Showing papers in "Biopolymers in 1973"

Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism

Abstract: Conformation of two-stranded DNA in H2O–methanol, H2O–ethanol, H2O–isopropanol, and H2O–dioxane solutions at different concentrations of alkaline ions has been studied with the aid of circular dichroism. The following conclusions are drawn: The conformation of DNA in H2O and H2O–methanol belongs to a family of B forms (B, C, T forms are the representatives of the family). The magnitude of the winding angle between adjacent base pairs (θ) is determined by the concentration and type of the cations. In H2O the cation action is nonspecific and leads to an increase in θ value. In 80% methanol the ions act specifically, Cs+ being to stabilize a form with a greater θ value, and Li+ being with a lesser one. The total θ change is likely within the limits of 33° ⩽ θ ⩽ 45°. At high content of ethanol, isopropanol, or dioxane (∼80%), but not with methanol, and in low ionic strength the conformation of DNA belongs to a family of A forms (A form is one of the members of the family) and is specified by the concentration and type of cation involved. The two-stranded regions of RNA in H2O are also of A type and winds with the rise of cation concentration. The range of θ variation is not narrower than 30° ⩽ θ 33°. The conformational transitions within the families (induced by ions) are of non-cooperative pattern, wheras the transitions between the families (induced by nonpolar component) are of cooperative pattern. The effect of cations, when specific, is discussed on the basis of steric correspondence between the width of DNA narrow groove and the size of a hydrated cation.

Structural components of alginic acid. II. The crystalline structure of poly-alpha-L-guluronic acid. Results of x-ray diffraction and polarized infrared studies.

Abstract: A structural investigation of the marine algal polysaccharide poly-α-L-guluronic acid is described. The molecular chains consist of 1 4 diaxially linked L-guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra-molecular O(2)H … O(6)D hydrogen-bond. The X-ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 A, b (fiber axis) = 8.7 A, c = 10.7 A. A structure corresponding to the space group P212121 is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.

Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs

Abstract: Absorbance-temperature profiles have been determined for the following self-complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A2GCU2, A3GCU3, A4GCU4, A6CG + CGU6, A8CG + CGU8, A4G2 + C2U4, A5G2 + C2U5, A4G3 + C3U4, and A5G3 + C3U5. In all cases cooperative melting transitions indicate double-helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single-strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of −15 kcal/mole. Due to the high degree of single-strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only −5 to −6 kcal/mole. (The corresponding parameters for AU pairs are −10.7 kcal/mole and −5 to −6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in ΔH were seen among the sequence isomers. The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 105 to 107M−1 sec−1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence AnGCUn recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec−1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on AnGCUn helix formation showed that the rates of recombination increase considerably with increased ionic strength.

Laser Raman studies of conformational variations of poly‐L‐lysine

Abstract: The frequencies and intensities of the laser Raman spectra of poly-L-lysine (PLL) have been observed in the following studies: (1) the thermally induced α-to-β transition which occurs with increasing temperature at high pH; (2) the ionized form to α transition at 10°C by increasing pH; and (3) the ionized form to α transition by ionic strength at low pH. The frequency-dependent bands which have been observed are the amide I (in H2O), amide I′ (in D2O), amide III, and C–C stretch. It has been found possible to assign an unique set of frequencies and intensities to each conformation of PLL of α, β, and ionized form. In this way the nature of the conformations intermediate in the transitions can be determined. The frequencies of the amide III and amide III′ are very weak in the α-helix and somewhat higher than usual in the β form. Hence it appears the amide III and amide III′ bands may differ from one type of polypeptide to another with the same backbone conformation.

An obligatory α-helical amino acid residue

Abstract: Stereochemical studies predict that α-amino isobutyric acid, one of the amino acids found in antibiotics, can fold only into left- or righthanded α-helical conformations Such residues will direct chain folding and should be useful in synthetic analogs of protein sequences to increase helix stability

Intensities and other spectral parameters of infrared amide bands of polypeptides in the beta- and random forms.

Abstract: The intensities and other spectral parameters of the main components of infrared amide bands for the random and anti-parallel pleated sheet forms have been determined for poly-S-carbobenzoxymethylcysteine, poly-S-carboxymethylcysteine, polylysine and silk fibroin of Bombyx mori in heavy water solutions and in organic solvents Assuming that the optical spectra of these two types of structure are additive, the method was proposed for determining relative contents and molar absorption coefficients of amide I band Integral intensity and maximum frequency values of the main components of the amide I band for all the samples in the β-form turned out to be specific In contrast to this the integral intensity of the band of amide I in the random coil form varied within certain limits, while the main maximum frequency for all samples remained the same

A dihedral angle-vicinal proton coupling constant correlation for the α–β bond of amino acid residues

Abstract: A coupling constant-dihedral angle correlation for the HCαCβH system of amino acid residues in peptides has been derived from a set of model compounds covering the full range of dihedral angles. The expression obtained, J = 11.0 cos2 θ −1.4 cos θ + 1.6 sin2θ, is close to those already used in pmr studies of peptide conformation, and provides a firmer foundation for them. A factor limiting the precision of this and other “Karplus relations” is illustrated.

Interaction of metallic cations with DNA VI. Specific binding of Mg++ and Mn++

Abstract: The binding of Mg2+ and Mn2+ by DNA by a divalent cation specific electrode and by ultracentrifugation. Both techniques give similar results for the stoichiometry of the reaction. An oscillating densiemete allowed us to detect small changes of volume accompanying the binding. The reaction was also followed by circular dichroism measurements. Interpretation of the results is only possible if one assumes an electrostate site-binding of Mg2+ to phosphate group, and a chelation Mn2+ between the phosphate group and the N7 of the guanine. Physical modifications accompanying these two types of binding are discused and compared to the role of these cations in some biological systems involving DNA.

Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride

Abstract: By analyzing the effect of urea and guanidine hydrochloride on the circular dichroism of many polypeptides and proteins, it is concluded that under conditions of high concentration of the perturbant and at low temperatures the resultant state approached is that of a local extended helix structure instead of a completely random coil. Intensification by urea and guanidine hydrochloride of the circular dichroism bands of poly-L-proline II leads to the proof that the mechanism of interaction of urea and guanidine hydrochloride with proteins is through hydrogen bonding to the backbone carbonyl group.

Investigation of DNA structural changes by infrared spectroscopy

Abstract: DNA-oriented samples of various origins were studied under different conditions of humidiity and sodium chloride content by means of infrared spectroscopy. (1) Oriented DNA (M. Lysodeikticus, E. coli, calf thymus and salmon sperm) films at 3–4% sodium chloride yield polarized spectra which show drastic changes at relative humidities (r.h.) between 94% and 0% indicative of conformational changes: B form → a form → disordered form The measurements of the infrared dichroism at frequencies of about 1230 cm−1 and at about 1090 cm−1 allow one to determine the orientation of the phosphate group, whereas the measurements at 1710 cm−1 characterize the base orientation. At humidities higher than 90% r.h. (B form) the bisector of OPO forms an angle of 70° relative to the helix axis, whereas at lower humidities, between 75% and 50% r.h. (A form) a rotation to about 45° is observed. Simultaneously, the 0—0 line of phosphate group changes its orientation from 55° to 65° to the helix when B → A transition takes place. The results are in general agreement with that of X-ray diffraction and allow one to determine the orientation of the phosphate group with greater precision. (2) The B–A conformational change is not observed for satellite DNA, isolated from Cancer pagurus, of which the guanine + cytosine content is below 5%. As a function of decreasing humidities, one observes the transition: B form → disordered form A diagram of conformational changes of DNA's as a function of base composition and of r.h., suggests that B–A transition will occur for DNA of relatively higher G + C content, whereas for high (A + T) content, base sequence may be of importance. The B–A transition is prevented in DNA at a relatively high or very low sodium chloride content.

Correlation between the backbone and side chain conformations in 5′-nucleotides. The concept of a ‘rigid’ nucleotide conformation

Abstract: Conformational energies of the 5'-adenosine monophosphate have been computed as a function of χ and ψ , of the torsion angles about the side-chain glycosyl C(1')-N(9) and of the main-chain exocyclic C(4')-C(5') bonds by considering nonbonded, torsion, and electrostatic interactions The two primary modes of sugar puckering, namely, C(2')-endo and C(3')-endo have been considered The results indicate that there is a striking correlation between the conformations about the side-chain glyocsyl bond and the backbone C(4')-C(5') bond of the nucleotide unit It is found that the anti and the Gauche-Gauche (gg), conformations about the glycosyl and the C(4')-C(5') bonds, respectively, are energetically the most favored conformations for 5'-adenine nucleotide irrespective of whether the puckering of the ribose is C(2')-endo or C(3')-endo Calculations have also shown that the other common 5'-pyrimidine nucleotides will show similar preferences for the glycosyl and C(4')-C(5') bond conformations These results are in remarkable agreement with the concept of the "rigid" nucleotide unit that has been developed from available data on mononucleotides and dinucleoside monophosphates It is found that the conformational 'rigidity' in 5'-nucleotides compared with that of nucleosides is a consequence of, predominantly, the coulombic interactions between the negatively charged phosphate group and the base The above result permits one to consider polynucleotide conformations in terms of a "rigid" C(2')-endo or C(3')-endo nucleotide unit with the major conformational changes being brought about by rotations about the P-O bonds linking the internucleotide phosphorus atom IT is predicted that the anti and the gg conformations about the glycosyl and the C(4')-C(5') bonds would be strongly preferred in the mononucleotide components of different purine and pyrimidine coenzymes and also in the nucleotide phosphates like adenodine di- and triphosphates

Hydration of stratum corneum

Abstract: A model for the hydration behavior of human stratum corneum has been developed from measurements on in vitro samples isolated in a manner which minimized tissue treatment and trauma. Water sorption/desorption rate measurements as a function of water activity, temperature, and tissue integrity are reported. These data, together with thermodynamic data (infrared and nmr results reported earlier) are consistent with a model in which rapidly sorbed/desorbed water (ca. 0.5 mg water/mg stratum corneum) is associated with (“bound” by) the tissue, while slowly sorbed/desorbed “free” water (up to 12 mg water/mg stratum corneum) is kinetically restricted and probably intracellular in location. Both equilibrium water binding and desorption kinetic data suggest structural changes of this cellular water barrier upon hydration. Evidence for hysteresis in water sorption isotherms (reported by others) could not be reproduced.

On the interaction of lithium salts with model amides

Abstract: Results of a study of the interaction of alkali metal salts on model aliphatic amides are reported. Lithium salts appear to interact more strongly with amides than those of other alkali metals. Spectroscopic investigations suggest that Li+ ion binds to the amide group at the carbonyl oxygen, causing a change in the spectroscopic properties and the geometry of the amide. Such binding of ions to amide groups may be of importance when one studies the spectral and conformational changes of polypeptides and proteins in high salt media.

Rotational relaxation of macromolecules determined by dynamic light scattering. II. Temperature dependence for DNA

Abstract: Correlation functions have been determined for the fluctuating intensity of the depolarized component of forward-scattered laser light from solutions of DNA. The molecular correlation function of calf thymus DNA (mol wt ∼15 × 106) appears to exhibit a longest relaxation time (τ25,w, ∼ 18 msec) close to what one would predict from the flowdichroism measurements of Callis and Davidson and, in addition, manifests a spectrum of faster times down to tenths of milliseconds. Furthermore, a major fraction of the amplitude of fluctuations in the angular distribution of segment axes is relaxed on a very much shorter time scale (of the order of 20 microseconds) that appears to be relatively insensitive to molecular weight of the DNA, or to near-melting temperatures. The temperature profile of the longest relaxation time has been obtained and found to exhibit a peculiar spike near Tm, which, together with the absence of a corresponding spike in the (high shear) viscosity, has been interpreted as indicative of an increase in the molecular weight of the DNA in a narrow temperature region near Tm. Correlation functions for polarized light scattered at finite angles were obtained in an attempt to determine the temperature dependence of the translational diffusion coefficient. Although the data contain an extremely slow component that does not admit a simple interpretation, there is some indication of a decrease in the translational diffusion coefficient near Tm, thus supporting the notion of an aggregation occurring near Tm. Finally, a “counterion escape” mechanisn is proposed for the apparent aggregation.

Oscillator strengths of the 1La and 1Lb absorption bands of tryptophan and several other indoles.

Abstract: The intensities of the indolyl 1La and 1Lb absorption bands were investigated by using 5-methoxyindole as a model compound. With 5-methoxyindole dissolved in weakly interacting solvents, almost the entire 1Lb electronic transition occurs at longer wavelengths than the 1La transition. The resolved spectrum of 5-methoxyindole permitted estimation of its oscillator strengths and also those of other indoles dissolved in cyclohexane: indole, 0.129 (1La), 0.019 (1Lb); 5-methylindole, 0.129 (1La), 0.027 (1Lb); 5-methoxyindole, 0.138 (1La), 0.045 (1Lb); 3-methylindole and N-stearyl-L-tryptophan n-hexyl ester, 0.127 (1La), 0.027 (1Lb). Hydrogen bonding to 1-methyl-2-pyrrolidinone does not measurably affect the total near-ultraviolet oscillator strength of indoles (less than 5% change). In water and ethanol, the oscillator strength of 3-methylindole and tryptophan is 15–20% less than that of 3-methylindole dissolved in cyclohexane. The spectra of the N-stearyl n-hexyl esters of tryptophan and 1-methyltryptophan dissolved in methylcyclohexane can be generated by using 1La and 1Lb bands having shapes similar to those observed for 5-methoxyindole, if the 1La and 1Lb bands are shifted so that their O-O bands overlap (289.5 nm for tryptophan and 299.5 nm for 1-methyltryptophan).

Induced optical activity in poly-L-lysine-methyl orange system.

Abstract: The absorption and cicular dichroism spectra of the complex of poly-L-lysine (PLL) in the random coil form with methyl orange (MO) have been measured in aqueous solution. A new absorption band is observed at the shorter wavelength compared with that of the free dye. Although MO does not show a formation of dimer or aggregation with an increase in concentration, circular dichroism bands are observed at the wavelength corresponding to the wavelength of the new absorption band. These induced circular dichroism bands may arise from the dimeric MO molecules bound to PLL in the random coil form. The main contribution to the interaction between MO molecules is shown to be the electro static interaction. The observed circular dichroism spectra and the configuration of dimeric MO molecules bound to PLL can be explained by the dipole couping mechanism.

Interactions of metallic ions with DNA. V. DNA Renaturation Mechanism in the Presence of Cu2

Abstract: New experimental data were obtained by means of circular dichroism, melting, renaturation, and kinetic experiments, upon Cu2+ binding to DNA, poly dAT, and poly dGdC. They enable us to propose a model of binding giving a satisfactory explanation to all of the data found in the literature. Two types of binding sites are proposed: (a) a “sandwich” of Cu2+ between two adjacent G-C pairs giving a charge-transfer complex, and (b) a chelate between a phosphate group and a nitrogen atom of the bases (N7 of guanine and N3 of cytosine at room temperature, N3 of adenine after thermal opening of A-T pair). Type (a) stabilizes the helix and keeps the two strands linked. Type (b) destabilizes the helix and explains why the kinetic rate of renaturation is the same as that of copper release.

Rotational relaxation of macromolecules determined by dynamic light scattering. I. Tobacco mosaic virus

Abstract: The intensity autocorrelation function for the depolarized component of forward-scattered light from a solution of large polymeric molecules is derived in terms of the correlation function for the amplitudes of the Y2,±1(θ,ϕ) fluctuations in the anglar distribution of segments in the solution without any assumptions regarding the statistical properties of the scatterad light field. Effects arising from the use of polychromatic incident light and from the mixing of the scattered and polychromatic incident light beams are examined in detail. Apparatus for observing the depolarized forward-scattered light, digitizing and storing the fluctuating phototube current at rates from 10 to 540,000 times per second, and computing the correlation functions directly in the time-domain is described herein. Correlation functions were obtained for 0.05 mg/ml solution of tobacco mosaic virus at pH 9.1 and also at pH 6. The degree of association of the virus appears to be independent of pH, and the monomer relaxation times (corrected to 25°C) extracted from the data by a least-squares procedure lie in the range 0.44–0.49 msec, also independent of pH. The absence of faster component in the correlation function between 6 μsec and 0.5 msec is used in conjunction with thermal fluctuation theory to infer a lower limit for the effective Young's modulaus of the rod, E ≤ 2.5 × 107 dynes/cm2.

Dielectric relaxation and orientation of DNA molecules.

Abstract: A conductivity dispersion has been measured at very low frequencies (VLF) on several concentrated DNA solutions. By measuring simultaneously their electric birefringence decay, it is shown that the dielectric relaxation (which is related to the conductivity dispersion) is due to the molecular orientation. Different polarization mechanisms are discussed. It is concluded that the DNA polarizability measured in the VLF range can only be explained by the orientation of a permanent ionic dipole. It is suggested that such permanent dipoles could be caused by small differences in the ionic composition between the two molecular “ends;” the difference could either be stable (asymmetrical localization of protein impurities for instance) or transient (fluctuating dipoles explained by the Kirkwood-Schumaker theory).

Electrical conduction in hydrated collagen. I. Conductivity mechanisms.

Abstract: The electrical conductivity of bovine Achilles tendon with various amounts of adsorbed water was measuredas a function of temperature The conduction appeared to be fully determined by the water of hydration The current is probably primarily carried by protons at water contents up to 45% and by small ions at water contents beyond 65% In both ranges of water content, a linear relation between activation energy and water and content was found As to the lower range, this is explained by the action of Coulombic forces during the separation of proton–hydroxyl ion pairs In two regions of water content a linear relation between the logarithm of the pre-exponential factor and the activation energy was found There are, however, indications that at certain water contents the dissociation constant of the adsorbed water is several orders of magnitude higher than in liquid water

Syn-anti effects on the spatial configuration of polynucleotide chains.

Abstract: Semiempirical energy calculations have beeb performed on model nucleic acid systems to assess the preferred conformation of the rotation χ about the glycosidic linkage and also the effect of this rotation on the spatial configuration of the sugar-phosphate chain backbone The rotation angle ϕ˝ about bond C5′–C4′ in purine polyribonucleotides and 5′-monoribonucleotides is found to depend on whether the conformational range of χ is syn or anti The preferred conformation of χ in these molecules is also found to depend upon the nature of the attached base The orientation of χ in poly rA chains is predicted to be predominantly anti, whereas in poly rG the syn conformer is expected to occur in significant proportions The syn conformer is preferred almost exclusively in certain unusual purine polynucleotides, such as poly 8Br-rA It is noted that the preferred conformation of x in polynucleotides is not necessarily the same as that calculated for 5′-mononucleotides and nucleosides On the basis of these calculations, the influence of the orientation and nature of a purine base on the spatial configuration of a polynucleotide chain as a whole has been examined The random coil dimensions of a syn polynucleotide chain are found to be larger than those of an anti chain as a consequence of the effect of a syn base on the local conformation of the chain skeleton Finally, it is found that the occurrence of a syn base in an ordered polynucleotide chain may prevent the formation of normal stacking with the preceding base

Flexibility of tropocollagen from sedimentation and viscosity.

Abstract: Sedimentation constant and intrinsic viscosity were measured on purified tropocollagens extracted from earthworm-cuticle and lathyritic ratskin A cartesian diver viscometer was used to make viscosity measurements at small shear stress and to avoid the effects of surface forces By comparing the experimental data with the hydrodynamic theories of wormlike-coil of Ullman a value of 1300 A has been assigned for the persistence length of these tropocollagens Other factors which may affect the estimate are discussed

Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized Rayleigh scattering and laser Raman spectroscopy.

Abstract: A new approach to the experimental conformational analysis of peptides in aqueous solution is presented and discussed. The basic idea is to combine laser Raman spectroscopy and depolarized Rayleigh scattering in order to interpret scattering properties of the dissolved molecule in terms of both local and global structure. We outline a simple method (anisotropic perturbation treatment) appropriate for solving conformational problems in large molecules by studying together slightly perturbed homologous compounds. This method is applied to the study of the molecular structure of simple glycine and alanine dipeptides. The preferred conformation for such molecules is the seven-membered chelated ring (C7) additionally stabilized by two intermolecular hydrogen bonds involving one molecule of water.

Theory of aggregation in solution. I. General equations and application to the stacking of bases, nucleosides, etc.

Abstract: Earlier theoretical work on aggregation in imperfect gases and in solutions of protein molecules is reformulated here in such a way as to be applicable to a number of aggregation systems in solution. The theory is most easily developed for an “osmotic” solution. It is exact, in principle, and in particular does not treat the aggregates as an ideal mixture as is usually done. If osmotic virial coefficients are diffcult to measure in a particular case, it is then necessary to relate these coefficients to properties of the more conventional “constant pressure” solution. An important special case is used as an example in the last three sections: The stacking of bases, nucleosides, etc., is represented by a statistical mecchanical model in which the aggregates resemble vertical stacks of checkers.

Interaction of metal ions with polynucleotides and related compounds. XXII. Effect of divalent metal ions on the conformational changes of polyribonucleotides.

Abstract: Changes in the conformation of poly(G), poly(C), poly(U), and poly(I) in the presence of divalent metal ions Mg2+, Ca2+, Mn2+, Co2+, Ni2+, Cu2+, Cd2+, and Zn2+ have been measured by means of ORD and u.v. spectra. Mg2+ and Ca2+ ions stabilize helical structures of all the polynucleotides very effectively at concentrations several orders of magnitude lower than the effective concentration of Na+ion. Cu2+ and Cd2+ destabilize the helical structure of polynucleotides to form random coils. Zn2+, Ni2+, Co2+, and Mn2+ions do not behave in such a clear-cut manner: they selectively stabilize some ordered structures, while destabilizing others, depending on the ligand strength of the nucleotide base as well as the preferred conformation of that polynucleotide.

Infinite-dilution viscoelastic properties of poly-gamma-benzyl-L-glutamate in helicogenic solvents.

Abstract: The storage and loss shear moduli, G, and G˝, have been measured for solutions of three samples of poly-γ-benzyl-L-glutamate with molecular weights from 16 to 57 × 104, by use of the Birnboim-Schrag multiple-lumped resonator. The frequency range was 106 to 6060 Hz, the concentration range 0.0015–0.005 g/ml, and the temperature 25°C. Two helicogenic solvents with widely different viscosities, dimethylformamide and m-cresol, were used to provide a broader effective frequency range. The intrinsic moduli, extrapolated to infinite dilution, were compared with the predictions of the theory of Ullman for rigid rods; agreement was rather good at the lowest frequencies, but unsatisfactory at high frequencies. The data over the entire frequency range of three of logarithmic decades could be described closely by a relaxation spectrum consisting of one terminal relaxation time separated by a gap from a sequence of relaxtion times spaced as in the Zimm theory. The terminal time agrees approximately with that calculated for end-over-end rotation of a rigid rod. The additional relaxation mechanisms are tentatively attributed to modes of flexural deformation of the helix.

Interaction of the polyelectrolyte heparin with copper(II) and calcium.

Abstract: The binding of copper(II) ions by heparin was investigated using equilibrium dialysi techniques, and the effects of this binding on solution properties determined In neus tral Tris buffer solutions, heparin binds a maximum of twenty-three to twenty-four copper ions in two classes of sites, one containing three to four binding sites, the other containing twenty to twenty-one sites Cooperative binding is associated with the larger class of sites In more acidic citrate buffer solution, only one class of sites is observed, containing about four to five binding sites Association constants are calculated for the classes and the possible chemical nature of the sites is discussed The binding of calcium ions in neutral buffer is also examined, and these ions appear to be bound by a group of twenty to twenty-one binding sites, with a larger association constant than that for the copper ions Definite effects on the solution properties of heparin, such as intrinsic viscosity, sedimentation coefficients, and partial specific volume, can be observed only in the cooperative binding of copper ions in neutral buffer The interpretation of these solution properties in terms of molecular size and shape is analyzed, and it is concluded that the metal ion interactions cause no major change in the apparently random coil conformation of heparin in buffered solution, although some minor changes can be associated with the cooperative uptake of copper ions

Heats of thermally induced helix-coil transitions of DNA in aqueous solution.

Abstract: Thermal denaturation of calf thymus DNA at both alkaline and neutral pH values was studied by differential scanning calorimetry. It was shown that the dependence of the enthalpy of transition on pH and salt concentration could be accounted for on the basis of a heat capacity change of +40 cal deg−1(base pair)−1. In the pH range between 10.3 and 11.3, a release of 0.6 proton per base pair was calculated from the pH dependence of the melting temperature. The heat effect associated with the release of this proton was calculated to be 5 kcal mole−1.

Investigation of the effect of amylose/iodine complexation on the conformation of amylose in aqueous solution†

Abstract: Using a potato amylose fraction of 8 × 105, molecular-weight viscosity studies were carried out at 25°C on solutions containing 0.176–0.042% polymer, 8.67 mM KI, 1% ethanol, and different concentrations of iodine. By a novel extrapolation method, the intrinsic viscosities of the amylose/iodine complex were determined under various conditions of iodine binding (0–0.133 g I2/g amylose). Contrary to the view long held in this research area, it was found that the intrinsic viscosity of amylose solutions decreases significantly upon complex formation with iodine. Taking into account the results of our previous kinetic studies, the present findings are interpreted in terms of an amylose model characterized by loose, extended helical regions which are interrupted by short disordered regions. It is proposed that the intrinsic viscosity decrease observed is due to a shortening of the linear dimension of the polymer chain. This conformation change is apparently caused by the contraction of loose helical regions of the amylose macromolecule due to the entrapment of iodine (and perhaps other) atoms inside the helical cavities.

Electrical properties of hydrated collagen. I. Dielectric properties

Abstract: The effect of water on the low-frequency (102-105 Hz) complex permittivitv of native, sold-state collagen has been investigated experimentally. Measurements at ambient temperature show that dry collagen exhibits essentially no frequency or temperature dependence. As water is absorbed, both dielectric constant and loss factor increase simultaneously and rise sharply upward at a hydration level which may be associated with the completion of the primary absorption layer as determined from independent water absorption studies. The behaviour is qualitatively identical to that observed for other proteins and related materials. Temperature-dependent measurements made under vacuum conditions in the range −196°C to +100°C are characteristic of the dielectric properties of the water in the sample. Dehydration produced by successive temperature recycling to the maximum temperature effectively eliminates any temperature or frequency dependence. A maximum in the temperature-dependent curves is found at about +40°C and is explained as the superposition of two processes: (1) the transition of water molecules from bound to free states, and (2) the difffusion of water molecules out of the system. The dielectric constant of dry collagen, after desorption at ambient temperature, is about 4.5. Desorption at elevated temperatures reduced the room temperature value to about 2.3 and the liquid nitrogen temperature value to a number indistinguishable from the optical value of n2 = 2.16.