The measurement of partial specific volumes and sedimentation coefficients by sucrose density centrifugation

The method of Martin and Ames (1961, J. Biol. Chem.236, 1372) gives good estimates of the s_20,w of proteins when the SW40 rotor is used with a sucrose gradient. Viscosities of sucrose in D₂O were measured, and the data were used in computer simulations to test alternate approaches to estimating $\text{v}$ and s_20,w values by comparisons with standards. The method of Meunier et al. (1972, FEBS Lett.24, 63) for $\text{v}$ was shown to be optimal. For s_20,w estimations, substantial errors were found with the methods of Bon et al. (1973, Eur. J. Blochem.35, 372) and especially Meunier et al. When standards and unknowns have the same $\text{v}$, and the gradient is made up in water or dilute buffer, the simple ratio method of Martin and Ames gives most accurate results for s_20,w. For all other cases, an alternative procedure is described.     

A low-cost integrator for preparative ultracentrifuges

An integrator is described for the measurement of the time integral ∫₀^t rpm²dt in preparative ultracentrifuge where linearity exists either (a) between tachometer generator ac voltage amplitude and rpm (e.g., Sorvall RC2-B) or dc voltage and rpm, or (b) between the square-wave frequency from the tachometer generator and rpm (e.g., Beckman L2-65B). The construction and the precision levels of an integrator for Sorvall RC2-B preparative ultracentrifuge in the range 0–10,000 rpm and for Beckman L2-65B preparative ultracentrifuge in the range 0–40,000 rpm are described.     

A permeabilized-cell assay for transaminase B activity in Escherichia coli K-12

The assay for transaminase B (EC 2.6.1.6) activity, developed by D. E. Duggan and J. A. Wechsler (1973, Anal. Biochem.51, 67–79) has been modified to allow for the measurement of activity in Escherichia coli cells made permeable by cetyltrimethylammonium bromide (CETAB). A concentration of 10 mg% CETAB was found to be most effective in treating the cells without having a significant effect on transaminase B activity. Extraction of the dinitrophenylhydrazone of 2-oxoisovalerate by toluene was not affected by the CETAB treatment. We further report that the Na₂CO₃ extraction step is not required to measure color formed by the dinitrophenylhydrazone of 2-oxoisovalerate. This CETAB-treated cell assay is accurate to study transaminase B activity through most of the logarithmic phase of growth of Escherichia coli.     

Rapid evaluation of the initial and equilibrium parameters of CsCl and RbCl in equilibrium ultracentrifugation.

Two types of tables and graphs have been calculated. One type relates the initial density of the gradient solution to its equilibrium density at the bottom of the tube. The other type lists the function I(p) (defined by C. R. McEwen, 1967, Anal. Biochem.19, 23–29) and can be used to obtain the equilibrium density at any radius from the axis, provided the equilibrium density at one radius is known. Tables are calculated for CsCl and RbCl as gradient materials, and for Beckman Instruments rotors SW 41 and SW 65.     

Low and high temperature asymmetric forms of pig kidney and rabbit muscle phosphofructokinases and reversible, temperature-dependent transitions.

Previous viscometric studies from this laboratory (Johnson, C. S., Vogtmann, L., and Deal, W. C., Jr. (1976) Biochem. Biophys. Res. Commun.73, 391–395) have shown that at 3.5 ° C, pig kidney phosphofructokinase (PFK) is markedly asymmetric and rabbit muscle PFK is moderately asymmetric. The present viscometric and ultracentrifugal studies show that both enzymes are also asymmetric at near-physiological temperatures, that both exist in high-temperature and low-temperature forms, and that the high-temperature forms of both are less asymmetric and more dissociated than the low-temperature forms. The risults also show that the transitions from low- to high-temperature forms are reversible if the exposure to 35 °C is short enough that no irreversible chemical modification occurs. For pig kidney PFK, intrinsic viscosity values of 34.0, 25.6, and 13.8 ml/g were obtained at 3.5, 20 and 35 °C, respectively, whereas rabbit muscle PFK yielded values of 6.9, 6.2, and 5.2 ml/g at the corresponding temperatures. These data clearly show a decrease in asymmetry with increase in temperature. However, both enzymes are still asymmetric at the higher temperature, inasmuch as most globular macromolecules have intrinsic viscosity values in the range of 3 to 4 ml/g, regardless of molekular weight. Studies from 1 to 45 ° C at a fixed protein concentration (4.8 mg/ml) showed that pig kidney PFK has reduced viscosity values of 51.0 ml/g (low-temperature form) and 20.4 ml/g (high-temperature form) in plateau regions of the viscosity graph at the temperature extremes; the mid-point of the transition between the two forms is at about 22–24 °C. Rabbit muscle PFK at 4.2 mg/ml reproducibly gave corresponding reduced viscosity values of 6.9 and 4.8 ml/g for the low- and high-temperature forms, respectively; the transition mid-point between the two forms is at about 16 °C. The first reported sedimentation velocity studies of rabbit muscle PFK at near-physiological temperature (35 °C) show that with near-physiological protein concentration (1.25 mg/ml), the enzyme is in a much more dissociated form, s_20,w(weight average) = 14. 5 S; s_20,w(peak leading edge) = 17 S, than that previously reported at lower temperatures, s_20,w(fastest peak) = 23–30 S. Similarly, the first sedimentation studies on the pig kidney enzyme indicate a lower sedimentation coefficient at 35 ° C (s^0.39%_20,w = 48 S) than at 3.5 ° C(65 S).     

Structure and physico-chemical properties of bacteriophage G: III. A homogeneous DNA of molecular weight 5 × 108

The physico-chemical properties of the DNA released from bacteriophage G (active on Bacillus megatherium) are described. Phage G, an unusually large bacteriophage, has a nucleic acid content of 4 to 6 × 10⁸ daltons.Sedimentation velocity analysis at low angular speed and examination by electron microscopy, indicate that a single DNA molecule, sedimenting with s_{20, w}⁰ = 125 ± 1.5 S and at least 200 ± 20 μm long, is released upon thermal or osmotic shock. Melting temperature data and chromatographic analysis indicate a mean base composition of 70% A + T. CsCl and Cs₂SO₄ buoyant density data, circular dichroism spectra and sensitivity to specific nucleases indicate that phage G DNA is similar to the DNAs from T-even phages and is more glucosylated than phage T6 DNA. Direct glucose determination indicates a 185% molar ratio of glucose to cytosine. Linear density extrapolated from literature data and contour length measurement yield a lower limit for the molecular weight of phage G DNA of 4.9 × 10⁸. Comparison of this value with the s_20,w⁰ measured with the analytical ultracentrifuge seems to confirm the validity of the empirical relationship proposed by Freifelder (1970), between s_{20, w}⁰ and molecular weight, over a larger range than that previously known. A possible systematic error in defect in length determination, however, prevents a discrimination between this and other empirical formulae proposed by various authors, which predict a molecular weight that is 20 to 25% higher.     

Studies on groundnut proteins. V. Physico-chemical properties of arachin prepared by different methods.

ORD,¹ CD, and fluorescence spectra of arachin prepared by Tombs' (Biochem. J., 96, 119; 1965), Dawson's (Anal. Biochem., 41, 305; 1971) or Shetty and Rao's (Anal. Biochem., 62, 108; 1974) procedure were measured; the effect of denaturants such as SDS, GuHCl, and acid was also determined. ORD and CD spectra showed differences, whereas fluorescence spectra did not show any difference. The effect of the denaturants was the same on the three arachins. At low concentrations of GuHCl (<2 m), the denaturant was bound by the protein molecule without causing any conformational change. The binding affinity varied among the arachins.     

Studies on groundnut proteins. III. Physicochemical properties of arachin prepared by different methods

The homogeneity of arachin prepared by different methods was determined by the techniques of polyacrylamide gel electrophoresis, DEAE-cellulose chromatography, and ultracentrifugation. Arachin obtained by the method of Tombs (Biochem. J.96, 119, 1965) or Dawson (Anal. Biochem.41, 305, 1971) appeared to be homogeneous by these techniques. Total groundnut proteins, extracted in 1 m NaBr solution and subjected to double precipitation with 23% (NH₄)₂SO₄, also gave a homogeneous arachin preparation. These three homogeneous arachin preparations differed in their rate of hydrolysis by alpha-chymotrypsin, heat coagulation, and dissociation into subunits. However, SDS¹ and GuHCl denatured them to the same extent, as could be judged by the difference spectra. The phosphorus and carbohydrate content of the three preparations did not differ significantly.     

Rapid purification of bacterial plasmids and coliphage M13 RF without CsCl centrifugation

A simple and rapid procedure for the purification of plasmids from Escherichia coli K12 has been developed. Bacterial cells are subjected to the boiling procedure [D. S. Holmes, and M. Quigley Anal. Biochem.114, 193–197 (1981)] followed by removal of contaminating RNA by chromatography on Sepharose 2B and of genomic DNA by acid-phenol extraction. Plasmids are recovered with good yield. They can be restricted and ligated and will transform host cells. A simple modification of the procedure allows it to be used for the isolation of coliphage M13 RF DNA.     

Molecular characteristics of bovine factor X activated in concentrated sodium citrate solution

Preparations of the zymogen form of bovine factor X were incubated in 25% $\text{w}\text{v}$ sodium citrate at room temperature. The rate of activation of factor X was dependent on the extent of contamination with factor VII, prothrombin, and thrombin. The activated factor X was isolated by DEAE-cellulose chromatography. Analysis of the final product by sedimentation velocity centrifugation coupled with measurements of the rate of boundary spreading, high-speed sedimentation equilibrium, and gel filtration chromatography provided evidence for a single molecular species undergoing reversible association-dissociation with a monomeric molecular weight of 48,000. In the absence of mercaptoethanol a single band was seen by disc electrophoresis and by SDS-acrylamide electrophoresis but after disulfide reduction two components of molecular weights 30,000 and 17,000 were visible. The protein contained large amounts of acidic amino acids but no carbohydrate. The N-terminal amino acids were alanine and isoleucine and 1 mole C-terminal arginine per mole protein was found. These characteristics are very similar to those of factor X activated with Russell's viper venom.When a BaSO₄ eluate of bovine plasma rich in prothrombin was allowed to stand in 25% sodium citrate both thrombin and activated factor X were generated. Chromatography of the isolated activated factor X on Sephadex G-200 as well as disc electrophoresis showed that it behaved identically with the enzyme obtained from purified zymogen and was clearly distinguishable from autoprothrombin c, a glycoprotein possessing qualitatively similar biological activity (Seegers, W. H., Cole, E. R., Harmison, C. R., and Marciniak, E. (1963) Can. J. Biochem. Physiol.41, 1047).     

A rapid DEAE disk assay for photoreactivation of pyrimidine dimers in [3H]DNA.

We have developed a rapid, sensitive, and specific assay for photoreactivation of pyrimidine dimers in ³H-labeled DNA. It is based on the nuclease resistance of dimercontaining sequences in DNA, and the adsorption of these sequences to DEAE-substituted paper (DE-81). The method maintains the advantages of the rapid dimer assay of B. M. Sutherland and M. J. Chamberlin (1973, Anal. Biochem., 53, 168–176), while avoiding its major drawback, the frequent preparation of high specific activity, ³²P-labeled, bacteriophage DNA. In addition, the use of scintillation spectrometry in our assay should allow more widespread use of this method.     

Isolation and characterization of kinetoplast DNA from Leishmania tarentolae

Kinetoplast DNA (? = 1.703 g/ml.) was isolated by preparative cesium chloride ultracentrifugation in a fixed-angle rotor from total cell DNA of Leishmania tarentolae and examined in terms of sedimentation properties, melting characteristics, and appearance in the electron microscope. It consisted of several molecular types, either free or bound together in associations of variable size: minicircles (molecular weight = 0.56 ± 0.03 × 10⁶), catenated minicircles, “figure 8” molecules, and long molecules. The associations seem to be held together by the long molecules threading through the smaller circles and catenanes. The large associations could be broken down by sonication, DNase II-treatment, or shear forces. Minicircles, catenated dimers, trimers, and small linear fragments were separated on preparative sucrose gradients of sonicated DNA, and S_20,w values were assigned to each molecular type by band sedimentation in the analytical ultracentrifuge.     

Calculation of s20,w values using ultracentrifuge sedimentation data from linear sucrose gradients,an improved,simplified method

A mathematical method is described for calculating the sedimentation coefficient (s_{20, w}) with ultracentrifuge data from linear sucrose gradients. Gradient density and viscosity functions are precisely described by regression equations, which permit continuous evalution (by integration) of the effects of gradient geometry on particle sedimentation. The results agree with previously used and more complex methods.     

Effect of thyroidectomy on the kinetics of ADP-ATP translocation in liver mitochondria

The role of adenine nucleotide translocase (AdNT) in the reduced oxidative metabolism of hypothyroidism has been examined. Both AdNT and respiratory activities in liver mitochondria of thyroidectomized rats were 30% below normal. Mitochondrial AdNT activities were determined by the back-exchange method of Pfaff and Klingenberg (Eur. J. Biochem.6, 66, 1968). The K_m and V_max of the enzyme were temperature dependent. At physiological temperature, the K_m and V_max of the normal rat AdNT were 10 μm (for external ADP) and 4.73% s^?1 (percentage efflux of the labeled adenine nucleotides), respectively. AdNT in hypothyroid rat liver mitochondria exhibited a 25–35% lower V_max and 75% higher K_m when assayed over the temperature range 0 to 37 °C. Dixonplot studies indicated that the AdNT in hypothyroidism was two- to threefold more sensitive to atractylate and palmitoyl-CoA inhibitions. In contrast the ADP-ATP translocase in hypothyroidism was more resistant than the control carrier to bongkrekate inhibition. The decrease in the transport of ADP, which is consistent with the decreased oxidative activity associated with hypothyroidism, apparently occurs secondary to changes in the lipid matrix of the inner mitochondrial membrane (F. L. Hoch (1977) Arch. Biochem. Biophys.178, 535.).     

A modification of the acetic acid-urea system for use in microslab polyacrylamide gel electrophoresis

A modification of the S. Panyim and R. Chalkley (1969, Arch. Biochem. Biophys.130, 337) acetic acid-urea polyacrylamide gel system to include a stacking gel has been devised. The modification makes possible the use of acetic acid-urea gels in the microslab system of P. T. Matsudaira and D. R. Burgess (1978, Anal. Biochem.87, 386).     

A simple micro-assay for inorganic phosphate

Modification of two assay procedures (Van Belle, H. (1970) Anal. Biochem.33, 132–142 and Itaya, K., and Ui, M. (1966) Clin. Chim. Acta14, 361) has allowed the development of a manual assay for inorganic phosphate of high simplicity and sensitivity. Total analysis requires only three reagents and is accomplished in less than 5 min, and smaples containing less than 1 μg/ml of inorganic phosphate may be detected. This assay retains a unique principle of the former two, complexation (instead of reduction) of the phosphomolybdate heteropoly complex with an appropriate triphenylmethane dye (malachite green, methyl green). Use of detergents has been eliminated and some further properties of the dyes, the assay, and the latter's applicability to a coupled enzyme system for phosphomonoester and phosphodiester analysis are discussed. Consideration is also given to the associated phenomena of transphosphorylation. (Dayan, J., and Wilson, I. B. (1964) Biochim. Biophys. Acta81, 620–623).     

Rapid, multisample isoelectric focusing in sucrose density gradients using conventional polyacrylamide electrophoresis equpiment: a two-peak transient in the approach-to-equilibrium.

Using a semiporous plug of agar gel to support a sucrose density gradient column without restricting electrical conductivity, Massey and Deal [J. Biol. Chem.248, 56 (1973)] were able to use a conventional polyacrylamide gel electrophoresis apparatus to carry out single tube isoelectric focusing experiments in density gradients in only 2 hr using minute amounts (50 μg) of sample and very little ampholyte (0.18 ml); no cooling apparatus was required. In this work we report that 1) polyacrylamide provides a superior gel plug and 2) that ten isoelectric focusing tubes can easily be run simultaneously in a conventional polyacrylamide gel electrophoresis apparatus. In addition, the isoelectric points of eight proteins, with pI values ranging from 5.1 to 8.8 have been determined and the kinetics of the approach-to-isoelectric-focusing-equilibrium have been analyzed. Of special interest is the discovery that in the initial stages of focusing, in these sucrose density gradients, a major peak is formed at each end of the column; these two peaks migrate toward each other and finally coalesce into a single peak. Similar, although less pronounced, effects were previously observed by Catsimpoolas and Wang [Anal. Biochem.39, 141 (1971)] in focusing experiments in polyacrylamide gels. With all other conditions constant, the time required to reach equilibrium is 1) less in broad range (e.g., 3–10) pH gradients than it is in narrow range (e.g., 5–8) pH gradients and 2) generally greater with higher molecular weight substances than with lower molecular weight substances. Explanations are given for all of these kinetic phenomena.     

Measurement of the binding of antifibrinolytic amino acids to various plasminogens

A method for studying the binding of various antifibrinolytic amino acids to plasminogen has been devised. This method is based upon the ability of inhibitors of the streptokinase-induced conversion of plasminogen to plasmin to produce an alteration in the s_20,w⁰ of native plasminogen accompanying their binding to plasminogen. Typical examples of antifibrinolytic amino acids, e.g., 6-amino hexanoic acid, trans-4-aminomethyl cyclohexane-1-carboxylic acid, and l-lysine cause alterations in the s_20,w⁰ of streptokinase-insensitive plasminogens as well as streptokinase-sensitive plasminogens from 5.1–5.6 S to 4.1–4.7 S depending upon the particular plasminogen used. Titration of the s_20,w⁰ of human plasminogen (streptokinase-sensitive) using absorption optics in the analytical ultracentrifuge with the above three compounds led to dissociation constants of 4.5 ± 0.8 × 10⁻⁴m, 8.0 ± 0.8 × 10⁻⁵m, and 6.8 ± 0.8 × 10⁻²m, respectively. When duck plasminogen (streptokinase-insensitive) was used, dissociation constants of 5.6 ± 0.7 × 10⁻⁴m, 9.0 ± 0.8 × 10⁻⁵m, and 8.8 ± 0.7 × 10⁻²m, were obtained.     

Plasmid replication in DNA Ts mutants of Bacillus subtilis.

In an attempt to increase our understanding of plasmid replication in Bacillus subtilis we determined the effect of various dna Ts mutations [Gass, K. B., and Cozzarelli, N. R. (1973). J. Biol. Chem. 248, 7688–7700; Gross, J. D., Karamata, D., and Hempstead, P. G. (1968). Cold Spring Harbor Symp. Quant. Biol.33, 307–312; Karamata, D., and Gross, J. D. (1970). Mol. Gen. Genet.108, 277–287] on pUB110 replication. pUB110 is a kanamycin resistance plasmid originally isolated in Staphylococcus aureus and introduced into B. subtilis by transformation. At temperatures nonpermissive for chromosomal DNA synthesis dnaA13, dnaB19, dnaC6, dnaC30, dnaD23, dnaE20, and dnaI102 permit replication of the plasmid. In several cases this “amplification” continues until approximately equal amounts of plasmid and chromosomal DNA are present. dnaG34, dnaH151, dnaF133, mut-1, and polC26 affect both pUB110 and host DNA synthesis at nonpermissive temperatures. The last three mutations are known to affect the activity of DNA polymerase III (PolIII). When polC26 is incubated at a nonpermissive temperature, there is an accumulation of plasmid DNA with a density on EtBr-CsCl gradients intermediate between that of covalently closed circular (CCC) and open circular DNA. pUB110 can replicate in a strain which is deficient in DNA polymerase I (PolI). Finally, chloramphenicol (Cm) inhibits the replication of pUB110 as well as of chromosomal DNA.