Conformation of sequential and random copolypeptides of lysine and alanine in sodium dodecyl sulfate solution

A series of sequential polypeptides, (Lys_i-Ala_j)_n, and random copolypeptides, (Lys^x, Ala^y)_n, were synthesized. The competitive effect of Ala, a helix former, and Lys, whose homopolymer has a β-form in neutral NaDodSO₄ solution, was determined by CD and absorption spectroscopy. All the polypeptides studied were unordered in neutral solution without the surfactant. Of the six sequential polypeptides only (Lys-Ala)_n adopted a stable β-form in NaDodSO₄ solution. Most striking is the difference between this polypeptide, (Lys₂-Ala₂)_n and (Lys^x, Ala^y)_n, even though they all have equimolar Lys and Ala. (Lys₂-Ala₂)_n was partially helical in 2.5–5 mM NaDodSO₄ but approached the unordered form in 50 mM NaDodSO₄, whereas (Lys⁵⁰, Ala⁵⁰)_n was completely helical in all NaDodSO₄ concentrations. Even Lysrich (Lys₂-Ala)_n and (Lys₃-Ala)_n formed a partial helix and a trace of the β-form, respectively, in low NaDodSO₄ concentrations; both reverted to the unordered form in high NaDodSO₄ concentrations. These results can be explained by Pauling-Corey's model for β-pleated sheets. Only (Lys-Ala)_n has all DodSO-bound Lys⁺ residues on one side and Ala residues on the other side of the polypeptide chain. They can nestle quiet efficiently in a β-sheet and between neighboring β-sheets. Our results further imply that random copolypeptides are not completely random; they comprise varying segments of (Lys_k-Ala_m), where k and m could vary from zero to a small integer.     

Sequential polypeptides containing arginine as histone models: synthesis and conformational studies

The sequential polypeptides (L -Arg-X-Gly)_n, where X represents amino acid residues Ala, Val, and Leu, were prepared as models of arginine-rich histones to be used in studying their structure and their interactions with DNA. The polymerization was carried out on the pentachlorophenyl active esters of the appropriate tripeptides, while the toluene-4-sulfonyl group was used for protecting the arginine guanido group. CD was employed to investigate the conformation of (L -Arg-X-Gly)_n polymers in aqueous solutions, at different pH, as well as in trifluoroenthanol and hexafluoroisopropyl alcohol solutions. In aqueous solutions (at pH 7 and 12) the prepared sequential polymers behaved as a random coil. The CD spectra in various trifluoroethanol–water or hexafluoroisopropyl alcohol–water mixtures indicated that the degree of helical conformation of the studied polytripeptides increased in the order of Ala → Val → Leu. The opposite was true for the β-structure. Characteristics of β-turn are excluded from the poly(L -Arg-L -Leu-Gly), which assumed the most pronounced helical conformation. The poly(L -Arg-L -Val-Gly) exerts a significant preference to the β-turn structure compared to that of poly(L -Arg-L -Ala-Gly). Thus the probability for helical, β-structure or β-turn conformations of the polymers was analyzed in relation to the bulkiness and length, and to the special features of the X-residue side chain (β-branching). We concluded that the prepared sequential arginine-containing polypeptides are plausible models for histone fractions, f₃ and f₂α₁.     

Conformation of amylose in aqueous solution: Optical rotatory dispersion and circular dichroism of amylose–iodine complexes and dependence on chain length of retrogradation of amylose

The dependence on chain length of two characteristic properties of amylose, i.e., retrogradation and complex formation with iodine, have been studied by using enzymatically synthesized, homodisperse amyloses. The association rates of amyloses in water containing 5% dimethyl sulfoxide have a sharp maximum at a degree of polymerization P?_n of 80; shorter and longer molecules are much more soluble. The iodine complexes of amylose exhibit a strong Cotton effect in the range of the long-wave absorption maximum (position depending on chain length) and two weaker Cotton effects at 480 and 350 nm. The long-wave Cotton effect is most intense at about P?_n 50 and decreases rapidly for shorter and longer chains. This behavior is unexpected and is not in accordance with the further increase of λ_max and λ_max. The experiments can best be interpreted by assuming well ordered, stiff chains in the low molecular weight range (P?_n 50–80). For longer chains, the findings are discussed in the light of current concepts of amylose conformation in aqueous solution, namely the model of the broken helical chain (alternating stiff helical segments and unordered regions) and the model of a flexible coil without a significant helical content. However, according to the results given in this paper, a wormlike helical chain seems to be the most adequate model for amylose conformation in neutral solution.     

Dissipative particle dynamics simulation on the meso-scale structure of diblock copolymer under cylindrical confinement

The meso-scale structure of symmetric diblock copolymer under cylindrical confinement is studied by dissipative particle dynamics (DPD). The simulation results show that coiled cylindrical geometry is favored in the presence of larger cylinder radius (R/L ₀>～1.5), and the number of rings depends on the cylinder radius. Because of the cylinder wall's selectivity, each block can form the central core, but only the preferential block forms the outmost layer. An approximately linear relationship exists between structure transition point, which is approximately in proportion to the 3/5 exponential of chain length of copolymer and number of layers. As the cylinder radius is decreased, a helical morphology is found. Lamellae parallel to the underside of the cylinder appear when the cylinder radius is made smaller (R/L ₀ < ～1.1).     

Intra- and intermolecular charge-transfer interactions between terminal electron donor and acceptor attached to poly(γ-benzyl-L-glutamate) in solution

Poly(γ-benzyl-L -glutamate) having a terminal dimethylaminoanilide group as an electron donor (D) and a terminal 3,5-dinitrobenzoyl group as an electron acceptor (A) (A-[Glu(OBzl)]_n-D) was synthesized by the N-carboxyanhydride method. Polymer samples were fractionated by gel chromatography and their number-average degrees of polymerization n were determined by the absorbances of the terminal chromophores. These polymers in chloroform and dimethylformamide solutions showed a charge-transfer (CT) absorption band around 455 nm, and the fraction of the polymer forming the CT complex was evaluated as a function of the chain length. CT absorption for short chains (n = 5 ～ 20) was attributed to intramolecular CT complex in which the A-[Glu(OBzl)]_n-D chain takes cyclic conformations. An optimum chain length for the intramolecular CT was found to be n ? 10, where the [Glu(OBzl)]_n chain may most easily bend back to form cyclic conformations. Stronger CT absorption observed for longer chains than n = 20 was shown to be intermolecular, and an intermolecular head-to-tail aggregation was found to be a cause of the strong CT interaction. All helical A-[Glu(OBzl)]_n-D chains were found to form the head-to-tail dimers in chloroform solution.     

Conformational studies of poly-L-alanine in water

The conformational properties of poly-L -alanine have been examined in aqueous solutions in order to investigate the influence of hydrophobic interactions on the helix–random coil transition. Since water is a poor solvent for poly-L -alanine, water-soluble copolymers of the type (D , L -lysine)_m–(L alanine)_n-(D , L -lysine)_m, having 10, 160, 450, and 1000 alanyl residues, respectively, in the central block, were synthezised. The optical rotatory dispersion of the samples was investigated in the range 190–500 mμ, and the rotation at 231 mμ was related to the α-helix content, θ_H, of the alanine section. In salt-free solutions, at neutral pH, the three large polymers show high θ_H values, which are greatly reduced when the temperature is increased from 5 to 80°C. No helicity was observed for the small (n = 10) polymer. By applying the Lifson-Roig theory, the following parameters were obtained for the transition of a residue from a coil to a helical state: ν = 0.012; ΔH = ?190 ± 40 cal./mole; ΔS = ?0.55 ± 0.12 e.u. Since ΔH and ΔS differ from the values expected for a process involving only the formation of a hydrogen bond, and in a manner predicted by theories for the influence of hydrophobic bonding on helix stability, it is concluded that a hydrophobic interaction is also involved. In the presence of salt (0.2M NaCl), or when the ε-amino groups of the lysyl residues are not protonated (pH = 12), the helical form of the two large polymers (n = 450 and n = 1000) is more stable than in water. Since the electrostatic repulsion between the lysine end blocks is greatly reduced under these conditions, the alanine helical sections fold back on themselves, and this conformation is stabilized by interchain hydrophobia bonds. This structure was predicted by the theory for the equilibrium between such interacting helices, non-interacting helices, and the random coil.     

N‐terminal diproline and charge group effects on the stabilization of helical conformation in alanine‐based short peptides: CD studies with water and methanol as solvent

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine‐based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N‐terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine‐based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac–Pro–Pro–Ala–Lys–Ala–Lys–Ala–Lys–Ala–NH₂) is designed to assess the effect of N‐terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac–Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) and A3 (Ac–d Pro–Pro–Glu–Glu–Ala–Ala–Lys–Lys–Ala–NH₂) with N‐terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i , i  + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1 , A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature‐dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β‐strand conformation, which is consistent with the previous studies. The results illuminate the effect of N‐terminal diproline and charged side chains in dictating the preferences for extended‐β, semi‐extended PPII and helical conformation in alanine‐based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Theoretical π-π* absorption and circular dichroic spectra of helical poly(L-proline) forms I and II

Absorption and CD spectra of the π-π* transition near 200 nm are calculated for helical (Pro)_n I and II (n = 6, 10) using the dipole interaction model, including interactions among all atoms, with optical parameters obtained from previous studies of related molecules. Calculated spectra for (Ala)_n and (Pro)_n in the same conformation show marked differences. The spectra for (Pro)_n are sensitive to side-chain structure but are found to agree reasonably well with exeriment for forms I and II when the side-chain C? C bond length is set at 1.54 Å, with structural data otherwise obtained from x-ray diffraction studies.     

Helical Inversion of Gel Fibrils by Elongation of Perfluoroalkyl Chains as Studied by Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low‐molecular mass weight gelator, N,N’‐diperfluoroalkanoyl‐1,2‐trans‐diaminocyclohexane. Attention was focused on the winding effects of (–CF₂)_n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6–8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle‐like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C‐F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361–364, 2016. © 2016 Wiley Periodicals, Inc.     

Conformational study of linear alternating and mixed D- and L-proline oligomers using electronic and vibrational CD and fourier transform IR

Vibrational CD (VCD) spectra of a series of blocked linear, alternating D - and L -proline containing oligopeptides, dissolved in D₂O and in CDCl₃. are reported. For the Boc-LDL -Pro₃ to Boc-DLDLDLDL-Pro₈ oligomers. The VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L -Pro)_n oligomers. While this admits the possibility of their favoring a right-handed helical chain conformation, the amide I ir spectra for these dl oligomers in D₂O indicate a mixed, apparently alternate, cis-trans conformation that prevents a simple conclusion. Their VCD in D₂O evidence no narrowing and has a progressive loss in intensity (measured as Δ /A,) with an increase in chain length. In CDCl₃a similar pattern of positive VCD couplets decreasing in intensity with length was seen, but their spectra are narrower. Their electronic CD (ECD) in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N-terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases. © 1995 John Wiley & Sons, Inc.     

Molecular configuration of amylose and its complexes in aqueous solutions. Part II. Relation between the DP of helical segments of the amylose–iodine complex and the equilibrium concentration of free iodine

The iodine which is added to an aqueous amylose solution is bound only partly by the amylose while forming the blue complex and partly remains free. The equilibrium normality of the free and the bound iodine at half-saturation of amylose by iodine is designated as [I_f]_v and [I_b]_w, respectively. The stability of the poly iodine chain formed within the axis of amylose helices depends on its length, i.e., indirectly on the DP of the amylose helices: the greater this stability, the lower the [I_f]_v value. The amylose molecule consists of helical segments. Such a molecule may behave as a random coil. The average length of the helical segments in freshly prepared amylose-iodine complexes depends on temperature, pH, iodide concentration, the presence of other complex-forming agents, and the DP of the amylose. This latter factor is investigated in the present paper. By the aid of an automatically recording photometrictitrating device the coherent values of [I_b] and [I_f] were determined. Plotting these values against DP _n for mechanochemically degraded as well as for periodateo-xidized amyloses resulted in curves consisting of two linear sections. The break of the curves occurred between DP _n 110 and 130. It was concluded that below DP _n = 100 the DP of helical segments (= sDP _n) is identical to the DP _n of the total molecule, i.e., the molecule consists of only a single, relatively stiff helix. Above this limit the molecule contains several helical segments. The DP of these helical segments can be calculated as follows: sDP _n = 141.1 ? 10.2 × 10⁵[I_f]_v. This equation is considered to be valid for 0.5–0.6 mg. amylose in 100 ml. 0.1N HCl at 20°C., λ = 650 mμ, euuvet diameter 3.4 cm., the feed rate of the iodate-iodide titrating solution (in acid medium resulting in a 5 × 10^?3N I₂ solution with a molar iodide to iodine ratio of 1.5) is 0.4ml./min. Amylose molecules of, e.g., DP ⁿ = 1380 consist of an average of 11.4 segments having a DP of about 120 and consisting of an average of 15–18 helical turns.     

Secondary structure of peptides: 15. 13C n.m.r. CP/MAS study of solid elastin and proline-containing copolyesters

In order to study the chemical shifts and the cis—trans isomerism of prolyl units neighbouring glycine or other amino acids, 75.4 MH_z¹³C nuclear magnetic resonance (n.m.r.) cross-polarization/magic angel spinning (CP/MAS) spectra of the following solid oligopeptides and sequence polypeptides were measured: Z-Gly-Pro-OH,Z-Gly-Pro-Gly-Gly-OEt,Z-Gly-Pro-Ala-Ala-OMe,(Gly-Pro-Gly)_n,(Gly-Pro-Ala)_n,(β-Ala-Pro)_n and $\text{(δ-Ava-Pro)}{}_{\mathrm{<mtext>n</mtext>}}\text{(δ-Ava=δ-}\text{aminovaleric acid}$). Whereas all these oligo- and polypeptided contain exclusively trans X-Pro bonds, both cis and trans peptide bonds were found in a polypeptide prepared by copolymerization of glycine- and $\text{proline-}\text{N}\text{-carboxyanhydrides}$ in pyridine. On the basis of these model compounds, the ¹³C n.m.r. CP/MAS spectra of solid elastin allows the following conclusions. Almost all X-Pro bonds assume the trans conformation, most alanine and leucine units form α-helical chain segments, whereas only a small fraction of β-sheet structure is present. A 30.3 MHz ¹⁵N n.m.r. CP/MAS spectrum of solid elastin confirms that ～25% of all amino acids assume the α-helical structure. A model of elastin is discussed consisting of an amorphous phase, α-helical chain segments and helical segments of still unknown pitch.     

CD studies of synthetic polypeptides as histone models: Poly(L-Arg-L-Ile-Gly), poly(L-Arg-L-Nva-Gly), and poly(L-Arg-L-Nle-Gly)

Sequential polypeptides (L -Arg-X-Gly)_n were prepared as synthetic models of arginine-rich histones to study their structure and their stereospecific interactions with DNA. In our previous work the conformational characteristics of poly(L -Arg-L -Ala-Gly), poly(L -Arg-L -Val-Gly), and poly(L -Arg-L -Leu-Gly) have already been analyzed. To obtain further insight into the influence of the X residue side chain on the conformation of the (L -Arg-X-Gly)_n polytripeptides, we now report their synthesis and cd properties when X represents the amino acid residues Ile, Nva, and Nle. The pentachlorophenyl active esters of the appropriate tripeptides were used to perform the polymerization, and the toluene-4-sulfonyl group was used to protect the arginine guanido group. CD spectroscopy showed that, in 100% trifluoroethanol, the degree of helical conformation increased in the order Ile → Nle → Nva. An equilibrium between β-turn, α-helix, and random-coil conformers occurred in 100% hexafluoroisopropyl alcohol, while a rise in the temperature or the addition of water favored the α-helix, the highest percentage of which was observed in a mixture of hexafluoroisopropyl alcohol: water (20 : 80) and in the order Ile → Nle → Nva. In aqueous solutions (at pH 7 and 12) the polymers behaved as a random coil, but they were forced to a less aperiodic structure, over a range of ionic strengths (0–0.5M NaF). A rise in temperature of up to 70°C in 100% trifluoroethanol resulted in a decrease of the α-helix percentage of the polymers, while in aqueous solutions the aperiodic structure decreased with increasing temperature. This study proved the importance of the nature of the X residue (length, C_β branching) in relation to the structural order of the sequential polypeptides. We concluded that the polymers prepared are suitable models for arginine-rich histones.     

Application of the augmented theory of alpha-helix-to-random-coil transitions of two-chain, coiled coils to extant data on synthetic, tropomyosin-analog peptides

The statistical mechanical theory for the helix-to-random-coil transition in two-chain coiled coils is applied to extant data for two synthetic coiled-coil polypeptides. These peptides have the primary structure K(LEALEGK)_n, in which n = 4, 5. This repeating heptet sequence mimics the pattern of hydrophobic, acidic, and basic residues characteristic of the 284-residue tropomyosin molecule, the prototypical coiled-coil protein. Theoretical calculations for single chains show that such model peptides cannot be directly compared to proteins like tropomyosin because of differences in chain length (29 and 36 residues vs 284) and in intrachain interactions, the latter caused by the differences in amino acid composition and seqeunce between protein and model. Application of the theory to extant data on the two synthetic peptides provides a semiquantitative fit and results in an assessment of the interhelix interaction in the model peptides. The value obtained, ～ 2000 cal · (mol of turn pairs)^–1, is four to five times larger than has been obtained for tropomyosin. This probably is a result of greater regularity in the structure of the synthetics and of the exclusive presence of leucine in the hydrophobic interface. The theory employed here insists that this powerful interhelix interaction in the synthetic is the principal reason that such short chains can be so highly helical at moderate and low temperatures. Theory predicts, indeed, that a tropomyosin-length chain with a sequence homologous to these synthetics would be completely thermally stable in the entire temperature range accessible in aqueous solutions. Theory also predicts a much more pronounced effect of concentration on the 29- and 36-residue synthetic polymers than is predicted or observed in the case of tropomyosin, and it also predicts a pronounced stabilizing effect of pH-reduction on the thermal curves. On the last two points, sufficient data are not yet available with which to test the theory.     

Use of sequence-specific tri-block copolymers to determine the helix-forming tendencies of amino acids

In order to examine the helix-coil transition of water-insoluble polypeptides, without requiring interspersion of charged or polar residues within the sequence, a tri-block copolymer strategy has been developed to determine the helix propensity of amino acids in short (15-residue) peptides. The method is also well suited to evaluate specific interactions that contribute to helix formation. In this approach, measurement is made of the helix content of the central block of tri-block copolymers of the type Lys₁₅-X-Lys₁₅, where X is the 15-residue peptide whose helix content is being investigated. The suitability of tri-block copolymers of this type has been verified experimentally by using the water-soluble peptide (Ala₂GlnAla₂)₃ as the central block. The CD spectrum of the central block in the tri-block copolymer and of Ac-(Ala₂GlnAla₂)₃-NH₂ are indistinguishable within experimental error. © 1996 John Wiley & Sons, Inc.     

Design,synthesis, MTT assay,DNA interaction studies of platinum(II) complexes

The square planar Pt(II) complexes of the type [Pt(Lⁿ)(Cl₂)] (where Lⁿ = L^1?3 = thiophene-2-carboxamide derivatives and L^4?6 = thiophene-2-carbothioamide derivatives) have been synthesized and characterized by physicochemical and various spectroscopic studies. MIC method was employed to inference the antibacterial potency of complexes in reference to free ligands and metal salt. Characteristic binding constant (K_b) and binding mode of complexes with calf thymus DNA (CT-DNA) were determined using absorption titration (0.76–1.61 × 10⁵ M^?1), hydrodynamic chain length assay and fluorescence quenching analysis, deducing the partial intercalative mode of binding. Molecular docking calculation displayed free energy of binding in the range of –260.06 to –219.63 kJmol^?1. The nuclease profile of complexes towards pUC19 DNA shows that the complexes cleave DNA more efficiently compared to their respective metal salt. Cytotoxicity profile of the complexes on the brine shrimp shows that all the complex exhibit noteworthy cytotoxic activity with LC₅₀ values ranging from 7.87 to 15.94 μg/mL. The complexes have been evaluated for cell proliferation potential in human colon carcinoma cells (HCT 116) and IC₅₀ value of complexes by MTT assay (IC₅₀ = 125–1000 μg/mL).     

The chain length dependence of the conformation for oligomers of L-lysine in aqueous solution: Optical rotatory dispersion studies

The optical rotatory dispersion of L -lysine oligopeptides (Lys_n, n = 2–22) in solution was measured in water and in 50% methanol. A gradual change with increasing chain length in the ORD curves of the oligomers was observed at pH 4. 3. Not even a chain of 22 residues had ORD identical with that of high molecular weight poly-L -lysine. A plot of the average molar residue rotation at 233 nm versus 1/n (where n is the chain length) resulted in a straight line with an intercept of ?1900, representing the internal residue rotation of a lysine residue in the random conformation, and a slope of +6200 representing the large end effect. At pH 11.9 a stright line is obtained up to n = 12 after which it deviates from the initial slope indicating onset of helicity. Extrapolation of the initially straight line to tire higher n's provided the necessary zero-helicity values for calculation of helicity. The highest oligolysine (n = 22) showed at pH 11. 9 13% helicity, which on adding methanol to 50% increased to about 50% helicity. It is shown that helix-coil data which are usually obtained from the temperature dependence of helicity can be obtained from the dependence of helicity on chain length applying the statistical theory. For the methanol-water system the cooperativity parameter v was calculated to be in the range 0.024–0.060, with corresponding equilibrium constants w of 1.32–1.43. The helical structure was calculated to be less stable in water than in methanol-water by about 250 calories per residue.     

Basic polypeptides as histone models. Synthesis, conformation, and interaction with DNA of statistical copolymers (Lys x,Ala y)n.

Statistical copolymers (Lys^x,Ala^y)_n were synthesized by copolymerization of N-carboxyanhydrides of L -amino acids. The conformation of copolymers in aqueous solutions was investigated using circular dichroism (CD). Calculations based on the CD data showed that polymers (Lys^x,Ala^y)_n can exhibit a random conformation, an α-helix, and a β-structure in various ratios. CD spectra of complexes of copolymers with DNA prepared by gradual dialysis from a high ionic strength to 0.15 M NaCl can be correlated with the copolymer conformation in medium and high ionic strength. For copolymers forming an α-helix and β-structure, these spectra show resemblance with similar spectra of complexes of those histones that are able to exhibit ordered conformations.     

Renaturation of triple helical polysaccharide lentinan in water-diluted dimethylsulfoxide solution

Triple helical lentinan, a β-(1→3)-d-glucan from Lentinus edodes, was denatured in dimethylsulfoxide (DMSO) into single random coils. The randomly coiled lentinan/DMSO solutions were diluted with pure water to w_H (the weight fraction of water in the mixed solvent) of 95%, and their intrinsic viscosity [η], weight-average molecular weight M_w, radius of gyration R_g, and hydrodynamic radius R_h were investigated at 25 °C after over 5-day storage. The [η] and M_w values, especially the conformation parameter ρ (≡R_g/R_h), of the renatured lentinan were close to those of the originally extracted one, suggesting that random lentinan chains in DMSO were reassembled into triple helical structures. Moreover, the renatured lentinan in 95% water/5% DMSO solution exhibited a unique behavior of triple helical glucans that shear modulus G′ decreased sharply at temperature from 8.4 °C to 13.3 °C with increasing temperature, which was ascribed to the intramolecular conformation transition from ordered triple helical I to disordered triple helical II. The AFM images gave was suggested intuitively evidence that the renatured lentinan mainly existed as rod-like chains, supporting that formation of triple helical structure. The optimal lentinan concentration for triple helical configuration formation was estimated to be over 0.04%. The time dependence of R_h and UV absorption of the water-diluted lentinan/DMSO solution with an indicator of azo dye of Congo red suggested that renaturation of triple helix was a very rapid process. Moreover, the blue-shift of UV-vis absorption spectra suggested that the dye molecules of Congo red were assembled into supramolecular structure in the hydrophobic cavity of the renatured triple helical lentinan. All the results showed that the triple helical structure formed once the randomly coiled lentinan/DMSO was diluted to the final water content of 95%.     

Complexes of DNA bases and Watson–Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study

We study the binding of the neutral Ag_n (n = 8, 10, 12) to the DNA base-adenine (A), guanine (G) and Watson–Crick –adenine-thymine, guanine-cytosine pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential was used for silver and 6–31 + G^** was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Ag_n–A,G/WC complexes were also studied using time-dependent density functional theory. The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Ag_n–WC complexes. The vertical ionization potential, vertical electron affinity, hardness, and electrophilicity index of Ag_n–DNA/WC complexes have also been discussed.