Polymer concentration effects on helix–coil transition widths

A theoretical study of effects of excluded volume intermolecular interactions on the sharpness of helix–coil transitions in solutions of polyamino acids or simple proteins indicates that the transition width may vary appreciably as a function of polymer concentration. The analysis is based on a second virial approximation for the excess free energy of mixing of a solution of polymers of varying degrees of helicity. The virial coefficients involved are roughly estimated on the basis of gross polymer geometry. For large N (degree of polymerization) the transition is found, typically to sharpen with increasing concentration, becoming second order and then first order at sufficiently high concentrations. The critical polymer concentration is found to be roughly of the order N^?1.2 ??₀^?1 for an “all or none” model and of order σ^1/2 N^?0.2 ??₀^?1 for a model with continuously variable degree of helicity (??₀ is the volume of a single helical molecule and σ^1/2 the normalized statistical weight of a helix–coil interface). In the second case for N ～ 10³ and σ ～ 10^?2–10^?4, the predicted critical concentration is in the range 10^?1–10^?3 g/cm.³ Comparison is made with experiments on solutions of poly(γ-benzyl-L glutamate).     

Triple helix–coil transition of covalently bridged collagenlike peptides

The thermal triple helix–coil transition of covalently bridged collagenlike peptides with repeating sequences of (Ala-Gly-Pro)_n, n = 5–15, was studied optically. The peptides were soluble in water/acetic acid (99:1) and were found to form triple-helical structures in this solvent system beginning with n = 8. The thermodynamic analysis of the transition equilibrium curves for n = 9–13 yielded the parameters ΔH°_s = ?7.0 kJ per tripeptide unit, ΔS°_s = ?23.1 J deg^?1 mol^?1 per tripeptide unit for the coil-to-helix transition, and the apparent nucleation parameter σ ? 5 × 10^?2. It was suggested through double-jump temperature experiments that the rate-limiting step during refolding is not only influenced by the difficulties of nucleation, but also by cis–trans isomerization of the Gly-Pro peptide bond.     

Adsorption of polypeptides on the solid surface. II. Effect of secondary chain structure and helix–coil transition

The theory of adsorption of semistiff chains on a planar surface developed by the authors previously has been used to consider the helix–coil transition in single-stranded macromolecule interacting with an adsorbent plane. The cases of nonselective interaction when the adsorption energy is independent of the unit conformation (a) and selective interaction with only helical (b) or coiled (c) sequences active in adsorption were investigated. In case (b) the existence of secondary structure favors chain bonding to the surface. This leads to the increase in the stability of the helical state and complete polypeptide chain spiralization. The profile of the conformational helix–coil transition acquires an asymmetrical shape inherent to the second-order phase transition. In case (c) the bonding of a partially helical chain to the surface is similar to the adsorption of Gaussian coils and is accompanied by the destruction of secondary structure, this destruction being appreciable even if the helical state in space was favorable.     

Dependence of polynucleotide helix–coil transition theory on the ring closure exponent

Formulas are derived which relate the maximum slope of the helix-coil transition in synthetic polynucleotides to the stacking free energy and to the exponent k in the expression for the probability of ring closure for polymer chains. The exact value of k has not yet been determined. By use of the derived formulas, it is then shown that estimates of the stacking free energy are sensitive enough to the value chosen for k, so that exact values of these energies must await a precise determination of k.     

Deuteration and solvent composition effects in the helix–coil transition of poly-γ-beiizyl-L-glutamate

The effects of deuteration and of changes in solvent composition on the thermo dynamics of the helix–coil transition have been studied by calorimetric and optical measurements in the poly-γ-benzyl-L -glutamate–dichloroacetic acid–1,2-dichloro-ethanc system. For a given solvent composition, deuteration of the polypeptide and of the acid lowers the transition temperature T_c, while an increase in the volume fraction of acid in the solvent raises T_c. A rise in T_c is accompanied by a decrease in both the van't Hoff and the calorimetric heats of transition, but at different rates. The result is a temperature dependency in the Zimm-Bragg cooperation parameter σ. Possible causes of this result and its implications are discussed.     

Coupling between the helix–coil transition and nematic–isotropic transitions in polypeptide solutions

The lattice model of Flory has been extended in order to consider equilibrium between isotropic and nematic phases containing helix–coil type chains. Nearly complete exclusion of coil sequences from the lyotropic nematic phase produces an enhanced cooperativity in the helix–coil transition. In poor solvents this enhancement begins to occur at concentrations typical of some experiments.     

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.     

Effects of calcium and manganese ions on the helix–coil transition of DNA

The thermal denaturation method was employed to study the effect of Ca²⁺ and Mn²⁺ ions on the DNA helix–coil transition parameters at Na⁺ concentrations of 10^?3–10^?1M. At low ion concentrations, thermal stability increases, the melting range passes through a maximum, and the denaturation curves become asymmetric. These changes are quantitatively similar for Mn²⁺ and Ca²⁺ ions. With a further increase in the concentration of bivalent ions, the conformational transition temperatures pass through a maximum, and the melting range first tends to saturation and then rapidly decreases to 1–2°C. The Mn²⁺ concentrations, at which the above effects occur, are an order of magnitude lower than the Ca²⁺ concentrations. Comparison of experimental results and calculation in terms of the ligand theory permitted estimation of binding constants characterizing association between Mn²⁺ and Ca²⁺ ions and bases of native and denatured DNA. We show that, unlike the interaction with phosphates, bivalent ion–DNA base binding is weakly dependent on monovalent ion concentration in the solution.     

DNA sequencing and helix–coil transition. III. DNA sequencing

We show that the fine oscillatory structure of the DNA melting curve can be used to determine explicitly the nucleotide composition and the order of certain domains within the DNA. If DNA is specifically fragmented, the order of fragments can be learned directly from a comparison of the differential melting curves of the nonfragmented and fragmented DNA. The indicated information may complement exact methods of DNA sequencing. The proposed analysis is applied to bacteriophage ?X-174, whose melting curve is known. Compared to the known ?X-174 DNA sequence, the results of the analysis are found to be very accurate.     

Pressure-induced helix–coil transition of DNA copolymers is linked to water activity

We have investigated the effect of reduced water activity on the pressure-stability of double-stranded DNA polymers, poly[d(A-T)] and poly[d(I-C)]. Water activity was modulated by the addition of ethylene glycol and glycerol. The ionic strength of the medium was such that pressure had a destabilising effect on the polymers in the absence of cosolvents. The molar volume change of the heat-induced helix to coil transition (ΔV_T) becomes more positive as the activity of water was reduced, suggesting that the pressure-induced denaturation of DNA polymers would not occur at very low water activity. This would imply that water plays a crucial role in the pressure denaturation of DNA, much like that in pressure denaturation of proteins where the driving force of the process is the penetration of water molecules into the protein core [Hummer et al., Proc Natl Acad Sci USA 1998, 95, 1552–1555].     

DNA sequencing and helix–coil transition. IV. Very long DNAs

Helix–coil transition in very long DNA (containing hundreds of thousands of nucleotides or more) is considered. Certain statistical information about DNA nucleotide sequence is obtained.     

On the two kinds of nucleation in the helix–coil transition theory of polypeptide chains

The nucleation of a helical sequence from a random chain of the polypeptide molecule as well as the nucleation of a random-coil sequence from the helical conformation of the molecule are considered simultaneously in evaluating the partition function of the system. This partition function is then used for a comparative analysis of the theories of Zimm and Bragg, Gibbs and DiMarzio, and Lifson and Roig. It is shown that while all three account properly for the essential nature of the nucleation phenomenon the first considers in detail the random-coil nucleation, the second emphasizes the details of the helix nucleation, while the third neglects the fine details of both in a symmetric way.     

Effects of Na+ and Mg++ ions on the helix–coil transition of DNA

The effects of monovalent (Na⁺) and divalent (Mg⁺⁺) cations on the temperature and breadth of the helix–coil transition of phage DNA have been investigated. The experimental results confirm the findings of Dove and Davidson [J. Mol. Biol. 5 , 467–478 (1962)] for the limiting cases of zero divalent ion concentration and saturating levels of divalent ion, and extend their findings to the intermediate region of Mg⁺⁺ concentrations. A theory for the dependence of transition temperature on the ion concentrations is developed, utilizing the approach of Wyman [Adv. Protein Chem. 19 , 223–286 (1964)], modified to account for electrostatic nonideality of the polyelectrolytes. The theory is in agreement with Manning's treatment of the experiments of Dove and Davidson [Biopolymers 11 , 937–949, 951–955 (1972)] and is in fair agreement with experimental data over the entire range of ion concentrations. Further investigation of the structure and ion-binding properties of the denatured form will be required before a quantitative comparison between theory and experiment can be performed.