Kinetic studies of the helix–coil transition in aqueous solutions of poly(L-lysine)

The rate of conformational change of aqueous poly(α-L -lysine) solutions was measured using the electric field pulse relaxation method with conductivity detection. The relaxation time as a function of pH exhibits two maxima. One is assigned to a proton transfer reaction and the other to the helix–coil conformational transition. The helix nucleation parameter and the maximum relaxation time yield the rate constant of helix growth process (k_F) according to Schwarz's kinetic theory as k_F = 2 × 10⁷ sec^?1, which is comparable to that of the poly(glutamic acid) solution. The thermodynamic parameters of the helix growth process are compared with those of poly(glutamic acid).     

Polypeptides. LVI. Effect of lithium bromide and of temperature on the conformation of a copolymer of glutamic acid and lysine

By using optical rotatory dispersion measurements, the helix content of poly Glu⁵⁰Lys⁵⁰ has been investigated and compared with that of poly Glu²⁰Lys²⁰Ala⁶⁰ in aqueous solutions. Measurements were made at pH 3 and at pH 8 in various concentrations of lithium bromide. Various factors affecting helix stabilization are considered and their perturbation by lithium bromide is related to the shape of the observed transition curves. A residual helix content of 12% in 8M LiBr, based upon a b₀ of +100 for a fully random conformation, was observed for poly Glu⁵⁰Lys⁵⁰ at pH 3 and 8. The loss of helix content of poly Glu⁵⁰Lys⁵⁰ as a function of temperature is also reported. ΔH is approximately ?6.9 kcal./mole for the overall transition, compared to ?6.5 kcal./mole for poly Glu²⁰Lys²⁰Ala⁶⁰. The midpoint of the broad transition is near 40°C. at pH 3, but much lower, at ?10 to 0°C., at pH 8. These results are discussed in terms of the stabilizing factors for the partial helix content of the polypeptides.     

Helix–coil transition kinetics in aqueous poly(α,L-glutamic acid)

A polarimetric electric-field-jump relaxation apparatus is described and used to determine the relaxation spectrum for the helix–coil transition of poly(α,L -glutamic acid) in water at 24°C. A maximum relaxation time of 1.7 μc occurs at the transition midpoint (pH = 5.9) yielding a rate constant for helical growth of 6 × 10⁷ sec^?1.     

Infinite dilution viscoelastic properties of poly(gamma-benzyl-L-glutamate) in m-cresol.

The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ-benzyl-L -glutamate) in m-cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights M_r are 6.4 × 10⁴–17 × 10⁴. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with M_r > 10⁵ is interpreted in terms of three mechanisms appearing from low to high frequencies: end-over-end rotation, flexural deformation, and side-chain motion. For a sample with M_r < 10⁵, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side-chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].     

Kinetic properties and the electric field effect of the helix-coil transition of poly(gamma-benzyl L-glutamate) determined from dielectric relaxation measurements

Dielectric relaxation of poly(γ-benzyl L -glutamate) in solution has been studied in the 5 kcps-10 Mcps range for various values of the helix content. The results give first experimental evidence for three effects of major significance. (1) The system exhibits dielectric relaxation due to a chemical rate process (namely helix formation). This confirms recent theoretical predictions. (2) The mean relaxation time τ* of the helix–coil transition could be evaluated as a function of the degree of transition. The results are in excellent agreement with a previously developed theory. At the midpoint of transition it is found τ*_max = 5 × 10^?7 sec. The elementary process of helical growth turns out to be practically diffusion-controlled (with a rate constant of hydrogen bond formation of 1.3 × 10¹⁰ sec^?1). (3) There is a considerable electric field effect of the helix–coil transition. This indicates that conformation changes in biological systems could be potentially caused by direct action of an electric field.     

Ultrasonic absorption in aqueous solution of lysozyme.

The titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74 , 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton-transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm³/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH-independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′_p ? iβ″_p of lysozyme molecule is evaluated as β′_p = 7.2 × 10^?12 cm²/dyne and β″_P = 4.3 × 10^?14 cm²/dyne from the increments over solvent in absorption as well as in sound velocity.     

Synthesis and physicochemical properties in aqueous solution of the sequential polypeptide poly(Tyr-Ala-Glu)

A polypeptide having the repealing sequence (Tyr-Ala-Glu)_n was synthesized by the polymerization of the N-hydroxysuccinimide ester of O-benzyl-L -tyrosyl-L -alanyl-γ-benzyl-L -glutamate, followed by the removal of the benzyl groups by means of hydrogen bromide. The main fraction obtained on gel filtration had an average molecular weight of over 60, 000, corresponding to over 500 amino acid residues per polypcptide chain. The polymer is soluble in water above pH 5.5, and precipitates on lowering the pH. The x-ray powder photographs show features of an α-helical structure. The dependence of the ultraviolet absorption spectrum, the optical rotatory dispersion, and the fluorescence of poly(Tyr-Ala-Glu) on pH, in salt-free as well as in salt-containing aqueous solutions, was compared with the corresponding properties of a copolymer containing equimolar proportions of tyrosine, alanine, and glutamic acid in a random sequence. From these measurements it was concluded that poly(Tyr-Ala-Glu ) has a helical con formation at low pH and a random coil conformation at high pH, the transition taking place at pH 6 in the absence of salt and pH II in the presence of salt. Thus, in the range pH 7 to l0. random coil-to-helix transition can be achieved by merely increasing the ionic strength. A model is proposed for the structure of the helical poly peptide which accounts for the Stability of the helical conformation by assuming hydrogen bonding between the carboxylate group of the ith glutamic acid residue and the hydroxyl group of the (i + 4 )th tyrosine residue. The complex ORD of helical poly(Tyr-Ala-Glu) is explained as being due to a superposition of the ORD of an α-helix and that of a regular array of phenolic ehroniopholes originating from the immobilization of the aromatic rings in the specific structure of the polymer.     

Kinetics of helix-coil transition of polypeptides in solution by the relaxation methods

Relaxation phenomena were studied in aqueous solutions of poly (alpha-L-glutamic acid) (Glu)n and poly (alpha-L-lysine) (Lys)n under various conditions using the electric field pulse method with detection by conductivity change. The relaxation time for the (Glu)n has a maximum value at the midpoint of the helix-coil transition. Some possible mechanisms are discussed and the observed relaxation phenomenon is attributed to the helix-coil transition. In the case of (Lys)n, the relaxation time as a function of pH exhibits two maxima. One is assigned to a proton transfer reaction and the other to the helix-coil transition. Using the Schwarz's theory the rate constants of the helix growth step for both (Glu)n and (Lys)n are estimated. The difference in the activation parameters for (Glu)n and (Lys)n is discussed.     

Determination of the relaxation time of the helix–coil transition of poly(γ-benzyl-L-glutamate) by the nmr technique

NMR measurements of poly(γ-benzyl-L -glutamate) are reported in several different strengths of magnetic field to determine the relaxation time of the helix–coil transition. Nmr spectra of various samples had line shapes varying from the double to single, depending on the extent of the polydispersity of the sample. This result indicated that the correct line shape of a polypeptide is obscured in the overlapping of multipeaks, which are due to the heterogeneity of the molecular weight in the sample. Thus, the conventional line-shape analysis could not be applied to the kinetic study of the helix–coil transition of polypeptides without consideration of this polydispersity effect on the line shape. To overcome this difficulty, we measured linewidths of nmr spectra for fairly monodisperse samples, using various nmr spectrometers, having field strengths from 60 to 220 MHz. The results were analyzed by a quadratic equation, which involves an additional term proportional to the frequency difference of two sites. The equation differs from the conventional quadratic equation, usually utilized in the case of the fast-exchange limit, only in this additional term. This modification is required to evaluate correctly the unusual broadening of the linewidth resulting from the polydispersity effect and to determine the relaxation time reflected in nmr. Nmr spectra of three samples (DP-35, 85, and 250) were measured by 220-, 100-, and 60-MHz spectrometers in trifluoroacetic acid/chloroform at 28°C and linewidths were analyzed. Relaxation times of the helix–coil transition obtained at the transition midpoint are 2.5 × 10^?4, 7 × 10^?4, and 1.1 × 10^?3 sec, for DP-35, 85, and 250, respectively.     

Untenability of the Heteronomous DNA Model for Poly(dA) · Poly(dT) in Solution. This DNA Adopts a Right-Handed B-DNA Duplex in Which the Two Strands are Conformationally Equivalent. A 500 MHz NMR Study Using One Dimensional NOE

Abstract

ID NOE ¹H NMR spectroscopy at 500 MHz was employed to examine the structure of poly(dA)·poly(dT) in solution. NOE experiments were conducted as a function of presaturation pulse length (50, 30, 20 and 10 msec) and.power (19 and 20 db) to distinguish the primary NOEs from spin diffusion. The 10 msec NOE experiments took 49 hrs and over 55,000 scans for each case and the difference spectra were almost free from diffusion.

The spin diffused NOE difference spectra as well as difference NOE spectra in 90% H₂O + 10% D₂O in which TNH3 was presaturated enabled to make a complete assignment of the base and sugar protons. It is shown that poly(dA) ·poly(dT) melts in a fashion in which single stranded bubbles are formed with increasing temperature.

Extremely strong primary NOEs were observed at H2′/H2″ when AH8 and TH6 were presaturated. The observed NOEs at AH2′ and that AH2″ were very similar as were the NOEs at TH2′ and TH2″. The observed NOEs at AH2′ and AH2″when AH8 was presaturated were very similar to those observed at TH2′ and TH2″ when TH6 was presaturated. In addition, presaturation of H1′ of A and T residues resulted in similar NOEs at AH2′/H2″ and TH2′/H2″ region and these NOEs at H2′ and H2″ were distinctly asymmetric as expected in a C2′-endo sugar pucker. There was not a trace of NOE at AH8 and TH6 when AH3′ and TH3′ were presaturated indicating that C3′-endo, × = 30–40° conformation is not valid for this DNA. From these NOE data, chemical shift shielding calculations and stereochemistry based computer modellings, we conclude that poly(dA)·poly(dT) in solution adopts a right- handed B-DNA duplex in which both dA and dT strands are conformationally equivalent with C2′-endo sugar pucker and a glycosyl torsion, ×, of ?73°, the remaining backbone torsion angles being φ′ = 221°, ω′ = 212°, ω = 310°, φ = 149°, ψ = 42°, ψ′ = 139°. The experimental data are in total disagreement with the heteronomous DNA model of Arnott et. al. proposed for the fibrous state. (Arnott, S., Chandrasekaran, R., Hall, I.H., and Puigjaner, L.C., Nucl. Acid Res. 11, 4141, 1983).     

Kinetic studies on the helix-coil transition of fluorescent labeled poly(-L-lysine) by the temperature-jump technique

Fluorescent dansyl labels were covalently attached to poly (L-lysine) (poly(Lys)) with a degree of polymerization of 300 to 600. The degree of labeling was 0.01 to 0.085 (mol label to mol amino acid residues). From the decay of the anisotropy of fluorescence it was concluded that the labels were highly mobile both in the coiled and helical state. A decrease of fluorescence intensity accompanied the helix-coil transition. Identical pH induced transition curves were measured by circular dichroism and fluorescence. The midpoint of the transition was at pH 10.2. The kinetics of the transition were studied by temperature-jump relaxation using fluorescence detection. A single relaxation phase was observed. The relaxation time tau exhibited a distorted bell shaped dependence on the degree of helicity f with a maximum value tau(max) = 15 micros at f = 0.3 and 20 degrees C. It was independent of polymer concentration and of the degree of labeling. A rate constant of helix propagation kF = 10(7) s(-1) was calculated from tau(max) and published values of the nucleation parameter sigma. The activation energy was 16 kJ mol . The observed rate constant is comparable to that of poly(L-glutamic acid) but two orders of magnitude smaller than that found for polyamino acids with nonionizable side chains.     

Synthesis and conformational study of poly(N -benzyl-L-lysine) and its benzyloxycarbonyl derivative

The solvent-and pH-induced conformational changes are examined in order to investigate the influence of benzyl group. Polymer was prepared via N^?-benzyloxycarbonyl, N^?-benzyl-N^α-carboxy-L -lysine anhydride. The resulting poly (N^?-benzyloxycarbonyl, N^?-benzyl-L -lysine) was obtained in high yield and had a high molecular weight. The protected polymer was removed into poly (N^?-benzyl-L -lysine) by treating it with hydrogen bromide. From the results of the ORD and CD, the protected polymer has a righthanded α-helix, showing [m′]₂₃₃ = –10,300, [θ]₂₂₀ = –27,600 and [θ]₂₀₇ = –25,100 in dioxane. The breakdown of the helical conformation is found to occur at 8% dichloroacetic acid in chloroform-dichloroacetic acid mixture. In the pH range 3.35–6.90, poly (N^?-benzyl-L -lysine) is in a random coil structure. In the pH range 7.50–13.0, the polypeptide has a right-handed α-helix structure; [m′]₂₃₃ = –12,000, [0]₂₂₀ = –27,200, and [0]₂₀₇ = –27,000. In comparison with poly-L -lysine, the coil-to-helix transition is observed at lower pH range in 50% n-propanol. Above pH 8 by heating, the α ? β transition of poly (N^?-benzyl-L -lysine) is not observed in an aqueous media.     

Proton magnetic relaxation and anion effect in solutions of acid ferricytochrome c.

Measurements of the longitudinal relaxation rates of water protons in aqueous solutions of ferricytochrome c and their temperature dependence, were used for the elucidation of the heme iron ligands at acid pH. The relaxation rates increased with a decrease in pH and pK values of 2.5 and 4.48 were evaluated for the aqueous and 6 m urea solutions, respectively. The results at acid pH are compatible with a structure in which two water molecules exchange rapidly between the coordination sphere of high spin heme iron and the bulk. They suggest that concomitantly with the low-high spin transition the histidine-18 and methionine-80 iron bonds break simultaneously. Addition of various anions, including methanesulfonate at pH 1.95 caused a 85% decrease in the net longitudinal relaxation rate. However, neither the chemical shift nor the width of the methyl proton nmr line of methanesulfonate in solution of acid ferricytochrome c were affected indicating that the effect of anions is not due to a direct binding to the heme iron. The relaxation mechanism of the water molecules in the first coordination sphere of the ferric ion in acid cytochrome c is discussed. It appears that the longitudial relaxation rate is modulated by the electronic correlation time of the ferric ion which was calculated to be τ_s = 6 × 10^?11 sec at 60 MHz.     

Viscosometric investigation of the ordinary–extraordinary phase transition in dilute polylysine solutions

Low shear viscosities have been determined for a 1 mg/ml poly(L -lysine) solution as a function of added salt concentration in the region of the previously reported ordinary–extraordinary phase transition. The measured viscosities indicate that the polyions are far from completely extended at the transition. Estimates of the longest internal relaxation time for an equivalent free-draining Rouse-Zimm chain give τ ? 10^?5 sec, similar to that of the rapid, angle-independent component previously observed in the dynamic light-scattering correlation function at the transition. An unusual peak and valley are observed in the curve of [η]₀ versus [NaBr] in the transition region. Possible interpretations of these features, and their bearing on the nature of the extraordinary phase, are discussed.     

Studies of the helix–coil transition of poly-L-lysine in film and solution

Water-insoluble films of poly-L -lysine, crosslinked with formaldehyde, were suspended in aqueous media and their relative lengths measured as a function of pH. A sharp transition of the polymer was observed in the pH range which corresponded with that observed in polylysine solutions by optical rotation or dilatometry. In NaBr and NaCl solutions the coiled form of the polylysine film shrinks with increasing salt concentration, but in NaHCO₃ solution the extent of the contraction is larger, and the coil–helix transition of polylysine occurs at lower pH when NaHCO₃ is added to the medium. If one assumes the formation of amino carbamate in this case, this phenomenon can be well explained. Urea does break up the hydrogen bonds in helical polylysine film, but not completely. This result is interesting compared with that obtained for poly(L -glutamic acid). After the coil–helix transition region was found by film experiments, the volume change associated with the coil-to-helix transition was measured and found to be about 1–l.5 ml. per amino residue after taking electrostatic interaction into consideration. This value is nearly same as that obtained for poly(L -glutamic acid). By contrast, the value for poly-γ-benzyl-L -glutamate was reported to be ?0.077 ml./mole of repeating unit. So it is still necessary to determine the magnitude and direction of the volume change for various kinds of polypeptides.     

A proton NMR spin-lattice relaxation study of the imino proton exchange kinetics in calf-thymus DNA

The results of semiselective ¹H-nmr inversion recovery experiments on sonicated calf thymus DNA fragments are reported. The measurements were conducted in aqueous solutions containing 85% D₂O, in order to reduce the dipolar contribution to the observed relaxation rates. In solutions containing 0.2M NaCl, 0.4 mM EDTA, and 10 mM cacodylate at pH = 7.0, the exchange rates of the imino protons in A-T base pairs confirm values published earlier in the literature, extrapolating to 0.25 s^?1 at 25°C. Corresponding values for the G-C base pairs are published for the first time, and are about sixfold slower. The addition of up to 0.1M Tris buffer (pH = 7.3 at 25°C), caused a striking increase in the measured exchange rates for both the A-T and G-C imino protons, resembling the effect recently observed for poly(rA)-poly(rU) and poly(rI)-poly(rC), and suggesting that the exchange rates measured for nucleic acid duplexes in low buffer concentrations at neutral pH do not reflect base-pair opening rates as assumed in the past. Lower limits to the base-pair opening rates could be estimated from extrapolation of the experimental data to infinite buffer concentration, and are 1 × 10³ s^?1 for the A-T, and 50 s^?1 for the G-C, base paris at 62°C.     

Mutagen–nucleic acid complexes at the polynucleotide duplex level in solution: Intercalation of proflavine into poly(dA-dT) and the melting transition of the complex

The nmr chemical shifts and line widths of the nucleic acid base and sugar proton resonances and the proflavine ring protons can be monitored through the melting transition of the proflavine + poly(dA-dT) complex, phosphate/dye (P/D) ratio = 24 and 8 in 1M salt solution. The nucleic acid and mutagen protons in the complex are in fast exchange between duplex and strand states with the midpoint of the melting transition monitored at the nucleic acid resonances increasing from 72.6°C for poly(dA-dT) to 78.1°C for the P/D = 24 complex and 83.4°C for the P/D = 8 complex in 1M salt solution. The melting transition monitored by the proflavine resonances were 80.0°C for the P/D = 24 complex and 84.3°C for the P/D = 8 complex in 1M salt solution. Since the nucleic acid is in excess at high P/D ratios, the nucleic acid transitions are an average for the opening of mutagen-free and mutagen-bound base-pair regions, while the proflavine transitions monitor the melting of mutagen-bound base-pair regions. The observed 0.75 to 0.95 ppm unfield shift at all four proflavine protons on formation of the complex with poly(dA-dT) provides direct evidence for intercalation of the mutagen between base pairs of the nucleic acid duplex. We have deduced the approximate overlap geometry between the proflavine ring and nearest-neighbor base pairs at the intercalation site from a comparison between experimental proflavine complexation shifts and those calculated for various stacking orientations. The experimental chemical shift of the poly(dA-dT) adenine H-2 resonance in the duplex state in the absence and presence of proflavine suggests that intercalation occurs preferentially at dT-dA sites. The selective chemical shift changes at the sugar H-2′,2″ and H-3′ resonances of the poly(dA-dT) duplex on complex formation demonstrates changes in the sugar pucker and/or torsion angles of the sugar phosphate backbone at the intercalation site.     

Volume and sound velocity changes associated with coil- transition of poly(S-carboxymethyl L-cysteine) in aqueous solution

The measurements were made for the volume and the sound velocity changes (ΔV and ΔU) on titrating the sodium salt of poly (S-carboxymethyl L -cysteine) with dilute HCl. For the reaction, ? COO^? + H⁺ → ? COOH, ΔV per mole of H⁺ bound was + 12. 7 ml and +11. 4 ml in salt-free and 0. 2 M NaCl solutions, respectively. Corresponding ΔU was about ?13 cm/sec in salt-free polymer solution where 11.5 mM carboxylate ion reacts with equimolar hydrogen ion. ΔV associated with the coil-to-β transition was found to be +2. 35 ml in H₂O and +1. 90 ml in 0. 2 M NaCl per mole of amino acid residue, respectively. These values are larger than those obtained for the coil-to-helix transition of poly (L -glutamic acid). ΔU for the transition was about ?30 cm/sec in salt-free solution of polymer concentration 0.0115 mole/liter. Possible sources of ΔV and ΔU for reaction; coil → β, are (1) the formation of void volume and (2) the changes in the extent of solvation in amide linkage and in side chain.     

A Raman spectroscopic study on 5′-rGMP gel and self-aggregate

In order to analyze the melting behavior of 5′-rGMP gel at acidic pH and self-aggregate near neutral pH we have obtained Raman spectra of aqueous solutions of 5′-rGMP at various temperatures. At low temperature the intensities of Raman peaks at 502, 585, 1083, 1179, 1322, 1366, 1487, and 1578 cm^?1 decrease due to the formation of ordered structure (Raman hypochromism). In contrast, the peaks at 671, 725, 813, and 1338 cm^?1 become stronger at low temperature (Raman hyperchromism). The Raman hyperchromism of the 671- and 813-cm^?1 peaks have been explained in terms of detailed structural models. Recently, the 668- and 682-cm^?1 peaks in the Raman spectrum of aqueous 5′-rGMP solution have been attributed to the guanine ring breathing vibrations in C3′- and C2′-endo conformers [Benevides, J. B., Lemur, D. & Thomas, G. J., Jr. (1984) Biopolymers 23 , 1011–1024]. On the basis of this information our Raman data can be interpreted to suggest that the continuous helix model of 5′-rGMP gel is right-handed. The 1487-cm^?1 peak intensity has been used to monitor the melting profies at several pHs. Near neutral pH the melting profile shows a single transition, whereas at acidic pH it shows two transitions. From these observations we propose possible pathways for the melting of 5′-rGMP gel formed at acidic pH and self-aggregate formed near neutral pH.     

Experimental theromodynamics of the helix-random coil transition. I. Influence of polymer concentration and solvent composition in the PBG-DCA-EDC system

The course of the reversible helix formation of poly(γ-benzyl L -glutamate) (PBG) dissolved in a mixture of dichloroacetic acid (DCA) and 1,2-dichloroethane (EDC) was followed by measuring the heat capacity and the optical rotation of the system through the transition region. The results of these measurements indicate that the transition enthalpy ΔH the transition temperature T_c, and the Zimm-Bragg parameter σ depend considerably on the PBG concentration as well as on the composition of the solvent. For the standard state of infinite dilution, however, a linear extrapolation of the measured ΔH if values results in a standard value ΔH° = 950 cal./mole, independent of the solvent composition. The results of the calorimetric measurements are discussed in relationship to changes in optical rotation. Some peculiarities in the measured thermodynamic and optical properties in solutions with relatively high content of dichloroacetic acid are reported.