Helix-coil stability constants for the naturally occurring amino acids in water. XIII. The presence of by-products in amino-acid analysis of copolymers and their effect on the guest parameters; recomputed values of σ and s for L-serine

Previously used procedures for processing the amino acids from 6N hydrochloric acid hydrolysis of poly[N⁵-(4-hydroxybutyl)-L -glutamine], poly[N⁵-(3-hydroxypropyl)-L -glutamine], and several random copolymers derived from these, led to the formation of spurious products. These have been isolated and characterized as the γ-ester of glutamic acid and the hydroxyalkyl amine, and chloro-alkyl amine hydrochloride. The former reduces the observed values for glutamic acid, but the latter has no effect on them. A method is used to avoid formation of these artifacts in the amino-acid analysis. Of all the copolymers studied previously in this series, the compositions of only those containing L -serine are in error as a result of the formation of the γ-ester. A redetermination of the amino-acid compositions of the copolymer fractions studied earlier leads to slightly revised values for the Zimm-Bragg parameters σ and s of serine.     

Helix–coil stability constants for the naturally occurring amino acids in water. XXI. Glutamine parameters from random poly(hydroxypropylglutamine-co-L-glutamine) and poly(hydroxybutylglutamine-co-L-glutamine)

Water-soluble, random copolymers containing L -glutamine and either N⁵-(3-hydroxypropyl)-L -glutamine or N⁵-(4-hydroxybutyl)-L -glutamine were synthesized, fractionated, and characterized. The thermally induced helix–coil transitions of these copolymers were studied in water. A short-range interaction theory was used to deduce the Zimm-Bragg parameters σ and s for the helix–coil transition in poly(L -glutamine) in water from an analysis of the melting curves of the copolymers in the manner described in earlier papers. The computed values of s indicate that L -glutamine is helix-indifferent at low temperature and a helix-destabilizing residue at high temperature in water. At all temperatures in the range of 0–70°C, the glutamine residue promotes helix–coil boundaries since the computed value of σ is large.     

Rigidity of α-helical polypeptides. A new method of obtaining the persistence length from viscosimetric data

The hydrodynamic properties of α-helical poly(L -glutamic acid), (Glu)_n in aqueous solutions and in mixtures of water with organic solvents have been interpreted in terms of the persistence length of the macromolecule. A modification of the method of Vitovskaya and Tsvetkov has been proposed in order to allow a more accurate determination of this parameter. The addition of an organic solvent increases strongly the rigidity of the helical conformation of (Glu)_n. A comparison is made with some data of the literature of poly[N⁵-(3-hydroxy propyl)L -glutamine], [Gln(CH₂)₃OH]_n, and poly(γ-benzyl-L -glutamate), [Glu(OBzl)]_n.     

Helix-coil stability constants for the naturally occuring amino acids in water. XIV. Methionine parameters from random poly(hydroxypropylglutamine,L-Methionine)

Water-soluble, random copolymers containing L -methionine and N⁵-(3-hydroxypropyl)-L -glutamine have been prepared, fractionated, and characterized. The thermally induced helix-coil transitions of these copolymers in water have been investigated, and it has been found that incorporation of L-methionine increases the helix content of the polymers at all temperatures in the range of 0–60°C. The Zimm-Bragg parameters σ and s for the helix-coil transition in poly(L -methionine) in water were deduced from an analysis of the melting curves of the copolymers using the methods described in earlier papers.     

Action of the Protease from Streptomyces cellulosae on l-Leu-Gly-Gly

We introduced efficient incorporation of unsaturated fatty acids into volicitin [N-(17-hydroxylinolenoyl)-L-glutamine] and N-linolenoyl-L-glutamine, insect-derived elicitors of plant volatiles, in the common cutworms Spodoptera litura by the incubation of larval gut tissues with unsaturated (linolenic, linoleic, and oleic acids) or saturated fatty acids (palmitic and stearic acids) sodium salt, and L-[α-¹⁵N]glutamine.     

Helix-coil stability constants for the naturally occurring amino acids in water. XII. Asparagine parameters from random poly(hydroxybutylglutamine-co-L-asparagine)

The synthesis and characterization of water-soluble random copolymers containing L -asparagine with N⁵-(4-hydroxybutyl)-L -glutamine, and the thermally induced helix-coil transitions of these copolymers in water, are described. The incorporation of L -asparagine was found to decrease the helix content of the polymers in water at all temperatures. The Zimm-Bragg parameters σ and s for the helix-coil transition in poly(L -asparagine) in water were deduced from an analysis of the copolymer melting curves in the manner described in earlier papers. The computed values of s indicate that asparagine destabilizes helical sequences at all temperatures in the range 0–60°C.     

Solution properties of synthetic polypeptides. VI. Helix-coil transition of poly-N5-(3-hydroxypropyl)-L-glutamine

A new procedure for evaluating u and σ characterizing σ-helix-forming polypeptides in solution was derived from Nagai's theory for the helix–coil transition of such polymers. Here u is the activity for helix formation from random coil, and σ is the helix initiation parameter. The necessary data are the helical content f_N at fixed solvent and temperature as a function of N, where N is the degree of polymerization of the polypeptide sample. Such data were obtained from ORD measurements on a number of fractionated samples of poly-N⁵-(3-hydroxypropyl)-L -glutamine (PHPG) in mixtures of water and methanol covering the complete range of composition and at various termperatures (5–40°C). When analyzed in terms of the proposed procedure, they yielded values of σ which were in the range (3.2 ± 0.6) × 10^?4, substantially independent of solvent composition and temperature. These values were much larger than those obtained recently for σ of poly(β-benzyl-L -aspartate) in m-cresol and in a mixture of chloroform and DCA. The data for [η] and s₀ (limiting sedimentation coefficient) as functions of molecular weight indicated that the molecular shape of PHPG in pure methanol is essentially rodlike, whereas that in pure water is not entirely randomly coiled but rather may be regarded as an interrupted helix. These indications were consistent with the results from ORD measurements. When plotted against the corresponding values of f_N, the values of [η] and [s₀] for PHPG in mixtures of water and methanol of various compositions and temperatures formed smooth composite curves, and we attributed these phenomena to the fact that σ of PHPG was nearly constant under these solvent conditions. Here [s₀] stands for a reduced limiting sedimentation coefficient which is equal to the inverse friction factor of the solute molecule.     

Conformational behavior of poly-N5-(3-hydroxypropyl)-L-glutamine in water-methanol mixtures studied by 13C Nmr and CD spectroscopy

The helix–coil transition of poly-N⁵-(3-hydroxypropyl)-L -glutamine (PHPLG) has been studied in methanol–water by CD and cmr spectroscopy. For polydisperse PHPLG, two separate peaks arising from residues in helical and random-coil conformations are observed during the transition for both main-chain carbons. These results are discussed and compared to those observed in the case of a polymer sample obtained by racemization of PHPLG in 0.1 M NaOH and of PHPLG samples of controlled molecular weight and dispersity. The dominant influence of the molecular-weight heterogeneity on the double-peak phenomenon has been verified. The linewidths and chemical shift of the ¹³C resonances are discussed in terms of side-chain–main-chain interactions and side-chain solvation.     

Experimental characterization of poly(hydroxyalkyl-L-glutamine) conformations in aqueous calcium chloride and sodium perchlorate solutions

Poly(hydroxyalkyl-L -glutamine) (alkyl = ethyl, propyl, butyl) solutions have been studied by CD as functions of temperature and activity of calcium chloride and sodium perchlorate. Helical content is altered by changes in salt activity and temperature. The helicity of poly(hydroxybutyl-L -glutamine) and poly(hydroxypropyl-L -glutamine) falls to zero in a monotonic fashion with increasing calcium chloride activity. A nonzero helicity reappears at activities in excess of 5–50 mol kg^?1. Poly(hydroxypropyl-L -glutamine) is much more sensitive to calcium chloride than is poly(hydroxybutyl-L -glutamine), and both polypeptides are more sensitive to calcium chloride than are typical proteins. Markedly different behavior is observed with sodium perchlorate. This salt acts as a helix stabilizer at low activities but becomes a destabilizer at activities higher than 0.3–1.0 mol kg^?1. In this respect the effect of sodium perchlorate on nonionic poly(hydroxyalkyl-L -glutamines) resembles that seen with cationic poly(L -lysine) and poly(L -arginine). Helix stabilization at low sodium perchlorate activity is moderate for poly(hydroxybutyl-L -glutamine) and large for poly(hydroxypropyl-L -glutamine) and poly(hydroxyethyl-L -glutamine).     

13C nmr study of the helix–coil transition of poly-N5-(3-hydroxypropyl)-L-glutamine

The helix–coil transition of poly-N⁵-(3-hydroxypropyl)-L -glutamine in methanol–water solutions has been observed using ¹³C nuclear magnetic resonance. Two signals appear in the α-CH region in the course of the transition; this is in contrast with previous proton magnetic resonance experiments carried out on this polymer in the same solvent system.     

Novel semicarbazones based 2,5-disubstituted-1,3,4-oxadiazoles: One more step towards establishing four binding site pharmacophoric model hypothesis for anticonvulsant activity

A series of novel N¹-{5-[(naphthalene-2-yloxy)methyl]-1,3,4-oxadiazol-2-yl}-N⁴-(4-substitutedbenzaldehyde)-semicarbazone, N¹-{5-[(naphthalene-2-yloxy)methyl]-1,3,4-oxadiazol-2-yl}-N⁴-[1-(4-substitutedphenyl)ethanone]-semicarbazone and N¹-{5-[(naphthalene-2-yloxy)methyl]-1,3,4-oxadiazol-2-yl}-N⁴-[1-(4-substitutedphenyl) (phenyl) methanone]-semicarbazone were designed and synthesized on the basis of semicarbazone based pharmacophoric model to meet the structural requirements necessary for anticonvulsant activity. The anticonvulsant activities of the compounds were investigated using maximal electroshock seizure (MES), subcutaneous pentylenetrtrazole (scPTZ) and subcutaneous strychnine (scSTY) models. Some of the selected active compounds were subjected to GABA assay to confirm their mode of action. The efforts were also made to establish structure activity relationships among synthesized compounds. The results of the present studying validated that the pharmacophoric model with four binding sites is essential for anticonvulsant activity.     

Facile synthesis of carbon-11-labeled cholesterol-based cationic lipids as new potential PET probes for imaging of gene delivery in cancer

Gene therapy based on gene delivery is a promising strategy for the treatment of various human diseases such as cancer. Cationic lipids represent one of the important synthetic gene delivery systems. There is a great interest in imaging of gene therapy using the biomedical imaging technique positron emission tomography (PET). Carbon-11-labeled cholesterol-based cationic lipids were first designed and synthesized as new potential PET probes for imaging of gene delivery in cancer. The [¹¹C-methyl]quaternary amine target tracers, N-[¹¹C]methyl-N-[4-(cholest-5-en-3β-yloxycarbonyl)butyl]pyrrolidinium iodide ([¹¹C]4a), N-[¹¹C]methyl-N′-[4-(cholest-5-en-3β-yloxycarbonyl)butyl]imidazolium iodide ([¹¹C]4b), N-[¹¹C]methyl-N-[4-(cholest-5-en-3β-yloxycarbonyl)butyl]piperidinium iodide ([¹¹C]4c), N-[¹¹C]methyl-N-[4-(cholest-5-en-3β-yloxycarbonyl)butyl]-4-methylpiperidinium iodide ([¹¹C]4d), and N-[¹¹C]methyl-N-[4-(cholest-5-en-3β-yloxycarbonyl)butyl]morpholinium iodide ([¹¹C]4e), were prepared from their corresponding tertiary amine precursors with [¹¹C]methyl iodide ([¹¹C]CH₃I) through N-[¹¹C]methylation and isolated by a simplified solid-phase extraction (SPE) method using a Silica Sep-Pak cartridge in 50-60% radiochemical yields decay corrected to end-of-bombardment (EOB), based on [¹¹C]CO₂, and 111-185 GBq/μmol specific activity at the end of synthesis (EOS).     

Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications

The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure–property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above ~0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA) · poly(dT) and poly(dG) · poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least ~11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]⁺. These structure–property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.     

Dansylcadaverine specific staining for transamidating enzymes.

Versatile fluorescent staining methodologies, based on the incorporation of dansylcadaverine[N-(5-aminopentyl)-5-dimethylamino-l-naphthalenesulfonamide] into N,N-dimethylcasein, are described for the detection of transamidating enzymes of the endo-γ-glutamine:ε-lysine transferase type. Activity staining was employed for comparing the electrophoretic behaviors of such transamidating enzymes derived from human and guinea pig tissues. Two enzymatically active forms of guinea pig liver transglutaminase were found.     

On the nature of interaction of dodecyl sulfate with proteins. Evidence from uncharged polypeptides

Circular dichroism and equilibrium dialysis measurements in aqueous solution reveal no strong interaction between dodecyl sulfate and the unionized polypeptides poly(N⁵-ω-hydroxyethyl-L-glutamine), poly(N⁵-ω-hydroxypropyl-L-glutamine) and poly(N⁵-bis(ω-hydroxyethyl)-L-glutamine). Dodecyl sulfate does not affect the stability of the helical forms of poly(N⁵-ω-hydroxypropyl-L-glutamine) and poly(N⁵-bis(ω-hydroxyethyl)-L-glutamine) in water.     

Synthesis and conformational study of poly(N -benzyl-L-lysine) and its benzyloxycarbonyl derivative

The solvent-and pH-induced conformational changes are examined in order to investigate the influence of benzyl group. Polymer was prepared via N^?-benzyloxycarbonyl, N^?-benzyl-N^α-carboxy-L -lysine anhydride. The resulting poly (N^?-benzyloxycarbonyl, N^?-benzyl-L -lysine) was obtained in high yield and had a high molecular weight. The protected polymer was removed into poly (N^?-benzyl-L -lysine) by treating it with hydrogen bromide. From the results of the ORD and CD, the protected polymer has a righthanded α-helix, showing [m′]₂₃₃ = –10,300, [θ]₂₂₀ = –27,600 and [θ]₂₀₇ = –25,100 in dioxane. The breakdown of the helical conformation is found to occur at 8% dichloroacetic acid in chloroform-dichloroacetic acid mixture. In the pH range 3.35–6.90, poly (N^?-benzyl-L -lysine) is in a random coil structure. In the pH range 7.50–13.0, the polypeptide has a right-handed α-helix structure; [m′]₂₃₃ = –12,000, [0]₂₂₀ = –27,200, and [0]₂₀₇ = –27,000. In comparison with poly-L -lysine, the coil-to-helix transition is observed at lower pH range in 50% n-propanol. Above pH 8 by heating, the α ? β transition of poly (N^?-benzyl-L -lysine) is not observed in an aqueous media.     

Amino acid conjugates as metabolites of the plant growth regulator dihydrojasmonic acid in barley (Hordeum vulgare)

The biotransformation of [2-¹⁴C](±)9, 10-dihydrojasmonic acid (DJA) was studied in excised shoots of 6-day-old barley seedlings after 72 h. From the ethyl acetate extract, some minor metabolites were isolated and purified by DEAE-Sephadex A-25 chromatography, thin-layer chromatography (TLC), C₁₈-cartridges, and high-performance liquid chromatography (HPLC). The structural identification of these metabolites was performed by gas chromatography-mass spectrometry (GC-MS), circular dichroism (CD), and amino acid analysis, and the following amino acid conjugates were found:N-[(–)9,10-dihydrojasmonoyl]valine,N-[(–)9,10-dihydrojasmonoyl]isoleucine,N-[9,10-dihydrojasmonoyl]leucine,N-[11-hydroxy-9,10-dihydrojasmonoyl]valine,N-[11-hydroxy-9,10-dihydrojasmonoyl]isoleucine,N-[12-hydroxy-9,10-dihydrojasmonoyl]isoleucine; and the cucurbic acid-related compoundsN-{[3-hydroxy-2(4-hydroxypentyl)-cyclopent-1-yl]-acetyl}isoleucine andN-{[3-hydroxy-2(5-hydroxypentyl)-cyclopent-1-yl]-acetyl}isoleucine. The results suggest conjugation with isoleucine and valine, as well as preferential hydroxylation at position C-11 or hydrogenation at position C-6, as being important steps in the metabolism of (±)DJA in barley shoots.     

The Synthesis of New Polymer Derivatives of ATP by Radical Copolymerization and Their Coenzymic Activity

Three polymerizable ATP derivatives, N⁶-[N-(6-methacrylamidohexyl)carbamoylmethyl]-, N⁶-[N -[2-[N -(2-methacrylamidoethyl)carbamoyl]ethyl]carbamoylmethyl]-, and N⁶ -[N -[N -(2-hydroxy- 3-methacrylamidopropyl)carbamoylmethyl]carbamoylmethyl]-ATP, were synthesized and radically copolymerized with comonomers [acrylamide, N -(2-hydroxyethyl)-, N -ethyl-, N, N - diethylacrylamide, acrylic acid, and 6-methacrylamidohexylammonium chloride] to obtain 18 new polymer derivatives of ATP. The molecular weight distributions were controlled by appropriate initiator concentrations. The monomeric and polymeric ATP derivatives were all coenzymically active against both hexokinase and glycerol kinase. The observed coenzymic activities (Km and V_max) are discussed in connection with the structures of the derivatives.     

Synthesis, characterization and X-ray crystal structure of [Re(L4)(CO)3]Br · 2CH3OH (L4 = N,N-bis[(2-diphenylphosphino)ethyl]methoxyethylamine): A model compound for novel cationic Tc(I)-tricarbonyl radiotracers useful for heart imaging

This report describes synthesis and evaluation of cationic complexes, [^99mTc(CO)₃(L)]⁺ (L = N-methoxyethyl-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L1), N-[(15-crown-5)-2-yl]-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L2) and N-[(18-crown-6)-2-yl]-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L3)) as potential radiotracers for heart imaging. Preliminary results from biodistribution studies in female adult BALB-c mice indicated that the cationic ^99mTc(I)-tricarbonyl complex, [^99mTc(CO)₃(L2)]⁺, has a significant localization in the heart at 60 min post-injection. To understand the coordination chemistry of these bisphosphine ligands with the ^99mTc(I)-tricarbonyl core, we prepared [Re(CO)₃(L4)]Br (L4: N,N-bis[(2-diphenylphosphino)ethyl]methoxyethylamine) as a model compound. [Re(CO)₃(L4)]Br has been characterized by elemental analysis, IR, ESI-MS, NMR (¹H, ¹³C, ¹H-¹H COSY, and ¹H-¹³C HMQC) methods, and X-ray crystallography. In solid state, [Re(CO)₃(L4)]⁺ has a distorted octahedron coordination geometry with PNP occupying one facial plane. The chelator backbone adopts a “chair” conformation with phosphine-P atoms at equatorial positions and the amine-N at the apical site. In solution, [Re(CO)₃(L4)]⁺ is able to maintain its cationic nature with no dissociation of carbonyl ligands or any of the three PNP donors.     

Conformational studies of sequential polypeptides containing lysine and tyrosine

The conformation of three sequential copolypeptides, poly(L -tyrosyl-L -lysine), poly(L -tyrosyl-L -lysyl-L -lysine), and poly[L -tyrosyl-(L -lysyl)₂-L -lysine] have been studied by a variety of techniques, including CD, ir spectroscopy, analytical ultracentrifugation, and x-ray diffraction. Depending upon the pH and sovent composition, poly(L -tyrosyl-L lysyl-L -lysine) and poly [L -tyrosyl-(L lysyl)₂-L -lysine] can adopt either the α-helical or random-coil conformation, while poly(L -tyrosyl-L -lysine) forms either inter- or intramolecular β-structures.