A theory of aggregation in the thermal denaturation region of multistrand biopolymers

Model for the Temperature-Induced Conformational Change in Xanthan Polysaccharide

Xanthan is an extracellular bacterial polysaccharide. It is manufactured commercially by fermentation of Xanthomonas campestris and used extensively in food and other industries to control the viscosity and texture of various products. Its useful properties stem from its occurrence both as a relatively rigid double-helical polymer and as a branched polymer network presumably crosslinked by the same noncovalent interactions that stabilize the double-helical form. Interconversion of these two forms can be achieved through heating and cooling processes. This paper describes a model for this thermally induced transformation under conditions of very dilute aqueous polymer concentration, where the characteristics of double-helical and crosslinked aggregates can be studied experimentally using light scattering. Because xanthan is a regularly repeating copolymer, there is no requirement for specific registration of the two strands of the duplex structure as is required in naturally occurring nucleic acid double helices. Here, we demonstrate the important role of the resulting xanthan structural degeneracy in dictating the characteristics of the temperature-induced conformational transition.

Higher order structure of (1,3)-beta-D-glucans and its influence on their biological activities and complexation abilities

(1,3)-beta-D-Glucans form a group of biologically active biopolymers that exist in different structural organizations depending on the environmental conditions. The biological effect of (1,3)-beta-D-glucans is a core issue stimulating large research efforts of the molecular properties and their consequences for action as biological response modifiers. The fascination for these molecules increased further following the finding of their ability to form complexes of defined geometry with a number of structures, ranging from linear architectures as polymers or carbon nanotubes, to globular structures as gold particles or dye molecules. The fascinating information concerning the relationship between sample treatment history and molecular organization has not yet reached out to all the contributors within the field, resulting in unnecessary apparent inconsistencies in the literature. In addition to environmental conditions, the sample history is known to influence on the precise structural organization of these molecules. The present knowledge related to the structure of native as well as denatured, renatured and annealed (1,3)-beta-D-glucans is reviewed. The influence of their structural organization on the biological activity and complexation abilities is discussed, and some factors hindering progress in the understanding of their biological effects or complexation abilities are pointed out.

DNA melting in aggregates: impeded or facilitated?

How does DNA melt in columnar aggregate relative to its melting in diluted solution? Is the melting temperature increased or decreased with the aggregate density? Have DNA-DNA interactions, predominantly of electrostatic nature, an effect on the character of the melting transition? In attempt to answer these questions, we have incorporated the theory of electrostatic interactions between DNA duplexes into the simplest model of DNA melting. The analysis shows that the effect of aggregate density is very different for aggregates built of homologous (or identical) DNA fragments relative to the case of DNA with random base pair sequences. The putative attraction between homologous DNA helices hampers their melting and increases the melting temperature and can even dramatically change the character of the transition. In the aggregate of nonhomologous DNAs, the pattern of electrostatic interactions is more complicated, and their effect could be opposite; in some cases we may even expect electrostatically induced melting. These findings define new directions for melting experiments in dense DNA assemblies.

The effect of temperature on DNA structural transitions under the action of Cu2+ and Ca2+ ions in aqueous solutions

The work examines the structural transitions of DNA under the action of Cu2+ and Ca2+ ions in aqueous solution at temperatures of 29 and 45 degrees C by ir spectroscopy. Upon binding to the divalent ions studied, DNA transits into the compact state both at 29 and 45 degrees C. In the compact state DNA remains in B-form limits. The compaction process is of high positive cooperativity. As temperature increases the divalent metal ion concentration required to induce DNA compaction decreases in the case of Cu(2+)-induced compaction and increases in the case of Ca(2+)-induced compaction. It is suggested that the mechanism of the temperature effect on DNA compaction in the presence of Cu2+ ions possessing higher affinity for DNA bases differs from that of the temperature influence on Ca(2+)-induced DNA compaction. In the case of copper ions the determining factor is the increase of binding constants of the Cu2+ ions interacting with the denatured parts formed on DNA while in the case of calcium ions it is the decreased screening action of counterions upon the increase of their hydration with temperature. The efficiency of divalent metal ions studied in inducing DNA compaction depends on hydration of counterions. DNA compaction occurs in a narrow interval of Cu2+ concentrations. As the Cu2+ ion concentration increases, DNA compaction is replaced with Cu(2+)-induced DNA aggregation. At elevated temperatures Cu(2+)-induced DNA compaction could acquire a phase transition character.

DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation

Interaction of natural calf thymus DNA with Mn(2+) ions was studied at room temperature and at elevated temperatures in the range from 23 degrees C to 94 degrees C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn(2+) concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B-form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn(2+) ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55 degrees C. DNA aggregation was observed in the presence of Mn(2+) ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state.

Vibrational CD study of the thermal denaturation of poly(rA).poly(rU)

The vibrational cd (VCD) of a double-stranded RNA, poly(rA).poly(rU), at pH 7 and moderate added salt concentration (0.1 M) has been measured in both the base-stretching and phosphate-stretching regions of the ir as a function of temperature. The data in both cases show two distinct phase transitions. The first is from double- to a triple-stranded form, and the second is from triple- to single-stranded forms, which still retain substantial local order even up to 80 degrees C. The nature of these transitions has been identified by comparison of the VCD and ir absorption spectra of the initially double-stranded samples with those of single-stranded poly(rA) and poly(rU) and with triple-stranded poly-(rA).poly-(rU).poly(rU). The large differences in the VCD band shapes allows positive identification of the intermediate and final states. Thus under VCD-concentration conditions, a simple helix-to-coil transition can be eliminated for poly(rA).poly(rU) while such a two-step transition can be seen at low salt conditions. All of these observations are consistent with previous studies of the phase transitions of poly(rA).poly(rU) under various salt conditions. Additionally, the VCD is indicative of premelting for all the triple-, double-, and single-strand complexes studied. The triple-strand complex did not show disproportionation to double strand on heating under these added salt conditions. The unusual VCD pattern for low temperature poly(rA).poly(rU), as compared to high G--C content RNAs and DNAs, is qualitatively, but not quantitatively, explained using exciton coupling of localized dipolar transitions in each type of base within the strand.

Structure and dynamics of M13mp19 circular single-strand DNA: effects of ionic strength

Dynamic and static light scattering, CD, and optical melting experiments have been conducted on M13mp19 viral circular single-strand DNA as a function of NaCl concentration. Over the 10,000-fold range in concentration from 100 microM to 1.0 M NaCl, the melting curves and CD spectra indicate an increase in base stacking and stability of stacked regions with increased salt concentration. Analysis of dynamic light scattering measurements of the single-strand DNA solutions as a function of K2 from 1.56 to 20 X 10(10) cm-2 indicates the collected autocorrelation functions are biexponential, thus revealing the presence of two decaying dynamic components. These components are taken to correspond to (1) global translational motions of the molecular center of mass and (2) motions of the internal molecular subunits. From the evaluated relaxation rates of these components, diffusion coefficients D0 and Dplat are determined. The center of mass translational diffusion coefficient D0, varies in a nonmonotonic manner, by 10%, from 3.75 X 10(-8) to 3.39 X 10(-8) cm2/s over the NaCl concentration range from 100 microM to 1.0 M. Likewise, the radius of gyration RG, obtained from static light scattering experiments, varies by 15% from 699 to 830 A over the same NaCl range Dplat, the diffusion coefficient of the internal subunits, displays a different dependence on the NaCl concentration and decreases, by nearly 22% in a titratable fashion, from 12.46 X 10(-8) to 10.26 X 10(-8) cm2/s, when the salt is increased from 100 microM to 1.0 M. A semiquantitative interpretation of these results is provided by analysis of the light scattering data in terms of the circular Rouse-Zimm chain. Rouse-Zimm model parameters are estimated from the experimental results, assuming the circular chains are composed of a fixed number of Gaussian segments, N + 1 = 15. The rms displacement of the internal segments, b, is estimated to be the smallest (442 A) in 100 mM NaCl. Increases of b to 467 A in 100 microM and 524 A in 1.0 M NaCl are observed. Meanwhile, the hypothetical friction factor of the internal subunits, f, progressively increases as the NaCl concentration is raised. It is inferred from the evaluated Rouse-Zimm model parameters that both the static flexibility of the circular chain and diffusive displacements of the internal subunits decrease with increases in NaCl concentration from 100 mM to 1.0 M.(ABSTRACT TRUNCATED AT 400 WORDS)

A differential scanning calorimetric study of the conformational transitions of schizophyllan in mixtures of water and dimethylsulfoxide

The thermal conformational transitions of two sonicated samples of schizophyllan were studied in water-dimethylsulfoxide (DMSO) mixtures by high-sensitivity differential scanning calorimetry (DSC). Two transitions were observed over most of the range of solvent compositions. These were assigned to an internal change of the triple helix [T. Itou et al. (1986) Macromolecules 19, 1234-1240] and a triple-helix-single-coil transition [T. Sato et al. (1981) Carbohydr. Res. 95, 195-204], respectively. In water, the former transition observed at lower temperature for a low molecular weight sample, U-1, is centered at 3 degrees C and characterized by the specific enthalpy, delta hcal = 3.29 J g-1. A higher molecular weight sample, M-2, showed this transition at 7 degrees C with delta hcal = 4.39 J g-1. The transition temperature for both samples increased with increasing DMSO concentration up to about 50 degrees C at 70 weight % DMSO, and then rapidly decreased with increasing DMSO concentration, with about 3 degrees C higher for M-2 than for U-1 over the DMSO concentration. The transition was not observed when the concentration of DMSO exceeded 87%. It was found that delta hcal for both samples was a linear function of t 1/2, the temperature of half-completion in degrees C, delta hcal = 0.177t + 2.96. The triple helix-coil transition was observed at around 127 degrees C for U-1 and above 130 degrees C for M-2 in the range of DMSO composition below about 70%. The transition temperature decreased with increasing DMSO concentration at above 70%, and the transition finally disappeared when the DMSO concentration exceeded 90%. The plot of delta hcal vs. t 1/2 for the transition of both samples gave a linear relation, delta hcal = 0.253t - 10.58. The reversibility of the transition at lower temperature was demonstrated by the reversibility of the curves when the first heating was stopped before the second transition. Once the heating was performed over the second transition, the reheating DSC curves showed several endothermic peaks, indicating the irreversibility of the transition and heterogeneity in the conformation of the heated schizophyllan.

A differential scanning calorimetry analysis of the age-related changes in the thermal stability of rat skin collagen

Differential scanning calorimetry (DSC) has been applied to the study of connective tissue to evaluate the denaturation process of collagen. We have applied this technique to the study of the ageing of rat skin. We have tried to correlate the variations of the parameters measured by DSC and the modifications of collagen crosslinks with ageing. The thermograms obtained are composed of one main peak located between two shoulders. The relative size of each peak varies with time: the first peak diminishes regularly from 2 to 20 months whilst, at the same time, the third peak increases; the recovery temperature increases with age (+ 16 degrees C between 2 and 20 months); the total denaturation enthalpy does not vary: the main value obtained is 5.9 X 10(-2) J/mg collagen. On the other hand, the assay of reducible collagen crosslinks in rat skin, over the same age range, shows a decrease of heat-labile aldimine crosslink (essentially hydroxylysinonorleucine). These results and the study of thermograms obtained with altered rat skin (animals treated with beta-aminopropionitrile or skin reduced with NaBH4) allow us to conclude that heat-labile and heat-stable crosslinks account for a collagen thermal stabilization which can explain the delay of denaturation characterized by the third peak of DSC thermograms.

Conformational studies on the inactivation of glyceraldehyde-3-phosphate dehydrogenase from the facultative thermophile Bacillus coagulans KU

Among the various proposals that have been made in attempting to explain the ability of thermophiles to reproduce at high temperatures, there is no doubt that obligate and extreme thermophiles synthesize proteins (and other molecules) that have sufficient intrinsic molecular stability to withstand increased thermal stress. In contrast, the glyceraldehyde-3-phosphate dehydrogenase from the facultative thermophile Bacillus coagulans KU has been shown to be quite thermolabile in vitro. Thermal inactivation is not due to loss of bound NAD+. It has also been shown that the enzymatic activity can be thermostabilized in vitro by increased ionic strength. As previously reported [J. W. Crabb, A. L. Murdock, and R. E. Amelunxen (1975) Biochem. Biophys. Res. Commun. 62, 627; (1977) Biochemistry 16, 4840], the enzyme loses 94-97% of enzymatic activity after heat treatment at 55 degrees C for 5 min in 0.05 M sodium phosphate buffer (pH 7.1); however, by increasing the ionic strength to 1.8, complete protection was conferred at this temperature. Gel-filtration chromatography has been used to study the initial dissociation and subsequent aggregation of the glyceraldehyde-3-phosphate dehydrogenase after thermal inactivation. Aggregation occurs when the enzyme is heated at 50 degrees or 55 degrees C. Loss of enzymatic activity is correlated with changes in the tertiary structure as measured by the near-uv CD spectrum of the enzyme following heat inactivation, with essential disappearance of the peaks at 263 and 296 nm, and a blue shift of the far-uv spectrum, which is a measure of secondary structure. Estimation of secondary structure of the unheated protein from the far-uv CD data showed the enzyme contains approximately 26% alpha-helix, approximately 21% beta-structure, and approximately 53% disordered structure. Heat treatment at various temperatures resulted in only slight changes of the estimated secondary structure. Increased ionic strength prevents thermal alteration of the CD spectrum in both near- and far-uv regions. The data support the previous proposal that thermolabile enzymes such as the glyceraldehyde-3-phosphate dehydrogenase from the facultative thermophile B. coagulans are thermostabilized in vivo mainly by the intracellular charged macromolecular environment.