On the role of the macromolecular phase transitions in biology in response to change in solution volume or macromolecular composition: action as an entropy buffer

We have used numerical simulation to demonstrate the potential for macromolecular precipitate solution phase transitions existing within the cell, to play a role in the minimization of changes in location or quaternary state of other macromolecular components, predicted to accompany changes in cell volume. For our modeling we have employed thermodynamic relations that take into account the large effects upon the thermodynamic activity coefficient produced by a solution environment that is highly volume occupied due to the presence of high concentrations of soluble macromolecule. The theoretical approach adopted, along with the simulated results, provide a framework for the interpretation of certain proteins' behavior (e.g. cytoskeletal elements such as tubulin and actin and possibly some prion structures) in response to cell volume change.     

Dielectric Relaxation of Molecules with Fluctuating Dipole Moment

When a dissolved macromolecule is in chemical equilibrium with a free ionic species, the charge configuration, and hence the dipole vector, of the macromolecule is fluctuating. Expressions for the static dielectric constant and the relaxation spectrum of such a mixture are here derived in terms of the components of the mean moment and the root mean square fluctuation moment, the molecular relaxation time constants, and the chemical rate constants of the ionic binding reaction. Contrary to a previous treatment of this problem by Kirkwood and Shumaker (1), it is shown that fluctuations introduce no independent components into the relaxation spectrum.     

An electrophoretic device concentrating charged macromolecules to a predetermined final solution volume

An apparatus for electrophoretic concentration of charged macromolecules to a predetermined final solution volume has been developed. The concentration process has a yield of near 100%, which implies that it is possible to predetermine the final macromolecule concentration as well. Both the final macromolecule solution volume and concentration are nearly independent of the electrophoresis time when it exceeds a certain minimum value. The electric field strength across the boundary containing the concentrated macromolecule solution is very low. This considerably reduces macromolecule aggregation, adsorption, and denaturation at this boundary compared to conventional electrophoretic concentrator designs. Both one-stage and two-stage versions of the apparatus have been developed. The one-stage version easily yields a 10-fold and the two-stage version a 50-fold concentration of the macromolecules. Typical macromolecule solution start volumes are 20-50 ml.     

Small molecules as chromotropes in metachromasia

Summary Interactions of cationic dye methylene blue with small polyanions like inositol hexasulfate, adenosine-triphosphate, ammonium molybdate, potassium ferro- and ferricyanide have been studied spectrophotometrically and conductometrically to ascertain the chromotropic characters of these polyanions. Results show that while almost all of them bind the dye stoichiometrically, none of them except ammonium molybdate is a chromotrope in the sense in which heparin, chondroitin sulfate etc. are. Inositol hexasulfate induces an intermediate spectra, though not perfectly metachromatic as is the case with inositol hexaphosphate. It is concluded that a chromotrope need not be a macromolecule to induce metachromasia in a dye solution, but the minimum number of charges per polyanion to give it a chromotropic character will vary with the nature of the polyanion.University Research Scholar.     

Distinct clonal Ig diversification patterns in young appendix compared to antigen-specific splenic clones

The young rabbit appendix is a dynamic site for primary B cell repertoire development. To study diversification patterns during clonal expansion, we collected single appendix B cells from 3- to 9-wk-old rabbits and sequenced rearranged H and L chain genes. Single cells obtained by hydraulic micromanipulation or laser capture microdissection were lysed, PCR amplified, and products directly sequenced. Gene conversion-like changes occurred in rearranged H and L chain sequences by 3-4 wk of age. Somatic mutations were found in the D regions that lack known conversion donors and probably also occurred in the V genes. A few small sets of clonally related appendix B cells were found at 3-5 wk; by 5.5 wk, some larger clones were recovered. The diversification patterns in the clones from appendix were strikingly different from those found previously in splenic germinal centers where an immunizing Ag was driving the expansion and selection process toward high affinity. Clonally related appendix B cells developed different amino acid sequences in each complementarity-determining region (CDR) including CDR3, whereas dominant clones from spleen underwent few changes in CDR3. The variety of combining sites generated by diversification within individual clones suggests that at least some clonal expansion and selection, known to require normal gut flora, may be driven through indirect effects of microbial components rather than solely by their recognition as specific foreign Ags. This diversity of combining sites within B cell clones supports the proposed role of appendix in generating the preimmune repertoire.     

Alteration of mammalian cell metabolism by dynamic nutrient feeding

The metabolism of hybridoma cells was controlled to reduce metabolic formation in fed-batch cultures by dynamically feeding a salt-free nutrient concentrate. For this purpose, on-line oxygen uptake rate (OUR) measurement was used to estimate the metabolic demand of hybridoma cells and to determine the feeding rate of a concentrated solution of salt-free DMEM/F12 medium supplemented with other medium components. The ratios among glucose, glutamine and other medium components in the feeding nutrient concentrate were adjusted stoichiometrically to provide balanced nutrient conditions for cell growth. Through on-line control of the feeding rate of the nutrient concentrate, both glucose and glutamine concentrations were maintained at low levels of 0.5 and 0.2 mM respectively during the growth stage. The concentrations of the other essential amino acids were also maintained without large fluctuations. The cell metabolism was altered from that observed in batch cultures resulting in a significant reduction of lactate, ammonia and alanine production. Compared to a previously reported fed-batch culture in which only glucose was maintained at a low level and only a reduced lactate production was observed, this culture has also reduced the production of other metabolites, such as ammonium and alanine. As a result, a high viable cell concentration of more than 1.0 × 10⁷ cells/mL was achieved and sustained over an extended period. The results demonstrate an efficient nutrient feeding strategy for controlling cell metabolism to achieve and sustain a high viable cell concentration in fed-batch mammalian cell cultures in order to enhance the productivity. This revised version was published online in July 2006 with corrections to the Cover Date.     

Calculations of stability of A and B forms of dA6.dT6 and dG6.dC6 duplexes by molecular mechanics method in an aqueous solution and approximation of the statistical model. Analysis of unusual stability of the dA6.dT6 B form

The statistical model of the environment for estimating the influence of the aqueous electrolyte solution on the macromolecule has been developed. The energy of the water-fasteners between macromolecule atoms has been calculated. The calculations of A and B form dA6.dT6 and dG6.dC6 duplexes have been made. The unusual stability of B form in dA6.dT6 and their unstability in dG6.dC6 have been analysed. B form duplexes have optimal energy of Van-der-Waals interactions, but a more strained ribose-phosphate backbone, the latter being the reason of its high conformational lability. The aqueous solution stabilizes B form duplexes. The main types of sequence-dependent B form stabilizing interactions are: electrostatic interactions between phosphate groups and bases, the effect of the solvent molecular structure and energy of water fasteners between nucleic bases and ribose-phosphate backbone.     

Structural characterization of high 800 nm-absorbing light-harvesting complexes from Rhodospirillales from their resonance Raman spectra

Resonance Raman spectroscopy provided evidence that high 800 nm-absorbing antennae from Rhodopseudomonas (Rps.) acidophila and Rps. palustris have similar structures around their dweller bacteriochlorophylls. These host-site structures are different from those of B 850-800 complexes from Chromatiaceae, which also exhibit a high absorbance at 800 nm. As also shown by previous biochemical data, these complexes might be stoichiometrically different from other antenna complexes, having one more BChl per minimal size unit of protein. A new classification of B 850-800 complexes is proposed, on the basis of resonance Raman and biochemical data: this classification distinguishes a class of B 850-800 S (involving the B 850-800 complexes from sulfur purple bacteria), two classes of B 850-800 NS (involving the B 850-800 complexes from non sulfur purple bacteria) and a class of H 800 complexes (involving the B 850-800 complexes from non sulfur purple bacteria exhibiting a high absorbance at 800 nm).     

Dielectric increment and dielectric dispersion of solutions containing simple charged linear macromolecules. I. Theory

A theory is derived for the static and frequency dependent value of the electric permittivity for model systems representing a solution of a macromolecule bearing a large number of identical charges. The polyion is represented either as a charged rigid rod (A) or as a sequence of charged rodlike subunits in an arbitrary but fixed configuration (B) and it is assumed that a certain fraction of the counterions is closely associated to the macromolecule. The dielectric properties are described in terms of fluctuations in the distribution of the associated counterions along the polyion. These fluctuations can occur locally between potential barriers marking the ends of the subunits (if considered) but can also extend over the whole molecule. Neglecting correlations between different associated counterions expressions for the static value of the dielectric increment are obtained which reveal its dependence on the fraction of bound ions, on the charge of the counterions and on the length of the molecule for model A or the radius of gyration for model B. The dynamic behaviour of A is distinguishable from that of B as the former will present one single dispersion curve of the frequency dependent electric permittivity while the latter may give rise to two different dispersion regions. This will be the case if both the exchange between bound and free ions and the rotation of the complete molecule are relatively slow in comparison to the local bound counterion density fluctuations and if these fluctuations occur on a much shorter time scale than the ion density fluctuations extending over the complete macromolecule.     

Purification and molecular characterization of two inhibitors of yeast proteinase B.

A rapid purification procedure for large scale preparations of yeast proteinase B inhibitors 1 and 2 (IB1 and IB2) is described. By disc gel electrophoresis, amino acid analysis, and end-group determinations, each of the inhibitors is homogeneous. Both inhibitors are polypeptides with molecular weights of 8,500, containing 74 residues. No components other than amino acids could be detected. There is no significant difference in the amino acid compositions of the two inhibitors as analyzed after acid hydrolysis. Both polypeptides are characterized by the total absence of arginine, tryptophan, and sulfur-containing amino acid residues. The proteinase B inhibitors of yeast, therefore, differ fundamentally from proteinase inhibitors of many other organisms, which generally contain a large number of disulfide bridges. Both proteinase B inhibitors have threonine as the NH2-terminal residue and -Val-His-Thr-Asn-COO- as the COOH-terminal sequence. Comparison of peptide maps after tryptic digestion reveals that the two inhibitors differ definitely in only a few tryptic peptides. The inhibitors are rapidly inactivated by digestion with carboxypeptidase A from bovine pancreas at pH 8.5. Inactivation occurs stoichiometrically with the release of threonine, the penultimate residue at the COOH-terminal end of both inhibitors.     

Structure of phenylalanine-accepting transfer ribonucleic acid and of its environment in aqueous solvents with different salts

Yeast tRNA(Phe) was studied in different salt-containing solvents by UV absorbance and small-angle neutron scattering (SANS). This extends results obtained previously in NaCl and KCl solutions [Li, Z.-Q., Giegé, R., Jacrot, B., Oberthür, R., Thierry, J. C., & Zaccai, G. (1983) Biochemistry 22, 4380-4388]. As expected, at low concentrations of all salts studied, the tRNA molecule is unfolded. The importance of specific counterion interactions and the flexibility of the macromolecule are emphasized by the observation that it cannot take up its folded structure in N(CH3)4Cl solvents, even when that salt concentration is increased to 1 M, in the absence of Mg ions. In CsCl solvents, on the other hand, the folded conformation is obtained in salt concentrations above about 0.2 M, similar to NaCl or KCl. By a comparison of SANS results in CsCl H2O and CsCl 2H2O solvents with the data from NaCl and KCl solvents, thermodynamic and structural parameters were derived for the solvated macromolecule. All the data are accounted for, quantitatively, by a model for the particle in NaCl, KCl, or CsCl solution made up of tRNA76-, closely associated with 76 positive hydrated counterions, surrounded by an aqueous solvent layer that excludes salt (and, therefore, of density different from that of bulk solvent). The mass of water in that layer depends on salt concentration, and the values found are consistent with those predicted by the Donnan effect.     

Investigation of the conformational lability of serum albumin macromolecules in aqueous solution by the NMR spin-echo method.

The complex proton spin-echo decay curve was recorded for human serum albumin (SA) solutions with different concentrations in normal and heavy water. The curve included three fast-decaying components for SA, in addition to the slow-decaying component for the water. The total amplitude of these three components roughly corresponded to the number of protons in the SA (with isotopic exchange taken into account); the component ratio remained constant at different concentrations and different temperatures between 4 and 39 degrees. The relatively slow-decaying protein component, which accounted for similar to 10% of the SA protons, was produced by the side chains of the protein. The presence of two other faster-decaying SA components with approximately equal amplitudes indicated that only about half of the remaining protons in the SA macromolecule are incorporated into the comparatively rigid globule, the other half belonging to groups with high conformational lability in aqueous solution. The activation energy for the aqueous component was close to that for pure water, while the activation energies for the protein components were roughly twice as large.     

A simple, versatile, sensitive and volume-independent method for quantitative protein determination which is independent of other external influences.

A method is described which in principle is a quantitative "spot analysis". 0.5-5 microliter of a protein solution in the concentration range between 0.01-10 mg/ml is used for one determination. The sample is taken up by capillary attraction in a 0.5-, 1-, 2- or 5-microliters capillary and transferred to a cellulose acetate strip. The protein is fixed and stained simultaneously by dipping the cellulose acetate strip into a solution of Amido Black or a benzoxanthene derivative (Hoechst 2495) dissolved in in methanol/acetic acid. After elution of the excess of dye (3 x 5 min) the quantitative evaluation can be performed in different ways: 1) The sample is fixed and made transpartent by incubation in dioxane/1-butanol and evaluated densitometrically (Amido Black 10B) or 2) the evaluation is performed in situ by spot fluorometry (Hoechst 2495). 3 The sample can be dissolved together with the acetate layer completely in dioxane, dimethylsulfoxide or N,N-dimethylformamide and evaluated photometrically or 4) fluorometrically. 5) Highest sensitivity is reached if the fluorochrome (Hoechst 2495) bound to the protein is eluted with 15% NH4OH and measured fluorometrically. There is a linear correlation with a correlation coefficient of 0.999 between the fluorescence and a protein amount of 10 ng-20 micrograms. In addition to its simplicity, the method has the advantage of being independent of or well-defined against other external influences, e.g., sodium dodecyl sulfate, mercaptoethanol, Triton X-100, etc. The stainability of a protein with Amido Black is influenced stoichiometrically by sodium dodecyl sulfate (not by mercaptoethanol) whilst the staining with Hoechst 2495 is not at all affected. As there is linear correlation between the area of a spot on an acetate layer and the volume applied in the range between 0.5 and 5 microliters, (only influenced stoichiometrically by the protein concentration in that volume, which in turn is measured by staining with Amido Black), then with a simple iterative calculation on the basis of suitable calibration curves, it is easily possible to determine a protein concentration in mg/ml even in an unknown volume between 0.5 and 5 microliters.     

Fluorescence-activated cell sorter (FACS) analysis of rabbit cells

Monoclonal antibodies RB1, RB2, RT1, RT2 and RB3 were prepared against rabbit lymphoid cells by immunization with various fractions of rabbit lymphoid cells. The antigens detected by the antibodies are found on B and T cells in different densities. High proportions of polymorphonuclear and bone marrow cells which do not carry the RABELA and RTLA antigens carry the antigens of the RB and RT series. A subpopulation of appendix sIg-negative, RTLA-negative cells has a relatively high concentration of RT2. In general, B and T cells of the appendix show relatively small differences in the membrane densities of RB and RT antigens.     

Effect of cosolvents on solubility of protein in equilibrium between different states

This paper describes a theoretical work on the solubility of a protein in equilibrium between different forms such as isomerization (A ? B) and dimerization (2A ? B). Under the assumptions that A and B have different solubilities and form their own solid phases (in the form of either precipitation or crystal), it was shownthat only either A or B precipitates at a given condition, another form being in equilibrium in solution with the precipitating form, provided that the solubility ratio of A to B is not identical to their equilibrium composition in the solution phase determined by the equilibrium constant. It follows, then, that the total concentration of the protein in the solution phase can be calculated by summing the solubility of the precipitating form and the concentration in solution of another form in equilibrium with the precipitating form. Assuming various preferential protein-solvent interactions for the two forms in solution as well as solid phases, dependences of the total protein solubility on the additive concentration were examined. It was shown that this dependence may be complex, showing maximum, minimum, or inflection point, depending on the preferential protein interactions with solvent components.     

A novel reversible thiol-specific spin label: papain active site labeling and inhibition

A new, highly reactive, thiol-specific spin label, (1-oxyl-2,2,5,5-tetramethyl-Δ³-pyrroline-3-methyl)methanethiosulfonate was synthesized. Its unique specificity was demonstrated with the active thiol protease, papain, which was stoichiometrically inhibited within 5 min, resulting in a conformationally sensitive spectrum, which was identical over the pH range 4.5–7.5. The spin-label modification yielded a mixed disulfide between Cys 25 of papain and the 3-methylpyrroline nitroxide which was rapidly and completely reversed by exposing the labeled papain to mild concentrations of dithiothreitol. The concentration of released nitroxide corresponded exactly to the number of reactive thiol groups in the original enzyme. Full enzymatic activity was restored after the spin label was removed. This spin label is useful as a sensitive thiol titrating agent as well as a specific conformational probe of thiol site structure by virtue of its minimal rotational freedom and distance from the covalent disulfide linkage to the macromolecule under study.     

Contribution of the Excluded Volume of Bovine Serum Albumin for Solute Molecules to the Apparent Nonsolvent Water

Addition of a macromolecule to a solution will give rise to a large excluded volume for the centers of the solute molecules. This will cause an apparent increase in solute concentration which is of the same order of magnitude as that associated with the nonsolvent volumes reported in the literature. A critical examination of one of the procedures used for the determination of nonsolvent water—the vapor pressure method of Hill—is given, and it is concluded that, with the use of this method, it is impossible to detect any significant nonsolvent water surrounding bovine albumin for either sugars or polyols. Generally, data reported in the literature for the nonsolvent water of proteins or other macromolecules will be too high unless they are corrected for the excluded volume.     

THE COLLOIDAL BEHAVIOR OF EDESTIN

1. It has been shown by titration experiments that the globulin edestin behaves like an amphoteric electrolyte, reacting stoichiometrically with acids and bases. 2. The potential difference developed between a solution of edestin chloride or acetate separated by a collodion membrane from an acid solution free from protein was found to be influenced by salt concentration and hydrogen ion concentration in the way predicted by Donnan''s theory of membrane equilibrium. 3. The osmotic pressure of such edestin-acid salt solutions was found to be influenced by salt concentration and by hydrogen ion concentration in the same way as is the potential difference. 4. The colloidal behavior of edestin is thus completely analogous to that observed by Loeb with gelatin, casein, and egg albumin, and may be explained by Loeb''s theory of colloidal behavior, which is based on the idea that proteins react stoichiometrically as amphoteric electrolytes and on Donnan''s theory of membrane equilibrium.     

Reconstitution of Escherichia coli ribosomes containing puromycin-modified S14: functional effects of the photoaffinity labeling of a protein essential for tRNA binding

In previous work we have shown that puromycin photoaffinity labels two proteins, L23 and S14, from separate sites of high affinity on Escherichia coli ribosomes [Jaynes, E. N., Jr., Grant, P. G., Giangrande, G., Wieder, R., & Cooperman, B. S. (1978) Biochemistry 17, 561-569; Weitzmann, C. J., & Cooperman, B. S. (1985) Biochemistry 24, 2268-2274], that puromycin-modified S14 is separable from native S14 by reverse-phase high-performance liquid chromatography (RP-HPLC), and that ribosomal proteins prepared by RP-HPLC can be reconstituted into active 30S subunits [Kerlavage, A. R., Weitzmann, C. J., & Cooperman, B. S. (1984) J. Chromatogr. 317, 201-212]. In this work we definitively identify puromycin-modified S14 by tryptic fingerprinting, an analysis that also provides evidence that the single tryptophan-containing peptide in S14 is the site of puromycin photoincorporation. We show that reconstituted 30S subunits, in which all of the S14 present is stoichiometrically modified with puromycin and all other ribosomal components are present in unmodified form, lack Phe-tRNAPhe binding activity and further that 70S ribosomes containing such reconstituted 30S subunits have substantially diminished binding activity to both the A and P sites, as differentiated through use of tetracycline. Suitable control experiments strongly indicate that this loss of activity is a direct consequence of puromycin photoincorporation.     

The Demonstration of Beryllium Oxide in Paraffin Sections with Chromoxane Stains

Aqueous solutions of the arylmethane dyes Chromoxane pure blue BLD (C.I. No. 43825) and Chromoxane pure blue B (C.I. No. 43830) will stain beryllium oxide. In the presence of EDTA the staining of other metals is masked. As a specific stain for BeO, formol saline fixed paraffin sections are hydrated and stained for 1 hr with either 0.1 gm of pure blue BLD in 100 ml of pH 4.0 Na-acetate buffer or with 0.1 gm of pure blue B in 1 N NaOH adjusted to pH 9.0 with HCl. To mask interference from other metal ions, 9 gm of Na₂-EDTA is added to 100 ml of the stain solution. BeO is stained blue, organic tissue components are either unstained or pink. Results of tests against other materials show that a high degree of specificity may be expected from these dyes. A 1% aqueous solution of neutral red may be used as a counterstain.