Akihiro Kagemoto

Theoretical Conformational Analysis on Silk Fibroin Model Polypeptide with Ala-Gly Repeated Sequence

Theoretical conformational analysis was carried out for Ac-(Ala-Gly)12-NHMe, which was a model polypeptide of Bombyx mori silk fibroin, using ECEPP and the conformational energy minimization procedure. The hypothesis on the interaction in polypeptide molecules was also used for the analysis. Calculated results showed that right-handed α-helix and left-handed β4.6-helix were the lowest-energy and 2nd low-energy conformations, respectively. Several stable conformations, which were related to the already proposed model structures of silk fibroin, were also found in the theoretically obtained conformational ensemble of Ac-(Ala-Gly)12-NHMe.

Thermodynamic studies on interactions between DNA and dye

Abstract The interactions in solution between DNA, DNA-I (GC content 26.5%), DNA-II (GC content 42%), and DNA-III (GC content 72%), with various contents of guanine—cytosine base pair (GC content), and 9-amino-acridine (9-AA) or quinacrine with side chains were studied by microcalorimetry and spectrophotometry. The thermodynamic quantities for dye intercalated into adjacent base pairs of DNA were determined. From the results, the ΔG⊖ values in the DNA-I—, -II—, and -III—9AA systems were estimated to be about −32 kJ, virtually independent of GC content, although the absolute values of ΔH increase with increasing GC content of DNA, suggesting that an interaction between DNA and 9-AA forms a thermodynamically stable complex, depending on the GC content of the DNA. However, the ΔG⊖ value for the DNA-II—quinacrine system is lower than that for the DNA-I— or DNA-III—quinacrine systems, demonstrating that an interaction between DNA-II and quinacrine forms a thermodynamically stable complex, compared with those in the DNA-I— and DNA-III—quinacrine systems. An analysis for base specificity of dyes accompanying the intercalation was carried out according to Eq. (7) in the text. The thermodynamic quantities for dye intercalated into GC/GC, AT/AT, and GC/AT base pair sequences were estimated. From these results, the most stable base sequence with respect to the intercalation of 9-AA into adjacent base pairs was the AT/AT base pair rather than the GC/GC and AT/GC base pairs, its thermodynamic quantities being about −31 kJ mol−1 for ΔH, 5.0 J K−1 mol−1 for ΔS, and −33 kJ mol−1 for ΔG⊖. Therefore, 9-AA interacts preferentially with the AT/AT base pair sequence. However, in the quinacrine systems, the most stable base pair for intercalation of quinacrine into adjacent base pairs was the GC/AT base sequence, and its thermodynamic quantities being ΔH ≈ −64 kJ mol−1, ΔS ≈ −12 J K−1 mol−1, and ΔG⊖ ≈ −68 kJ mol−1 suggesting that interaction between DNA and quinacrine is governed by ΔH, and also, that the interaction mode of quinacrine is different from that of 9-AA.

Heats of dilution of water-soluble polymer solutions

Abstract In order to obtain information about the effects of water on water-soluble polymers, the heats of dilution of poly(acrylic acid)-water and poly(acrylic acid)-ethyl alcohol systems were measured at 298.15 ± 0.002 K with a specially constructed automatic microcalorimeter. The results obtained show that the heat of dilution is endothermic for the water system and exothermic for the ethyl alcohol system. In order to confirm the endothermic and/or exothermic heats of dilution of those systems, the excess volume of mixing of the systems was also measured at 298.15 ± 0.01 K using a densimeter. The sign of the excess volume for the ethyl alcohol system, but not for the water system, was in good agreement with that of the interaction heat parameter estimated by calorimetry. To obtain further information about the interaction, the interaction energies of the systems were calculated by means of ab initio molecular orbital (MO) calculations. The result obtained is about −12 kJ mol −1 for the ethyl alcohol system, suggesting that the interaction mode between poly(acrylic acid) and ethyl alcohol molecules may be based on the hydrogen bond between the COOH group in the chain of poly(acrylic acid) and the OH in the ethyl alcohol molecule from the agreement of the heats of dilution with the excess volume of mixing and/or ab initio MO calculations. However, for the water system, the interaction energy obtained is positive and its value is very large.

Thermodynamic characterization of the 9-aminoacridme intercalated into DNA

Abstract The interaction of DNA with 9-aminoacridine was studied by means of calorimetric and spectral measurements, and the thermodynamic quantities for 9-aminoacridine intercalated into DNA were determined. Changes in free energy ΔG, enthalpy ΔH, and entropy ΔS accompanying the intercalation process were estimated to be about −36kJ mol−1, −22kJ mol−1 and 47 J K−1 mol−1 respectively, suggesting that the interaction between DNA and 9-aminoacridine appears to form a stable complex from the viewpoint of free energy and that this complex formation is governed by both enthalpy and entropy.

The conformational change of DNA in aqueous alcohol solutions containing metallic ions determined by using differential scanning calorimeter

Abstract In order to obtain information about the conformational change of DNA by changing the environment surrounding DNA molecule, we measured the helix-coil transition of DNA solutions with various concentrations of ethanol at a given concentration of various kinds of metallic ion by means of an adiabatic differential scanning calorimeter. The observed heat of transition, ΔH increases, but the transition temperature, T 1 decreases with increasing the concentration of ethanol, demonstrating that the conformation of DNA may considerably change by environment surrounding DNA. In order to confirm the conformational change of DNA, we also measured the CD spectra at room temperature under the same experimental conditions as the DSC measurement. The concentration range of ethanol where molecular ellipticity ratio, [θ] max /[θ] min of positive maximum, [θ] max to negative minimum, [θ] min changes is in good agreement with that obtained from DSC measurements. We will discuss the conformational change of DNA in solutions with various proportions of ethanol and a definite concentration of metallic ion by combining the results obtained by the calorimetric and spectral measurements.

Thermal and optical properties of liquid crystal formation in an equimolar mixture of poly(A) and poly(U) by simultaneous measurement of differential thermal analysis and laser transmittance

Abstract A differential thermal analysis apparatus equipped with a laser was designed to allow simultaneous measurement of the thermal and optical properties of biopolymer solutions. The phase states of a concentrated solution of an equimolar poly(A)-poly(U) mixture were studied using this apparatus and a polarization microscope. This mixture shows an isotropic phase at concentrations below 3.0wt.%, a quasi-isotropic phase for the concentration range 4.0–6.0wt.%, a spherical liquid crystal phase for the concentration range 7.0–9.0wt.%, and a layer crystal phase for concentrations above 10.0wt.%. The thermal and optical changes for phase states estimated with the new apparatus correspond well with phase state changes observed with the polarization microscope.

Random-coiled conformation of polypeptide chains

SummaryRandom-coiled conformation of poly(L-leucine), which has γ-branched side-chain, was theoretically analyzed by a conformational energy calculation based on intra-residue interactions. Calculated characteristic ratio 7.62 was obtained by using the transformation matrix statistically averaged over the entire side-chain conformational space of L-Leu residue. This value is smaller than those of poly(L-phenylalanine) (11.24) and poly(L-tyrosine) (12.33) which have γ-branched side-chain.

Heats of dilution of water-soluble-polymer solutions (II) - heat interaction parameters of aqueous hydroxypropylcellulose and gelatin solutions determined by means of flow microcalorimeter

Abstract In order to obtain information about the intermolecular interaction between the water-soluble-polymers, we measured the heats of dilution of hydroxypropylcellulose(HPC)-water and gelatin-water systems at 298K by the flow microcalorimeter. The heat of dilution for gelatin-water system proved to be exothermic and the heat interaction parameter x1, determined by Van Laar equation was estimated to be about −1.00. However, the heat of dilution of HPC-water system moves from the exothermic to the endothermic with an increase of HPC concentration and x1-value in dilute solution was estimated to be about −0.91. We found that the interaction between gelatin and water depends linearly on the gelatin concentration, but for HPC-water system, the interaction depends considerably on the HPC concentration. From the results of these interactions, the hydrophilic effect of these water-soluble-polymers for water was the order of gelatin > HPC. We will discuss the hydrophilic and hydrophobic interactions from the results of heats of dilution.

Thermodynamic studies on the interaction between nucleic acid and drug by calorimetry

Abstract The heats of mixing of the DNA-AD, Duplex I-AD and Duplex II-one systems were measured at 298.15 ± 0.005 K by using an LKB batch type twin microcalorimeter with a help of spectral measurements. From the results of DNA-AD system obtained, the interaction between DNA and AD is mainly caused by intercalation manner by referring to the result of spectral measurement. And, we estimated the thermodynamic quantities based on the intercalation process. While, from the results of Duplex I-AD and Duplex II-one systems, we concluded that the interactions of these systems may be corresponded to an electrostatic force as binding process rather than an intercalation process.

Thermodynamic studies on selective recognition of bases in complex formation between base pairs. Formation of complexes by non-complementary interactions

Abstract In order to obtain information on non-complementary interaction in polynucleotide mixtures, the molecular conformations of the equimolar mixtures poly(A)—poly(C) (Mixture 1), poly(A)—poly(I) (Mixture 2), poly(C)—poly(U) (Mixture 3), and poly(I)—poly(U) (Mixture 4), in concentrated solutions, were studied by means of microcalorimetry, spectrophotometry, refractive index, and ab initio molecular orbital (MO) calculation. Mixtures 1 and 3 did not form complexes by non-complementary interaction under the experimental conditions of the present work, although possible interactions were considered for both systems from the standpoint of the net charge, using ab initio molecular orbital (MO) calculations. The phase state for the poly(I)—poly(C) mixture based on complementary interaction between purine and pyrimidine bases was observed using a polarization microscope. This indicated that the poly(I)—poly(C) mixture forms a layered liquid crystal, as reported previously for poly(A)—poly(U) mixture. It should be noted that Mixture 2 forms liquid crystals with a triple-stranded helical structure by non-complementary interaction between poly(A) and poly(I), both with purine base. Moreover, the change in enthalpy Δ H t (7.3 kJ) based on the helix—coil transition of Mixture 2 is approximately the same as those of poly(I)—poly(C) mixture (Δ H t = 6.2 kJ) and poly(A)—poly(U) mixture (Δ H t = 6.4 kJ), as reported previously. But the change in enthalpy (Δ H ord—disord = 2.7 kJ) based on the order—disorder transition of the layered liquid crystal for Mixture 2 is different from the value Δ H ord—disord = 5.8 kJ for an equimolar poly(I)—poly(C) mixture, and Δ H ord—disord = 6.6 kJ are for equimolar poly(A)—poly(U) mixture, in which liquid crystals are formed by complementary interaction, suggesting that the intermolecular interaction of the liquid crystals formed by non-complementary interaction between the purine bases of poly(A) and poly(I) is very weak compared with that formed by complementary interaction between purine base and pyrimidine base of nucleotides. Mixture 4 displays an isotropic phase at concentration below 5.0 wt%, and an anisotropic phase with a double-stranded helical structure appears above 5.0 wt%. But the changes in enthalpy (Δ H t = 4.0 kJ) and Δ H ord—disord = 1.0 kJ), for Mixture 4 are smaller than those for Mixture 3, poly(I)—poly(C), and poly(A)—poly(U) by complementary interaction, as reported previously, demonstrating that the molecular conformation formed between purine and pyrimidine bases of Mixture 4 is different from that formed between purines or between purine and pyrimidine bases.