Molecular mechanisms of receptor. II. Identification of the conformational transition of rhodopsin responsible for the leading edge of the photoresponse of artificial lipid membranes modified by fragments of the outer segment of rods

Kinetic parameters of photoinduced permeability increase of artificial lipid membranes, modified by ROS fragments (tau20 degrees C = 20 mesec Ea = 33 +/- 2 kcal/mole) coincides with appropriate parameters of photoinduced protein fluorescence intensity decrease and ROS fragments absorption spectra change (metarhodopsin I leads leads to metarhodopsin II transition). Hydroxylamine accelerates this process, its rate is proportional to hydroxylamine at concentrations lower than 0.6 M.     

Kinetic properties of gamma-glutamyltranspeptidase and leucine-amino-peptidase in developing rat intestine: effect of hormones

Administration of cortisone and thyroxine produced adult-type increase in the activities of soluble and membrane-bound gamma-glutamyltranspeptidase (gamma-GTP) in suckling rat intestine. Membrane-bound enzyme activity remained unaltered while the soluble enzyme activity was reduced (27%) in insulin-injected pups. Kinetic analysis revealed that the observed changes in the enzyme levels were a consequence of altered Vmax with no change in apparent Km. A 2-fold increase in the Km value was observed in adult gamma-GTP activity compared to that of suckling animals. Membrane-bound and soluble gamma-GTP yielded similar values of the Ea (9.7-13.1 kcal/mole) but exhibited apparent differences in heat stability in the control and hormone-injected groups. Leucine-amino peptidase(LAP) activity was reduced to adult levels in insulin-treated suckling animals. Thyroxine- and cortisone-treatment did not affect soluble activity but significantly (P less than 0.001) augmented the membrane-bound LAP levels. This increase was due to enhanced (54-82%) Vmax with no change in Km. The observed decrease in LAP activity in response to insulin was due to reduced Vmax. There was no change in Ea (8-11.6 kcal/mole) except the value was raised to 19.1 kcal/mole in cortisone-injected pups. Both the soluble and membrane-bound LAP activities were quite resistant to heat inactivation upto 30 min at 60 degrees C except in weanling rats. Thus, the kinetic behaviour of normally developed and precociously induced gamma-GTP and LAP is essentially similar but there are apparent differences in the mode of action of insulin, cortisone and thyroxine in affecting the development of these enzymes.     

Kinetic characteristics of soluble and brush border alkaline phosphatase and sucrase activities in developing rat intestine: effect of hormones

Suckling rat intestine contains 35 and 65% of the cytosolic and membrane-bound alkaline phosphatase (AP) activities. The corresponding values for sucrase were 20 and 80% respectively. The amount of the soluble enzymes was reduced to 7-11% in adult rat intestine. Administration of cortisone, thyroxine or insulin to suckling animals induced adult type distribution of the enzymes. There were apparent differences in kinetic characteristics of soluble and brush border enzymes, but the kinetic properties of the normally developed and hormone-induced AP and sucrase were essentially similar. This suggested identical nature of these enzymes under these conditions. A biphasic Arrhenius plot was obtained for AP in weaned and hormone injected pups with a break point around 18 degrees C, while the soluble enzyme yielded a monophasic curve (Ea = 8-11 kcal/mole). Arrhenius plot for sucrase was monophasic in the suckling, hormone-injected and adult rat intestine (Ea = 8.3-15.1 kcal/mole). Membrane-bound enzymes were generally labile, while soluble enzyme activities were stable to heat treatment (sucrase at 50 degrees C and AP at 60 degrees C) in various experimental groups.     

Changes of enzymes involved in DNA synthesis in the testes of cryptorchid rats

The activities of DNA polymerase alpha (EC 2.7.7.7) and topoisomerase I did not fluctuate up to 7 days after surgery to induce cryptorchidism and showed no significant difference from those in control testes (sham-operated). In contrast, the activity of DNA polymerase beta decreased by 43% at 5 days (P less than 0.01) and by 47% at 7 days (P less than 0.001). The activity of DNA polymerase gamma also decreased by 46% at 3 days (P less than 0.02) and by 78% at 7 days (P less than 0.01) after surgery. The amount of mRNA for DNA polymerase beta decreased in parallel with enzyme activity. Since the sensitivity to heat inactivation of testicular DNA polymerase beta was exactly the same as that from liver, the decrease in DNA polymerase beta activity may be, at least in part, due to reduced biosynthesis of enzyme protein. The morphological changes in cryptorchid testes suggested that the decrease in DNA polymerase beta and gamma activities might be related to the deleterious effects of elevated temperature on spermatogenesis.     

Inactivation of bacteriophage PM2 during storage

The kinetics of bacteriophage inactivation in the medium that is optimal for its storage has been studied at temperatures from 4 to 55 degrees C. The plot of Arrhenius dependence of the constant of inactivation rate consists of the two linear parts with the energies of activation Ea = 25 kcal/mol for 4-37 degrees C and Ea = 91 kcal/mol for 37-55 degrees C. The DNA of inactivated bacteriophage remained mostly in superspiralized form and completely preserved its biological activity as tested by transfection in spheroplasts. The analysis of inactivation kinetics suggests ageing of virions cultivated at 4 degrees C. The addition of watersoluble antioxidant amoxipin did not change the inactivation kinetics. The addition of antioxidant ionol with twin-80 increased the inactivation that was paralleled by the bacteriophage DNA degradation.     

Conformational and thermodynamic properties of apo A-1 of human plasma high density lipoproteins.

Conformational changes of apo A-1, the principal apoprotein of human plasma high density lipoprotein, have been studied by differential scanning calorimetry and ultraviolet difference spectroscopy as a function of temperature, pH, concentration of apoprotein, and urea concentration. Calorimetry shows that apo A-1 (5 to 40 mg/ml, pH 9.2) undergoes a two-state, reversible denaturation (enthalpy = 64 +/- 8.9 kcal/mole), between 43--71 degrees (midpoint temperature, Tm = 54 degrees), associated with a rise in heat capacity (deltaCvd) of 2.4 +/- 0.5 kcal/mole/degrees C. Apo A-1 (0.2 to 0.4 mg/ml, pH 9.2) develops a negative difference spectrum between 42--70 degrees, with Tm = 53 degrees. The enthalpy (deltaH = 59 +/- 5.7 kcal/mole at Tm) and heat capacity change (2.7 +/- 0.9 kcal/mole/degrees C) in the spectroscopic experiments were not significantly different from the calorimetric values. Below pH 9 and above pH 11, the calorimetric Tm and deltaH of denaturation are decreased. In the pH range of reversible denaturation (6.5 to 11.8), delatH and Tm are linearly related, showing that the heat capacity change (ddeltaH/dT) associated with denaturation is independent of Tm. In urea solutions, the calorimetric Tm and deltaH of denaturation are decreased. At 25 degrees, apo A-1 develops a negative difference spectrum between 1.4 and 3 M urea. Fifty per cent of the spectral change occurs in 2.4 M urea, which corresponds to the urea concentration obtained by extrapolation of the calorimetric Tm to 25 degrees. In urea solution of less than 0.75 M there is hyperchromicity at 285 nm (delta epsilon = 264 in 0.75 M urea), indicating strong interaction of aromatic amino acid residues in the native molecule with the solvent. Spectrophotometric titration of apo A-1 shows that 6.6 of the 7 tyrosine groups of apo A-1 titrate at pH less than 11.9, with similar titration curves obtained in aqueous solutions and in 6 M urea. The free energy of stabilization (deltaG) of the native conformation of apo A-1 was estimated, (a) at 37 degrees, using the calorimetric deltaA and deltaCvd, and (b) at 25 degrees, by extrapolation of spectroscopic data to zero urea concentration. The values (deltaG (37 degrees) = 2.4 and deltaG (25 degrees) = 2.7 kcal/mole) are small compared to typical globular proteins, indicating that native apo A-1 has a loosely folded tertiary structure. The low values of deltaG reflect the high degree of exposure of hydrophobic areas in the native protein molecule. The loosely folded conformation of apo A-1 allows extensive binding of lipid, since this can involve both surface hydrophobic sites and hydrophobic areas exposed by a cooperative, low energy unfolding process.     

NMR studies of conformations and interactions of substrates and ribonucleotide templates bound to the large fragment of DNA polymerase I

The large fragment of DNA polymerase I (Pol I) effectively uses oligoribouridylates and oligoriboadenylates as templates, with kinetic properties similar to those of poly(U) and poly(A), respectively, and has little or no activity in degrading them. In the presence of such oligoribonucleotide templates, nuclear Overhauser effects (NOE's) were used to determine interproton distances within and conformations of substrates bound to the large fragment of Pol I, as well as conformations and interactions of the enzyme-bound templates. In the enzyme-oligo(rU)54 +/- 11-Mg2+dATP complex, the substrate dATP has a high anti-glycosidic torsional angle (chi = 62 +/- 10 degrees) and an O1'-endo/C3'-endo sugar pucker (delta = 90 +/- 10 degrees) differing only slightly from those previously found for enzyme-bound dATP in the absence of template [Ferrin, L.J., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694]. Both conformations are similar to those of deoxynucleotidyl units of B DNA but differ greatly from those of A or Z DNA. The conformation of the enzyme-bound substrate analogue AMPCPP (chi = 50 +/- 10 degrees, delta = 90 +/- 10 degrees) is very similar to that of enzyme-bound dATP and is unaltered by the binding of the template oligo(rU)54 +/- 11 or by the subsequent binding of the primer (Ap)9A. In the enzyme-oligo(rA)50-Mg2+TTP complex, the substrate TTP has an anti-glycosidic torsional angle (chi = 40 +/- 10 degrees) and an O1'-endo sugar pucker (delta = 100 +/- 10 degrees), indistinguishable from those found in the absence of template and compatible with those of B DNA but not with those of A or Z DNA. In the absence of templates, the interproton distances on enzyme-bound dGTP cannot be fit by a single conformation but require a 40% contribution from a syn structure (chi = 222 degrees) and a 60% contribution from one or more anti structures. The presence of the template oligo(rU)43 +/- 9 simplifies the conformation of enzyme-bound dGTP to a single structure with an anti-glycosyl angle (chi = 32 +/- 10 degrees) and an O1'-endo/C3'-endo sugar pucker (delta = 90 +/- 10 degrees), compatible with those of B DNA, possibly due to the formation of a G-U wobble base pair. However, no significant misincorporation of guanine deoxynucleotides by the enzyme is detected with oligo(rU) as template.(ABSTRACT TRUNCATED AT 400 WORDS)     

Regulation of translation in rabbit reticulocytes and mouse L-cells; comparison of the effects of temperature.

Various parameters of protein synthesis were analyzed in rabbit reticulocytes exposed to various temperatures for up to five hours. Between 10 degrees C and 40 degrees C total protein synthesis exhibited two different apparent activation energies (36 kcal/mole, 10-24 degrees C; 22 kcal/mole, 24-40 degrees C), as did protein elongation and release (35 kcal/mole, 10-25 degrees C; 12 kcal/mole, 25-40 degrees C). However, the level of polysomes remained essentially unchanged between 0 degrees C and 42 degrees C which implies that the activation energy for polypeptide initiation is quite similar to that for elongation and is also biphasic. This situation is different from that in cultured mouse L-cells where the polysome level is dependent on temperatures. Nevertheless, reticulocytes and L-cells appear to be similar in their temperature dependence of initiation and in their rate of elongation (5-6 amino acids/second at 36 degrees C.     

Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase

We showed that the alpha-CH(2) --> NH substitution in octanoyl-CoA alters the ground and transition state energies for the binding of the CoA ligands to medium-chain acyl-CoA dehydrogenase (MCAD), and such an effect is caused by a small electrostatic difference between the ligands. To ascertain the extent that the electrostatic contribution of the ligand structure and/or the enzyme site environment modulates the thermodynamics of the enzyme-ligand interaction, we undertook comparative microcalorimetric studies for the binding of 2-azaoctanoyl-CoA (alpha-CH(2) --> NH substituted octanoyl-CoA) and octenoyl-CoA to the wild-type and Glu-376 --> Gln mutant enzymes. The experimental data revealed that both enthalpy (DeltaH degrees ) and heat capacity changes (DeltaC(p) degrees ) for the binding of 2-azaoctanoyl-CoA (DeltaH degrees (298) = -21.7 +/- 0.8 kcal/mole, DeltaC(p) degrees = -0.627 +/- 0.04 kcal/mole/K) to the wild-type MCAD were more negative than those obtained for the binding of octenoyl-CoA (DeltaH degrees (298) = -17.2 +/- 1.6 kcal/mole, DeltaC(p) degrees = -0.526 +/- 0.03 kcal/mole/K). Of these, the decrease in the magnitude of DeltaC(p) degrees for the binding of 2-azaoctanoyl-CoA (vis-à-vis octenoyl-CoA) to the enzyme was unexpected, because the former ligand could be envisaged to be more polar than the latter. To our further surprise, the ligand-dependent discrimination in the above parameters was completely abolished on Glu-376 --> Gln mutation of the enzyme. Both DeltaH degrees and DeltaC(p) degrees values for the binding of 2-azaoctanoyl-CoA (DeltaH degrees (298) = -13.3 +/- 0.6 kcal/mole, DeltaC(p) degrees = -0.511 +/- 0.03 kcal/mole/K) to the E376Q mutant enzyme were found to be correspondingly identical to those obtained for the binding of octenoyl-CoA (DeltaH degrees (298) = -13.2 +/- 0.6 kcal/mole, DeltaC(p) degrees = -0.520 +/- 0.02 kcal/mole/K). However, in neither case could the experimentally determined DeltaC(p) degrees values be predicted on the basis of the changes in the water accessible surface areas of the enzyme and ligand species. Arguments are presented that the origin of the above thermodynamic differences lies in solvent reorganization and water-mediated electrostatic interaction between ligands and enzyme site groups, and such interactions are intrinsic to the molecular basis of the enzyme-ligand complementarity.     

The pathways for fluid phase and receptor mediated endocytosis in rat hepatocytes are different but thermodynamically equivalent

In isolated rat hepatocytes fluid phase endocytosis, determined by the uptake of the fluorescent dye lucifer yellow (LY), and receptor mediated endocytosis, determined using a ligand for the asialoglycoprotein receptor (asialo-orosomucoid; ASOR), are different pathways based on their different sensitivities to hyperosmolarity induced by sucrose (Oka and Weigel, J. Cell. Biol. 105, 311a, 1987). LY uptake was unaffected by 0.2 M sucrose at all temperatures tested between 12 degrees and 37 degrees C whereas the uptake of 125I-ASOR was completely inhibited at any temperature. Since the two probes are taken up by different pathways it was possible to determine independently the activation energies (Ea) for the fluid phase versus the receptor mediated coated pit endocytic process. The Ea was 26.4 +/- 3.5 and 25.8 +/- 1.9 kcal/mole for, respectively, receptor mediated and fluid phase endocytosis. These values are not significantly different, and we conclude that the fluid phase and receptor mediated pathways are thermodynamically equivalent even though they are independent.     

Effects of temperature on the mitochondrial malate dehydrogenase of adult muscle of Toxocara canis

Purified mitochondrial malate dehydrogenase isoenzyme (m-MDH) of Toxocara canis muscle presented maximum activity at 48 degrees C. A clear change in slope of the Arrhenius plot was observed. The energy of activation calculated for the catalytic process showed values of 3.2 kcal/mol and 10.5 kcal/mol. Thermal inactivation of m-MDH showed that it is more thermolabile than the s-isoenzyme. The inactivation of the enzyme by heat could be reduced at least in part by the addition of 0.1 mM NADH. The heat denaturation showed to be a first-order process. The rate constant (k) was calculated as being of the order of 5.28 X 10(-4) s-1 at 40 degrees C. The activation energy for the heat inactivation process was 16.45 kcal/mol between 30 degrees C and 40 degrees C and 13.79 kcal/mol between 40 degrees C and 48 degrees C.     

Effect of glycerol and low pH on heat-induced cell killing and loss of cellular DNA polymerase activities in Chinese hamster ovary cells

A whole-cell assay technique for DNA polymerase alpha and beta was used to measure the activities of both enzymes in Chinese hamster ovary (CHO) cells after hyperthermic treatment of 42.2 - 45.5 degrees C in acidic or basic environment and in the presence or absence of 5% glycerol. Cell survival was measured at the same time, and the DNA polymerase activities were correlated with survival. The results show a positive correlation between cell killing by heat and loss of DNA polymerase beta activity, both when cells were sensitized to heat by treatment at pH 6.7 with or without glycerol and when cells were protected from heat by treatment with 5% glycerol at pH 7.4 or 6.7. The results show a poor correlation between loss of DNA polymerase alpha activity and cell survival; i.e., compared to cell killing, the loss of DNA polymerase alpha activity was sensitized to heat more by acidic treatment without glycerol and was protected less from heat by glycerol treatment at normal physiological pH (pH 7.4). However, cell killing and loss of polymerase alpha activity did correlate well for sensitization to heat by acidic treatment in the presence of glycerol and for protection from heat by glycerol treatment at low pH. These results considered with other hyperthermia-polymerase studies suggest that heat effects on membranes can apparently result in changes in environmental conditions within the cell (secondary effects), which can in turn alter polymerase activities and/or the direct or secondary effect of heat on the polymerase enzymes. Furthermore, loss of polymerase beta activity serves as a better index of thermal damage resulting in cell death than loss of alpha activity.     

Estimation and Analysis of Cucumber (Cucumis sativus L.) Leaf Cellular Heat Sensitivity

Triphenyl tetrazolium chloride (TTC) reduction by cucumber (Cucumis sativus L. cv Poinsett 76 and cv Ashley) leaf discs was used as a viability assay to examine the effect of temperature pretreatment on the tissue response to acute hyperthermia. Semi-logarithmic plots of TTC reduction as a function of incubation time at different temperatures from 40 to 60[deg]C resembled the heat survival curves of animal cells. Heat inactivation rates were obtained and subjected to "quasi" Arrhenius analyses by analytical methods derived from the animal studies. The Arrhenius plots of TTC reduction rates for cv Ashley leaf discs preincubated at 25 or 37[deg]C and for cv Poinsett 76 preincubated at 37[deg]C were linear with the same activation energy (Ea) of about 80 kcal mol-1. The Arrhenius plot of cv Poinsett 76 preincubated at 25[deg]C was nonlinear with an Ea of about 80 kcal mol-1 at temperatures below 46[deg]C and an Ea of about 27.5 kcal mol-1 at temperatures above 47[deg]C. The significance of these differences is discussed in terms of the role of protein denaturation in the thermal sensitivity of cucumber disc reduction of TTC and the applicability of these methods to the analysis of plant cellular heat sensitivity.     

Temperature dependence of enthalpy changes for ethidium and propidium binding to DNA: effect of alkylamine chains

Calorimetric titrations have been performed on the binding of ethidium and propidium to calf thymus DNA at temperatures in the 15-60 degrees C range. Enthalpy changes (delta HB) derived from these experiments performed with the new Omega reaction calorimeter have a precision of +/- 0.10 kcal/mol or less at all temperatures. For ethidium (a monocation), delta HB varies little with temperature, and the heat capacity change (delta CP) for the binding reaction derived from these parameters is 10 cal/deg/mol. In contrast, delta HB changes from -6.5 to -8.1 kcal/mol for DNA binding of propidium (a dication due to a charged amine group at the end of an alkyl chain attached to the phenanthridine ring nitrogen), and delta CP is -57 cal/deg/mol. At 21 degrees C a plot of delta HB vs mole ratio is curved downward for propidium in the 0.08-0.25 range, whereas the same plot at 45 degrees C is a straight line from 0.05 to 0.15 and sharply downward thereafter. Similar plots for ethidium follow the latter pattern between 25 and 50 degrees C. These observations and our analyses of delta HB and delta SB are consistent with the hypothesis that the location in the DNA complex and the rotational motion of the alkylamine chain change substantially over the temperature range in this study. Only near 50 degrees C is delta HB equal for the binding of these two cations to DNA, and caution must be used in analyses of enthalpic effects when the temperature dependence for delta HB is not available.     

Biochemical responses to temperature in the contractile protein complex of striped bass Morone saxatilis

The effects of acute and long-term changes in temperature upon catalytic and calcium regulatory function of red (slow oxidative) and white (fast glycolytic) muscle from striped bass (Morone saxatilis) were determined. Acclimation to 5 degrees C or 25 degrees C had no significant effect on catalytic function (ATPase activity) or regulatory sensitivity (Ca++-activation) of myofibrils from either muscle type. Substantial differences between red and white muscle were found in the intrinsic thermal sensitivity of maximally-activated Mg++-Ca++ myofibrillar ATPase. Arrhenius plots of myofibrillar ATPase from white muscle show one significant breakpoint at 29 degrees C, with activation energies (Ea) of 2.3 and 23.4 kcal mole-1 at temperatures above and below this transition, respectively. Arrhenius plots of myofibrillar ATPase from red muscle show two transitions occurring at 22 and 9 degrees C, with Ea of 7.6 kcal mole-1 above 22 degrees C and 18.3 kcal mole-1 between 9 and 22 degrees C. Activation energies for myofibrils from red muscle increase substantially to approximately 107.3 kcal mole-1 below the 9 degrees C breakpoint. Differences in the intrinsic thermal sensitivity of red and white muscle catalytic function are apparently due to interaction of actomyosins and calcium regulatory proteins which are specific to each muscle type. The results suggest that capacity for sustained swimming in striped bass, which is powered exclusively by red muscle, will be severely impaired at cold temperature unless compensations occur above the level of contractile proteins.     

Quenching of the zinc-protoporphyrin triplet state as a measure of small-molecule diffusion through the structure of myoglobin

The diffusion of small molecules through the myoglobin structure was studied. It has been shown that the fluorescent Zn-protoporphyrin substitutes easily for the native nonfluorescent Fe-protoporphyrin in myoglobin. The quenching rate of the E-type delayed fluorescence of Zn-protoporphyrin in a substituted myoglobin by the quenchers oxygen and anthraquinonesulfonate was used to measure their diffusion from the ambient solution through the protein to the ligand binding site. The quenching rate constant (at 21 degrees C) for oxygen is kq = (9.6 +/- 0.9) X 10(7) M-1 S-1, only 1 order of magnitude less than that for Zn-hematoporphyrin quenching in aqueous solution. The activation energy in the range between 2 and 40 degrees C is Ea = 6.0 +/- 0.6 kcal/mol. The corresponding data for anthraquinonesulfonate are kq = (2.1 +/- 0.3) X 10(8) M-1 S-1 and Ea = 5.8 +/- 0.6 kcal/mol. Taking into account the statistical factor involved in the oxygen quenching of the Zn-porphyrin triplet, the quenching rates are very similar. The data are discussed in terms of the "gated reaction" theory of Northrup and McCammon. The similar rate constants and activation energies indicate that the diffusion rate in the protein is determined by the frequency of the conformational changes that open "gates" for the passage of the quencher through the protein.     

Temperature dependence of the conductivity of individual potential-dependent K+-channels in mollusk neurons]

Using the patch-clamp method temperature dependences of the chord conductance of single potential--dependent slow and fast K+ channels in mollusk neurons were studied. Under control conditions (20 degrees C, 0 mV, [K+]o = 1.5 mM and [K+]i = 100 mM) the conductances of the fast and slow K+ channels were equal to 20-25 pS and 30-40 pS, respectively. Besides, the temperature dependences of the currents through the K+ channels of lesser conductance (5-20 pS) were studied. Some of these channels may be regarded as subtypes of the fast and slow K+ channels named above. It was found that for the channels of all types single channel currents arise with temperature. However, in the range of 10-20 degrees C an anomalous conductance decrease at temperature elevation was observed. For all channels except for the fast one at temperatures above 20 degrees C activation energy (delta Ea) calculated from the Arrhenius plots of the currents was about 4 kcal/mol. At the temperatures below 10 degrees C delta Ea was equal to about 12 kcal/mol. In this temperature range delta Ea had a pronounced potential dependency. Temperature dependences of the fast K+ channel conductance were opposite to those of the slow K+ channel to some extent.     

DNA helicase RepA: cooperative ATPase activity and binding of nucleotides

The steady-state kinetic parameters of the ATPase activity of the homohexameric DNA helicase RepA and the binding of the fluorescent analogue epsilonADP to RepA have been studied. ssDNA stimulates RepA ATPase activity optimally at acidic pH 5.3-6.0. The sigmoidal kinetic curves in both the absence and presence of ssDNA show strong positive cooperativity for ATP hydrolysis, with oligonucleotides longer than 10mer optimal for ssDNA-stimulated ATPase activity. Fluorescence titrations show that, at 25 degrees C and in the absence of DNA, the binding of epsilonADP to RepA is biphasic with three high (K(1) = 1.54 x 10(6) M(-1)) and three low (K(2) = 4.71 x 10(4) M(-)(1)) affinity binding sites differing by 30-40-fold in binding constants. In the absence of cofactors, RepA melts cooperatively at T(m) = 65.8 +/- 0.1 degrees C and is more stable in the presence of ATPgammaS, T(m) = 68.1 +/- 0.2 degrees C (DeltaDeltaG 0.95 kcal/mol), than in the presence of ADP, T(m) = 66. 5 +/- 0.1 degrees C (DeltaDeltaG 0.29 kcal/mol), indicating that the additional phosphate group in ATPgammaS has a significant influence on RepA structure. A model is proposed in which individual subunits of RepA sequentially and cooperatively perform a multistep ATP hydrolytic cycle.     

Nuclear Overhauser effect studies of the conformations and binding site environments of deoxynucleoside triphosphate substrates bound to DNA polymerase I and its large fragment

The conformations and binding site environments of Mg2+TTP and Mg2+dATP bound to Escherichia coli DNA polymerase I and its large (Klenow) fragment have been investigated by proton NMR. The effect of the large fragment of Pol I on the NMR line widths of the protons of Mg2+TTP detected one binding site for this substrate with a dissociation constant of 300 +/- 100 microM and established simple competitive binding of deoxynucleoside triphosphates at this site in accord with previous equilibrium dialysis experiments with whole Pol I [Englund, P. T., Huberman, J.A., Jovin, T.M., & Kornberg, A. (1969) J. Biol. Chem. 244, 3038]. Primary negative nuclear Overhauser effects were used to calculate interproton distances on enzyme-bound Mg2+dATP and Mg2+TTP. These distances established that each substrate was bound with an anti-glycosidic torsional angle (chi) of 50 +/- 10 degrees for Mg2+dATP and 40 +/- 10 degrees for Mg2+TTP. The sugar pucker of both substrates was predominantly O1'-endo, with a C5'-C4'-C3'-O3' exocyclic torsional angle (delta) of 95 +/- 10 degrees for Mg2+dATP and 100 +/- 10 degrees for Mg2+TTP. The consistency of these conformations with those previously proposed, on the basis of distances from Mn2+ at the active site [Sloan, D. L., Loeb, L. A., Mildvan, A.S., & Feldman, R.J. (1975) J. Biol. Chem. 250, 8913], indicates a unique conformation for each bound nucleotide. The chi and delta values of the bound substrates are appropriate for nucleotide units of B DNA.(ABSTRACT TRUNCATED AT 250 WORDS)