.00 988.80 1.13 – Mean (± SD) – 484.82 (55.39) 0.64 (0.08) – 1053.53 (86.40) 0.97 (0.10) Table 2. Apparent thermodynamic transition parameters of TetR and complex of TetR with Tc at various heating rates. The buffer for TetR was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, pH 8.0. The buffer for TetR + Tc was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, 10 mM MgCl 2 ,pH8.0. TetR TetR + Tc m (KÆmin )1 ) DH cal (kJÆmol )1 ) DH cal /DH vH m (KÆmin )1 ) DH cal (kJÆmol )1 ) DH cal /DH vH 0.10 541.22 0.78 0.10 920.25 0.81 0.50 550.27 0.91 0.50 911.66 0.88 1.00 495.84 0.78 1.00 1084.25 0.97 1.50 482.10 0.76 1.50 1030.15 0.99 2.00 452.73 0.70 2.00 1061.91 1.05 Mean (± SD) – 504.43 (40.94) 0.78 (0.08) – 1001.62 (80.62) 0.94 (0.09) Ó FEBS 2003 DSC study of tetracycline repressor (Eur. J. Biochem. 270) 4567 where DH is the enthalpy difference between the denatured and native state, m ¼ dT/dt is the scan rate, and E a is the activation energy. The thermal dependence of heat capacity (C exc p )forTetR was fitted to the experimental curves. The results are presented in Fig. 4. The mean value for the activation energy, E a , was calculated as 409.14 ± 30.5 kJÆmol )1 ,and the mean value of temperature T*wasdeterminedas 61.53 ± 0.9 °C. The results are presented in Table 3. To check further the validity of the two-state kinetic model, proposed for denaturation of TetR alone, the following equations proposed by Kurganov et al. [24] were used: d ln C exc p  d1=T ¼ 1 m  T 2  exp E a R  1 T à À 1 T  À E a R ð4Þ 1 T ¼ 1 T à À ln mC exc p Q t À Q  E a R ð5Þ The estimated Arrhenius equation parameters obtained from Eqns (3), (4), and (5) are in good agreement with each other and clearly support the proposed model of TetR denaturation in the absence of Tc. The temperature dependence of excess molar heat capacity of TetR in the presence of Tc, at various scan rates is presented in Fig. 5, and the dependence of the transition temperature, T max ,onscanrateforTetR– [Mg–Tc] + complexes is shown in Fig. 3. The T max rapidly increases in the range of low scan rates, but for higher scan rates, it reaches a noticeable plateau. Such a relationship between T max and scan rate indicates that this type of equilibrium thermodynamic analysis can be employed [21,25,26]. The enthalpy change associated with transition is equal to the area under the peak(s), i.e. DHðT max Þ¼ Z T F T 0 C exc p dT: The entropy change is given by DSðT max Þ¼ Z T F T 0 C exc p T dT; Fig. 4. Temperature dependence of excess molar heat capacity of TetR at a scan rate of 0.5 (n), 1.0 (h), 1.5 (s)or2.0(e)KÆmin )1 in buffer A. Solid lines are the best fit to each curve according to Eqn (3). Protein concentration was always 0.6 mgÆmL )1 . Fig. 3. Effect of scan rate on transition temperature. Data obtained from DSC experiments. (d) T max for TetR; (m) T max for the complex ofTetrepressorwithTc(5molexcessofTcover1molofthedimer was applied). The continuous lines have no theoretical meaning and are shown to guide the eye. Table 3. Arrhenius equation parameters estimated from the two-state irreversible model of thermal denaturation of TetR according to Eqns (3), (4) and (5). The buffer was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, pH 8.0. TetR m (KÆmin )1 ) DH (kJÆmol )1 ) E a (kJÆmol )1 ) T* (°C) Based on: Eqn 3 Based on: Eqn 3 Eqn 4 Eqn 5 Based on: Eqn 3 Eqn 4 Eqn 5 0.50 652.51 363.54 406.26 413.22 62.86 61.88 61.95 1.00 512.23 423.60 414.07 425.49 61.30 61.26 61.35 1.50 468.65 423.41 422.32 403.20 60.98 60.98 61.23 2.00 467.81 426.42 421.70 417.58 60.97 60.98 61.14 Mean (± SEM) – 525.30 (87.32) 409.24 (30.50) 418.95 (8.62) 415.11 (6.22) 61.53 (0.90) 61.28 (0.42) 61.42 (0.37) 4568 S. Ke˛dracka-Krok and Z. Wasylewski (Eur. J. Biochem. 270) Ó FEBS 2003 where T 0 and T F are lower and upper temperature limits of transition, respectively, and T max is the excess heat capacity associated with the transition. The Gibb’s free energy, DG ¼ DH ) TDS, and thus the entire transition energetics, can be calculated in a model-independent fashion [10,22]. Unfortunately, it was impossible to determine the change in heat capacity, because of insufficient signal-to-noise ratio of the experimental data. The thermodynamic parameters obtained are summarized in Table 4. Thermal transition of the TetR–[Mg–Tc] + complex was analyzed according to a two-state model. The best fit for scan rate curves above 1.0 KÆmin )1 is shown in Fig. 5. This model assumes that the total excess capacity is the sum of n independent thermal transitions. The heat capacity associated with thermal transition is deter- mined by a temperature derivative of enthalpy changes, as given by: C p ðTÞ¼ dH ðTÞ dT ð6Þ The enthalpy change is determined by the total enthalpy of the transition, which is assumed to be a constant multiplied by the fraction of the molecules that are unfolded: H(T) ¼ f u (T)DH. The fraction of unfolded molecules is determined by the equation: f u ðTÞ¼ KðTÞ 1 þ KðTÞ where the equilibrium constant is KðTÞ¼exp DH À T DH T max RT "# DSC curves were analyzed using the CpCalc software package provided by CSC. It turned out that a two-state model with one transition is good enough to describe denaturation of the complex of TetR with Tc. The enthalpy values obtained are listed in Table 4. CD measurements The CD measurements were performed in the same buffer as the DSC experiments. Figure 6 shows an example of a CD denaturation profile for TetR protein, and Fig. 7 presents a typical CD denaturation curve for TetR protein in complexes with Tc. Binding of Tc leads to increased symmetry of the thermal transition. Moreover, the results confirm the tendency of the behavior of the transition temperature observed with the DSC method (Fig. 2). Converted to mean residue ellipticity, CD thermal transition spectra for TetR were analyzed using nonlinear least squares fitting. The result is presented in Fig. 6. The fraction of denatured protein, F U , was calculated from the spectral parameter used to follow denaturation (y) before the minimization procedure accord- ing to the relation: F U ¼ðy À y N Þ=ðy U À y N Þ y N ¼ a 1 +a 2 T and y U ¼ b 1 +b 2 T are the means of y, characteristic of the native and denatured conformation, respectively. They were obtained by linear regression of the pre-transition and post-transition baselines. The parameter used to follow denaturation, y, can be expressed as a function of the kinetic parameters according to the follow- ing equation [24]: Fig. 5. Temperature dependence of excess molar heat capacity of the complex of TetR with Tc at five different scan rates: 0.1, 0.5, 1.0, 1.5 and 2.0 KÆmin )1 . Measurements were performed in buffer B with 5 mol excess of Tc over 1 mol of the protein. The solid lines represent the best one-transition two-state reversible model according to Eqn (6). Table 4. Summary of DSC measurements. The buffer for TetR was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, pH 8.0. The buffer for TetR + Tc was 10 mM Tris/HCl, 150 mM NaCl, 2 mM dithiothreitol, 10 mM MgCl 2 ,pH8.0. Species Effect E a (kJÆmol )1 ) T* (°C) DS (T max ) (kJÆmol )1 ÆK )1 ) DH a (kJÆmol )1 ) TetR Scan rate 418.40 ± 15.74 61.41 ± 0.56 – – TetR + Tc Concentration – – 3.06 ± 0.25 1077.2 ± 86.2 Scan rate – – 3.10 ± 0.08 1067.1 ± 36.3 a Values from fitting one-transition two-state model, according to Eqn (6). Ó FEBS 2003 DSC study of tetracycline repressor (Eur. J. Biochem. 270) 4569 y¼y U À½y U Ày N exp À 1 m Z T T 0 exp E a R 1 T à À 1 T  dT 8 < : 9 = ; ð7Þ The kinetic parameters obtained from the analysis of CD curves are 455.02 ± 2.83 kJÆmol )1 for E a and 61.44 ± 0.04 °CforT*. Additional quantitative validation of the two-state reversible interpretation of the denaturation of the [TetR– Tc] complex was obtained using a vant’Hoff analysis of the CD data. Taking into account that the intensity of CD signals is virtually insensitive to the aggregation process, and that the unfolding of the complex is a two-state process, the corresponding equilibrium constant is given by: K ¼ U 2 N 2 ; a ¼ K 1 þ K ) K ¼ f u 1 À f u where, f u is the degree of advancement of the denaturation process which refers to the unfolded fraction of a protein, resulting from normalization of thermal CD profiles. The denaturation CD profiles for the complex of TetR with Tc were analyzed according to the following equation: fðTÞ¼ ½f n þm n Tþ f u þm u ðTÞ exp DH mH R 1 T m À 1 T hinohi 1þexp DH mH R 1 T m À 1 T hino ð8Þ where f(T) is the native fraction of the protein in the temperature function, f n and f u are fractions of native protein for pre-transition and post-transition curves, respectively, obtained by extrapolation to 0 K, and m n and m u are slopes of the pre-transition and post-transition curves (Fig. 6). The DH vH and T m values obtained are 917.78 ± 5.99 kJÆmol )1 and 69.97 ± 0.01 °C, respectively. DLS measurements The buffer conditions in the DLS experiments were the same as in the DSC measurements. The curves showing the estimated hydrodynamic radius of wild-type TetR and its complex with Tc as a function of protein concentration are presented in Fig. 8. For evaluation of R theo H ,hydrationwas estimated to be 0.2 g H 2 O per g protein and the partial specificvolumetobe0.73cm 3 per g protein [18,27]. From the comparison of R H values obtained from linear extra- polation to zero concentration for wild-type TetR (2.98 ± 0.01 nm) and its complexes with Tc (3.04 ± 0.06 nm), it appears that there are no pronounced differences in hydrodynamic radii. The R H =R theo H ratio higher than 1 (always % 1.15) indicates similar discrepancies in the spherical shape of the protein in the absence and presence of the ligand. The increasing linear dependence of R H on the concentration of wild-type TetR suggests a strong tendency of the protein to aggregate. Tc binding makes this protein resistant to polymerization. Fig. 6. Temperature dependence of residue ellipticity at 222 nm for TetR in buffer A obtained on heating with a constant scan rate of % 1KÆmin )1 . The solid line is the best fit obtained using Eqn (7). Fig. 7. Temperature dependence of folded fraction ( f)oftheTetR complex with Tc in buffer A (5 M excess of Tc over 1 mol of the protein was used) obtained on heating with a constant scan rate of % 1KÆmin )1 . The solid line is the best fit obtained using Eqn (8). Fig. 8. Dependence of hydrodynamic radii on concentration of TetR (m) in buffer A and TetR–Tc (s) in buffer B (5 mol excess of Tc over 1 mol TetR). 4570 S. Ke˛dracka-Krok and Z. Wasylewski (Eur. J. Biochem. 270) Ó FEBS 2003 Discussion In this study, DSC, CD and DLS were used to show how binding of the [Mg–Tc] + inducer to TetR can influence the gross structure of the protein and the repressor stability in solution. Here we studied the TetR B homodimer variant, which is believed to have a similar structure to the TetR D variant [3]. Crystallographic studies of TetR D have shown that binding of [Mg–Tc] + is accompanied by conforma- tional changes in TetR, which in turn can abolish the specific interaction of the protein with the DNA operator sequences [28]. [Mg–Tc] + binds to the two tunnel-like cavities, which, in the absence of the inducer, are filled with disordered water molecules, and interact by both hydrogen bonding and hydrophobic interactions with the protein moiety [29]. Our previous CD studies in solution showed that, in the case of TetR B ,[Mg–Tc] + binding does not lead to dramatic changes in the secondary structure of the protein [30]. However, it has been suggested that a small decrease in the TetR helicity may occur as the result of partial unfolding of the DNA-recognition helix of the protein. This suggestion is supported by the observation that the fluorescence of Trp43, localized in the HTH structure of TetR, changes dramatically on inducer binding [30]. These findings are further supported by Trp43 fluorescence measurements of TetR B [31] and by infrared and Raman spectroscopy measurements [32], which showed nearly identical secondary conformation of TetR B with and without the inducer in solution. A variety of point mutations in TetR B have also been used to investigate how substitution of amino acids in the protein molecule results in inducer binding in the protein cavities [33]. These studies show that substitution of protein residues engaged in hydrogen bonding with [Tc–Mg] + results in reduced binding of the inducer by several orders of magnitude, whereas substitu- tion of residues engaged in hydrophobic interactions only marginally reduces the affinity for the inducer. The DLS results presented here show that TetR B alone has a Stokes’ radius of 3.04 nm, which decreases very slightly to 2.98 nm on binding of [Tc–Mg] + in the protein pocket. It should be pointed out that binding of the inducer to TetR does not lead to any changes in the global structure of the protein. However, a much stronger tendency to protein aggregation has been observed in the case of TetR B alone than for the complex of the protein with [Tc–Mg] + inducer. The DLS measurements indicate that at 20 °C TetR alone, as well as in the presence of [Mg–Tc] + ,was dimeric. As the binding of two molecules of [Mg–Tc] + to TetR leads to changes in the tertiary structure of the protein, one can expect that these changes may lead to a decrease in the tendency of the protein to aggregate. The DSC thermograms of TetR alone, presented in Fig. 1, show irreversible thermal unfolding of the protein, assuming an asymmetrical shape. The observed decrease in T max on increasing TetR concentration (Fig. 2) indicates that the dimeric protein aggregated at higher TetR concen- tration. The DH cal /DH vH ratio for TetR of 0.64 may also indicate protein oligomerization on unfolding. However, because of the irreversibility of the TetR transition, the volume DH cal /DH vH ratio can be treated only qualitatively. Detailed analysis of various theoretical models of the irreversible denaturation of proteins [21,24,34,35] has been performed in the literature. The simplest two-state kinetic model has been used to describe thermal transition of several proteins [23,36–39]. Analysis of the DSC results shows that TetR alone undergoes irreversible thermal denaturation during kinetically controlled reactions, which can be described by the simplest model called the two-state model, which is a limiting case of the Lumry–Eyring model [11]: N 2 À! k D 2 ; where k is first-order rate constant, and N and D are native and irreversible denatured monomer of the protein, respect- ively. This suggestion was verified by calculation of the activation energy using different analytical transformations to fit of the experimental data. The values of the average energy of activation, E a , presented in Table 3, together with T*(temperatureatrateconstant,k, equal to 1 min )1 )arein good agreement and further support the idea that the two- state irreversible model offers a good explanation of the TetR denaturation process. The model is also supported by the observation that the T max of dimeric TetR does not change significantly when the protein concentration is increased. Such behavior would be expected from a multimeric protein if its dissociation into monomers does not take place before the rate-determining step and the irreversible process shows first-order kinetics [21]. The average activation energy, estimated to be 414 ± 15 kJÆ mol )1 for TetR, is equal to (8.9 ± 0.3) · 10 )3 kJÆmol )1 after re-counting per gram of protein. This can be compared with the value of (7.1 ± 5.8) · 10 )3 kJÆmol )1 per g protein determined as an average value for several other proteins of different size, which undergo irreversible denaturation in the one-step model [40]. The thermal denaturation of TetR was also monitored by CD measurements; the irreversible rate- controlled process was fitted to eqn (7) and yielded the T* parameter and the activation energy for TetR. The values derived from CD measurements are in reasonable agree- ment with those obtained from the DSC measurements, and this independent experimental approach further supports the proposed model. Because the two-state irreversible mechanism occurs in the thermally unfolding TetR, one cannot use equilibrium thermodynamic analysis of these DSC transitions to estimate the entropy of denatur- ation and free energy. Nevertheless, the thermal denatura- tion process of TetR can be described by a denaturation enthalpy change of 504.9 kJÆmol )1 , calculated as an average from the data presented in Tables 1–3. Protein stability is often defined as the Gibbs free energy difference (D D N G) between denatured and native states at a given reference temperature (usually 25 °C). However, for practical purposes, the denaturation temperature T max may also be a useful measure of protein stability [11,41]. The mean temperature of TetR denaturation, T max ,determined for the protein concentration range 0.4–4.0 mgÆmL )1 is 60 °C. This value and that for denaturation enthalpy changes are very close to those determined for the structur- ally similar protein, cAMP receptor protein (CRP) (61 °C and 503 kJÆmol )1 , respectively) [42]. CRP, which has a very similar molecular mass to TetR, is a homodimeric molecule with a larger domain responsible for the cAMP binding and a smaller domain, which possesses HTH structure, respon- sible for the interactions with DNA sequences [32]. TetR Ó FEBS 2003 DSC study of tetracycline repressor (Eur. J. Biochem. 270) 4571 undergoes reversible chemically induced denaturation by urea, with simultaneous dissociation to monomers, charac- terized by a Gibbs free energy change DG (H 2 O, 25 °C) of 75 kJÆmol )1 [8]. It has been shown that CRP, which is structurally similar to TetR, undergoes reversible denatur- ation by guanidine hydrochloride, characterized by more rapid dissociation into monomers followed by co-operative unfolding of CRP monomers. The overall process of CRP unfolding is characterized at 20 °CbyaDG (H 2 O) of 77.8 kJÆmol )1 [43,44]. Analysis of the scan rate effect on the DSC transitions of the TetR–[Mg–Tc] + complex shows that at a higher scan rate the transition temperature, T max , approaches a plateau, which supports the idea that under these conditions equilibrium thermodynamics may be employed. Indeed, theoretical simulation has demonstrated that kinetic distor- tion caused by the irreversible process becomes negligible at sufficiently high scan rate (precisely at an infinitive scan rate, 1/m ¼ 0) [11,21]. Figure 3 shows no scan rate effect on transition temperature within the 1.0–2.0 KÆmin )1 range and, therefore, equilibrium thermodynamic analysis is permissible at least to the transition temperature of the DSC profile (the high temperature side is likely to be distorted by aggregation). Furthermore, the measured shape of the thermal transitions becomes more symmetrical with increasing heating ratio (Fig. 5), and the van’t Hoff enthalpy approaches calorimetric enthalpy, thereby render- ing the co-operativity ratio DH/DH vH equal to 1 (Table 2). In similar cases, where the T max was independent of scan rate in the high range of the heating ratio, the irreversible denaturation of annexin V E17G [25] and human phenyl- alanine hydrolase and human phenylalanine hydrolase with L -Phe [26] was described by application of the equilibrium thermodynamic analysis. A two-state reversible model was used to describe the thermal transition of the complex of wild-type TetR with Tc (at high scan rate). This model is based on the general Lumry–Erying model [21], simplified by excluding the kinetic irreversible step, which is negligible at a scan rate over 1 KÆmin )1 : N 2 Tc 2 ! K 2Tc þ U 2 This two-state model assumes that the total excess heat capacity is a sum of n independent two-state thermal transitions. As can be seen in Fig. 5, fitting of one- transition two-state model seems to be satisfied (Table 4). Applying the co-operative model to describe CD denatur- ation profiles of liganded TetR gives as a consequence high convergence of the experimental curve with the theoretical one (Fig. 7) and the values obtained for the thermody- namic parameters are in good agreement with those from DSC, which strongly supports the validity of the two-state reversible model. Analysis of DSC thermograms of TetR–[Mg–Tc] + complex as a function of the protein concentration does not show any significant changes on increasing the complex concentration. The lack of significant change in T max with concentration of the TetR–[Mg–Tc] + complex with accom- panying DH cal /DH vH values close to unity can be explained by this two-state model [11], in which a dimeric TetR complex undergoes denaturation without simultaneous dissociation into monomers, followed by protein aggrega- tion at higher temperature. The reduction in protein stability in the presence of Tc, observed at higher protein concen- tration (Fig. 2), may be explained on the basis of the complete Lumry–Erying model which can be depicted in the following scheme: N 2 Tc 2 ! K 2Tc þ U 2 À! k D According to this model, the dimeric native TetR in the presence of Tc undergoes two-state reversible unfolding with simultaneous dissociation into monomers U and ligand loss. The unfolded species thus obtained, U 2 , undergoes an irreversible alteration to yield a final, denaturated state D. 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