A theory on the effect of low molecular salts on the conformation of linear polyions

The effect of low molecular salts on the conformation of linear polyions is analyzed on the basis of the additivity law for the thermodynamic properties of polyelectrolytes in the presence of salts. In the case of flexible polyions the theory shows that the logarithm of the conformation parameter changes proportional to A ln (1 + γ_s0C_s/γ_pC_p) as a function of the salt concentration c_s, where c_p is the concentration of counterions from polyelectrolytes and γ_p and γ_s0 are the activity coefficient of counterions from polyelectrolytes in the absence of salts and from salts in the absence of polyelectrolytes, respectively. In the case of the discontinuous transition of the conformation of polyions, it is shown that the change of the transition point by salts is proportional to the same factor as the above. The constant A, which determines the magnitude of the effect of salts, is proportional to the sensitivity of the activity coefficient to the conformation of polyions in the absence of salts. A similar analysis is made for the conformational change due to dilution by the addition of solvent. These theoretical results are found to be in good agreement with experimental data on the viscosity of flexible polyions and on the helix–coil transition of biopolymers. The interrelation between these conformational changes and various thermodynamic properties of polyelectrolytes with salts is discussed.     

Effect of ionic strength on the pKa of ligands bound to DNA

The pK_a of 3,8-diamino-6-phenyl-phenanthridine (DAPP), a nonquaternary analog of ethidium bromide, has been determined spectrophotometrically as a function of sodium ion concentration both free in solution and complexed to DNA. Unwinding angle determinations with this compound were determined with Col El DNA using ethidium bromide as a standard. The unwinding angle for DAPP was 24 ± 2° relative to 26° for ethidium, and this suggests that DAPP binds in a manner quite similar to ethidium and with no significant outside bound DAPP under these experimental conditions. Isobestic behavior was obtained on spectrophotometric pH titration above pH 5 as long as the ratio of DNA-phosphate to ligand was between 100 and 300 and the DNA phosphate concentration was approximately 0.01M or greater. The loss of isosbestic behavior which occurred below pH 5 is probably due to titration of the 8 amino group of the ligand complexed to DNA. To circumvent this problem, pK_a values and the extinction coefficient of the acidic species were both determined by a computer program using experimental data obtained above pH 5. The pK_a of the free compound has only a minor dependence on ionic strength, while the pK_a of the ligand bound to DNA in an intercalated complex depends strongly on the sodium ion concentration. The pK_a of the DAPP-DNA complex is a linear function of –log[Na⁺] as predicted by the ion-condensation theory of polyelectrolytes. It was determined that DAPP is essentially completely bound to DNA under the conditions of these experiments by (1) determination of apparent pK_a values as a function of total DNA concentration, (2) calculation of binding constants for the neutral species of DAPP, and (3) spectral analysis of the protonated and neutral species of DAPP bound to DNA relative to DAPP free in solution. These results support the ion-condensation theory; provide an independent method for measuring ψ*, the average number of counterions associated per phosphate of DNA in the intercalated conformation; and illustrate that there are no specific pH effects or absolute pK_a values for ligands bound to DNA, but only ionic-strength-dependent results.     

Reassignment of the active site histidines in ribonuclease A by selective deuteration studies.

The C₂H resonance of the active site histidine residue designated AS-2, which has the lower pK_a of the two active site histidines, has been correlated in both RNase A and RNase S by comparing the pH 3 to 5.5 regions of the chemical shift titration curves, the effect of the inhibitor CMP-3′ on the chemical shifts at pH 4.0, and the effect of Cu II on the line widths at pH 3.6. It has been demonstrated that resonance AS-2 is absent in the spectrum of RNase S′ reconstituted using S-peptide deuterated at the C₂ of His 12, and in that of the RNase S′-CMP-3′ complex. We thus demonstrate that histidine AS-2 is in fact His 12 in both enzymes. This finding is in agreement with out previous assignment of the exchangeable NH proton in RNase A to His 12, but reverses the assignments of the active site histidine C₂H resonances made earlier by other authors.     

Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit

Backbone-side group conformations of amino acid residues including one or two δ-carbons in the side group have been investigated. Conformational energies of norvalyl, leucyl, phenylalanyl, tyrosyl, tryptophenyl, and histidinyl side groups in a dipeptide unit have been calculated by using classical energy expressions. The side group conformations about the C^α—C^β and C^β—C^γ bonds are restricted to specific values of the respective rotational angles. Thus, most favourable positions of γ- and δ-atoms of a linear side-chain (norvalyl) are restricted to (γ_I, δ_II) (γ_II, δ_I), (γ_II, δ_II), (γ_III, δ_II), and (γ_III, δ_III), whereas those of the side-chain branching at a sp³ γ-atom (leueyl) are further restricted. It is also shown that there is a definite correlation between the orientations of the two peptide planes and that of the planar group of the aromatic side chain of phenylalanyl type residues. The studies bring out an important fact that while the γ-atoms have definite and characteristic effects on the backbone rotational angles ? and ψ, the δ atoms and beyond have no effects on the preferred ? and ψ values. Thus, the preferred backbone conformations are independent of the preferred side group conformations beyond the γ-atom and vice versa. The observed ?, ψ, χ¹, and χ² values of amino acids, simple peptides, and of the three protein molecules lysozyme, myoglobin, and chymotrypsin have been compared with the theoretical predictions, and the agreement is found to be excellent.     

Mean activity coefficients for the simple electrolyte in aqueous mixtures of polyelectrolyte and simple electrolyte. V. common counterion mixtures of alkali-metal dextransulfates with alkali metal chlorides

Mean molal activity coefficients of simple electrolyte in aqueous solutions of Li, Na, K or Cs salts of dextransulfate (DS) with added LjCl, NaCl, KCl or CsCl are reported. The measurements were carried out by means of an electrochemical cell method using a cation exchange membrane as cation selective electrode and Ag/AgCl electrodes. For LiDS-LiCl, NaDS-NaCl and CsDS-CsCl systems the polymer concentration, m_p, was varied from 0.0088 to 0.113 m and at a given m_p the ratio X of the polymer to salt concentration was varied from 0.5 to 16. Due to the insolubility of KDS in high concentration of KCl, the measurements on KDS-KCl system were performed in the m_p range of 0.0088–0.089 m and some of the smaller X values were omitted. The activity coefficient results are compared to Manning's limiting laws, the additivity rule, and to new limiting laws. The additivity rule can give an excellent representation of the data for all m_p values when γ_p is used as an adjustable parameter.     

Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein

Many macromolecular interactions, including protein‐nucleic acid interactions, are accompanied by a substantial negative heat capacity change, the molecular origins of which have generated substantial interest. We have shown previously that temperature‐dependent unstacking of the bases within oligo(dA) upon binding to the Escherichia coli SSB tetramer dominates the binding enthalpy, ΔH_obs, and accounts for as much as a half of the observed heat capacity change, ΔC_p. However, there is still a substantial ΔC_p associated with SSB binding to ssDNA, such as oligo(dT), that does not undergo substantial base stacking. In an attempt to determine the origins of this heat capacity change, we have examined by isothermal titration calorimetry (ITC) the equilibrium binding of dT(pT)₃₄ to SSB over a broad pH range (pH 5.0–10.0) at 0.02 M, 0.2 M NaCl and 1 M NaCl (25°C), and as a function of temperature at pH 8.1. A net protonation of the SSB protein occurs upon dT(pT)₃₄ binding over this entire pH range, with contributions from at least three sets of protonation sites (pK_a1 = 5.9–6.6, pK_a2 = 8.2–8.4, and pK_a3 = 10.2–10.3) and these protonation equilibria contribute substantially to the observed ΔH and ΔC_p for the SSB‐dT(pT)₃₄ interaction. The contribution of this coupled protonation (∼ −260 to −320 cal mol⁻¹ K⁻¹) accounts for as much as half of the total ΔC_p. The values of the “intrinsic” ΔC_p,0 range from −210 ± 33 cal mol⁻¹ °K⁻¹ to −237 ± 36 cal mol⁻¹K⁻¹, independent of [NaCl]. These results indicate that the coupling of a temperature‐dependent protonation equilibria to a macromolecular interaction can result in a large negative ΔC_p, and this finding needs to be considered in interpretations of the molecular origins of heat capacity changes associated with ligand‐macromolecular interactions, as well as protein folding. Proteins 2000;Suppl 4:8–22. © 2000 Wiley‐Liss, Inc.     

1H nuclear magnetic resonance studies of histidine-containing di- and tripeptides. Estimation of the effects of charged groups on the pKa value of the imidazole ring.

The nmr titration curves of chemical shifts versus pH were observed for the protons of various histidine-containing di- and tripeptides. With these results, the macroscopic pK_a values and the chemical shifts intrinsic to each ionic species were determined by a computer curve-fitting based on a simple acid dissociation sequence. The pK_a value of the imidazole ring in N-acetyl-L -histidine methylamide was assumed to represent the intrinsic (or unperturbed) pK_a of the imidazole rings of histidine having peptide linkages at both the CO and NH sides. The pK_a values of the imidazole rings observed for most di- and tripeptides were reasonably reproduced by simple calculations using the intrinsic value and the perturbations due to the CO₂^? and NH₃⁺ groups located at various positions. Some other factors affecting the pK_a value of the imidazole ring are also discussed.     

The First and Second Dissociation Constants of Subtilisin BPN′-Plasminostreptin Complex Determined by a Polarographic Method,and the Effects of pH on Them

A polarographic method based on the Brdi?ka current (the polarographic catalytic hydrogen evolution current produced by proteins in the presence of cobalt salts) was applied to direct titration of subtilisin BPN′ (S.BPIST) with plasminostreptin (PS) at a concentration level of 10”⁸ m. The first and second dissociation constants of the S.BPN-PS complex were determined by fitting theoretical curves to the titration data, in which the multiple equilibria involving microscopically distinct forms of S.BPN-PS complex were taken into account. The intrinsic free energy change in the first binding of S.BPN′ to dimeric PS was larger than that in the second binding. The dependence of the microscopic dissociation constants of S.BPN′-PS complex on pH indicates the participation of ionizable groups of pK_a 8.0 and 9.4 in the complex formation. The repulsive effect between negatively charged molecules of S.BPN′ and PS in the complex formation at elevated pH is suggested.     

Experimental study on aggregation of model monopeptide molecules: 6. A model for peptide β-structures?

Homo- and hetero-aggregates of monopeptide molecules Bu^tCONHCHRCONHPrⁱ have been studied by ¹H-n.m.r. Two pairing modes of the molecules are found for both types of aggregate, according to the bulkiness of side chains R. Their hydrogen bond patterns are closely related to the interstrand interactions in β_a (antiparallel) and β_p (parallel) sheets of globular proteins. The pairing mode Γ₁₄ of these molecules, similar to that of the residues in β_a-structures, is the most stable disposition if the side-chains are not C^β or C^γ-branched simultaneously. When both side chains are bulky C^β or C^γ-branched groups, the pairing mode Γ₁₂ found in β_p-structures is favoured. This observation is in agreement with the lower content of β_p compared to β_a-structure in globular proteins and the preferential occurrence of C^β and C^γ-branched residues in β_p structures.     

1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH

The ¹H-nmr chemical shifts and the spin–spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H-Gly-Gly-X-L -Ala-OH in D₂O and H₂O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pK_a values obtained in D₂O, with the use of pH-meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pK_a values in H₂O. This suggests that the present data are suitable “random-coil” ¹H-nmr parameters for conformational studies of polypeptide chains in D₂O and H₂O solutions.     

1H-Nuclear magnetic resonance study on imidazole–imidazole interaction in L-histidyl-L-histidine and D-histidyl-L-histidine: Analysis including microscopic dissociation series

The ¹H-nmr titration curves of chemical shifts versus pH were observed for the protons of _D,L-histidyl-_D,L-histidine as representative of cases with two or more ionizable groups with similar pK_a values. The titration curves of L -histidyl-L -histidine and D -histidyl-L -histidine were individually analyzed according to two mathematical models: one of a macroscopic dissociation series and one of a microscopic dissociation series. Most-probable values and standard deviations were obtained for pK_a values and intrinsic chemical shifts. An analysis including the microscopic dissociation series yielded an electrostatic interaction between twoimidazole rings of about 0.3 pH units for L -histidyl-L -histidine and about 0.7 pH units for D -histidyl-L -histidine. The difference of the magnitude of imidazole-imidazole interactions between L -histidyl-L -histidyne and D -histidyl-L -histidine was interpreted in terms of the spatial arrangement of two imidazole rings in each molecule based on the solution conformation estimated from Gd(III)-induced relaxation enhancements.     

Potentiometric studies of hydrophobic effect on ion binding of ionic dextran derivatives

In order to clarify the effect of degree of substitution of ionic and hydrophobic group on the polyelectrolytic behavior of polysaccharides, potentiometric titration and activity measurement of counterions were made for carboxymethyldextran (Cm-dextran) having various degrees of substituted carboxyl group and for carboxymethylbenzyldextran (Cm-Bzl-dextran) containing various degrees of substituted benzyl group. From the shape of titration curve, no conformational change was observed for both Cm-dextran and Cm-Bzl-dextran. The pK₀ value of Cm-dextran was independent of the degree of the degree of substituted carboxy group. However, the pK₀ of Cm-Bzl-dextran increased with an increasing degree of substituted benzyl group. The suppression of dissociation of a carboxyl group, caused by the surrounding hydrophobic groups, was discussed mainly in terms of the change of water structure around such groups. From the results of activity measurement for counterions of these dextran derivatives, we proposed the possibility of ion selectivity based on the hydrophobicity.     

Water permeability of bilayer lipid membranes: Sterol-lipid interaction

Summary Bilayer lipid membranes were generated in an aqueous medium from synthetic, egg or plant phosphatidyl choline (PC) or from plant monogalactosyl diglyceride (MG). The water permeability of the black membranes was determined by measuring the net volume flux produced by a NaCl gradient. The osmotic permeability coefficient,P _os, was markedly affected by the number of double bonds in the fatty acid conjugates of the lipids: the greater the degree of unsaturation, the higher the value ofP _os. The temperature dependence ofP _os of the lipid membranes was studied over a range of 29 to 40°C. The experimental activation energy,E _a , estimated from the linear plots of log (P _os)versus 1/T, was significantly higher for MG membranes (17 kcal/mole) than for the various PC membranes (11 to 13 kcal/mole), probably owing to hydrogen bonding between MG and water molecules. In comparison with PC membranes, the membranes generated from PC and cholesterol (11 molar ratio) had lowerP _os but similarE _a values. Likewise, either stigmasterol or -sitosterol decreasedP _os of MG membranes, whileE _a was not affected by the sterols. MG-cholesterol membranes were specifically characterized by a unique value ofE _a (–36 kcal/mole) thus indicating temperature dependent structural changes.     

The effects of experimental conditions of fluorescence quenching on the binding parameters of apigenin to bovine serum albumin by response surface methods

A fluorescence quenching technique is often used to study interactions between small molecules and serum albumin. However, the results are quite different by using spectroscopic techniques on the same drug‐protein interaction research and they may be affected by different conditions (e.g. working solution of pH and ionic strength). In this research, using apigenin as an example, the effect of experimental conditions of fluorescence quenching on the binding parameters of drug to bovine serum albumin was investigated using a response surface method (RSM). The effect of pH, the concentration of NaCl and the concentration Mg²⁺ on the quenching constant (K_SV), the apparent association constant (K_a) and the number of binding sites (n) was studied by single‐factor experiments with pH, [NaCl] and [Mg²⁺] as independent variables and K_SV, K_a and n as response values. Prediction models were fit to a quadratic polynomial regression equation and the results showed that both K_SV and n displayed a second‐order model, whereas Ka displayed linear relation dependence on pH, [NaCl] and [Mg²⁺]. Under these experimental conditions, [NaCl] was the most significant (p < 0.05) impact factor on K_SV and K_a, whereas n was most affected by pH (p < 0.05). Copyright © 2013 John Wiley & Sons, Ltd.     

The equivalent conductivity of aqueous salt-free solutions of DNA: Influence of univalent counterions

The equivalent conductivity of salt-free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10^?4 to 4 × 10^?3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where C_p is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10^?4 Sm m² equiv.^?1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H⁺-DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.     

Polyelectrolyte theory. I. Counterion accumulation,site-binding,and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations

We have computed the Poisson-Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations. The polyelectrolytes considered here are highly charged in the sense that ξ > 1, ξ being the linear charge density parameter for cylinders, which is generalized by us to other shapes. Contrary to the situation at zero salt concentration, the counterion distribution is not strongly shape dependent, being similar for cylinders or spheres which have the same superficial charge density and radius of curvature R_c. The distribution resembles that in the neighborhood of a plane with the same charge density. Three regions are distinguished. (1) In the “inner region” which extends up to a distance R_c/2ξ from the surface, the counterion distribution is essentially salt independent. The counterion concentration in the immediate vicinity of the polyelectrolyte surface (CIV) is quite high, typically 1–10M, and proportional to the square of the surface charge density, which is its main determinant. (2) An intermediate region extends out to a distance where the electrostatic potential is equal to κT/e. This distance is comparable to λ for plane and cylinder, and smaller for the sphere. (3) In the outer region, the distribution is hardly influenced by the details of the inner region, on which it cannot, therefore, give much information. Colligative properties are dependent on the distribution in the outer region and are fairly well predicted even by a rudimentary theory. The large value of the CIV implies that site binding must often be significant. It can be computed by applying the mass-action law to site-bound counterions in equilibrium with the counterions in the neighborhood, whose concentration is the CIV, the relevant equilibrium constant being that for the binding of counterions to isolated monomer sites. Because the CIV is insensitive to salt concentration, this will also be the case for site binding. With the graphs provided, one can compute the extent of sitebinding within the Poisson-Boltzmann framework. The “condensation radius,” i.e., the radius encompassing a counterionic charge 1 ? ξ^?1 around a cylinder, is found to be large. It varies with salt concentration and tends to infinity as the salt is diluted. Neither this radius nor the charge fraction 1 ? ξ^?1 of condensation theory plays any special role in the counterion distribution. The “finite-salt” results apply to salt concentrations, typically as low as 1–10 mM. This encompasses, among others, all experiments on biological polyelectrolytes.     

Self-association of glutamic acid-rich fusion peptide analogs of influenza hemagglutinin in the membrane-mimic environments: Effects of positional difference of glutamic acids on side chain ionization constant and intra- and inter-peptide interactions deduced from NMR and gel electrophoresis measurements

Two glutamic acid-rich fusion peptide analogs of influenza hemagglutinin were synthesized to study the organization of the charged peptides in the membranous media. Fluorescence and gel electrophoresis experiments suggested a loose association between the monomers in the vesicles. A model was built which showed that a positional difference of 3, 7 and 4, 8 results in the exposure of Glu3 and Glu7 side chains to the apolar lipidic core. Supportive results include: first, pK_a values of two pH units higher than reference value in aqueous medium for Glu3 and Glu7 CγH, whereas the deviation of pK_a from the reference value for Glu4 and Glu8 CγH is substantially smaller; second, Hill coefficients of titration shift of these protons indicate anti-cooperativity for Glu3 and Glu7 side chain protons but less so for Glu4 and Glu8, implying a strong electrostatic interaction between Glu3 and Glu7 possibly resulting from their localization in an apolar environment; third, positive and larger titration shift for NH of Glu3 is observed compared to that of Glu4, suggesting stronger hydrogen bond between the NH and the carboxylic group of Glu3 than that of Glu4, consistent with higher degree of exposure to hydrophobic medium for the side chain of Glu3.     

Hydration of polyacids

The hydration of several polyacids has been investigated with special attention to the effects of neighboring charged groups and hydrophobic groups on the hydration regions. The molar volume change due to the structural change of water by the hydration was obtained by the method of refractivity measurement. The polyacids employed were poly(acrylic acid), poly(methacrylic acid), poly(L -glutamic acid), and a copolymer of maleic acid and vinyl acetate. The measurement of the refractive index was performed for the solutions of these polymers neutralized to varying degrees by tetrabutyl-ammonium hydroxide and sodium hydroxide. The results confirm the characteristics of the previous model of the hydration of polyelectrolytes, that is, the cooperative action of neighboring charged groups induce the second hydration region in addition to the intrinsic hydration region. The stiff structure of water in these regions restricts the mobility of counterions forced to enter into these regions by the strong electrostatic potential of polyions. The results indicate also that hydrophobic groups induce an additional hydration region around their neighboring charged groups. Small but negative volume changes were observed for conformational changes of poly(L -glutamic acid) and poly(methacrylic acid) induced by the neutralization of carboxyl groups.     

Thermodynamic analysis reveals that GTP binding affects the interaction between the alpha- and gamma-subunits of translation initiation factor 2

Eukaryotic and archaeal translation initiation factors 2, heterotrimers that consist of α-, β-, and γ-subunits, deliver methionylated initiator tRNA to a small ribosomal subunit in a manner that depends on GTP. To evaluate correlation of the function and association of the subunits, we used isothermal titration calorimetry to analyze the thermodynamics of the interactions between the α- and γ-subunits in the presence or absence of a nonhydrolyzable GTP analog or GDP. The α-subunits bound to the γ-subunit with large heat capacity change (ΔC_p) values. The ΔH and ΔC_p values for the interaction between the α- and γ-subunits varied in the presence of the GTP analog but not in the presence of GDP. These results suggest that the binding of both the α-subunit and GTP changes the conformation of the switch region of the γ-subunit and increases the affinity of the γ-subunit for tRNA.     

Evidence for a plasmalemma-based CO2 concentrating mechanism in Laminaria saccharina

A kinetic analysis of the photosynthesis inhibition by buffers allowed quantification of some components of the carbon concentrating mechanism (CCM) of the brown macroalga Laminaria saccharina. The CCM was based on the presence of acid regions outside the plasma membrane that increased the CO₂ concentration available for photosynthesis by 10–20 times above that of the bulk medium at alkaline pH. Furthermore, the results suggested that the CCM is located mainly on the cell membrane and not in the chloroplast, as suggested for most macroalgae. The degree of dissipation of the acid regions by a buffer was related to the buffer anion concentration (B⁻), estimated from the titration of the buffer from bulk medium pH to a pH endpoint value close to the first pK _a of the carbonic acid system. A kinetic model describing the relationship between inhibition of photosynthesis by a buffer and B⁻ was developed suggesting that buffers act as competitive inhibitors with IC₅₀ (the concentration of the buffer anion which reduces the reaction velocity by half) of 5.0 mol m⁻³. This model can be used to estimate the inhibitory effect of any buffer on the photosynthesis of L. saccharina. Nevertheless, some buffers tested showed a lower effect than that predicted from the hyperbolic model suggesting that their strength as inhibitors depended on: (1) the pK _a in relation to the first pK _a of the carbonic acid system and (2) its molecular weight (i.e. its mobility).