bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymerization of L‐ and DL‐phenylalanine N‐carboxyanhydride by poly(N‐methyl‐L‐alanine)
Authors: Imanishi Yukio , Kugimiya Kazuya , Higashimura Toshinobu 
Published: December 2004

AbstractPolymerizations of L‐ and DL‐phenylalanine N‐carboxyanhydride in nitrobenzene by poly (N‐methyl‐L‐alanine) of varying degrees of polymerization (n = 1–30) were investigated. Poly(N‐methyl‐L‐alanine) was prepared by the polymerization of N‐methyl‐L‐alanine NCA with N‐methyl‐L‐alanine diethylamide and the degree of polymerization was controlled by the molar ratio [NCA]/[Catalyst] + 1. This polymer was shown to be an asymmetrically selective catalyst which polymerized L‐phenylalanine NCA at a faster rate than DL‐phenylalanine NCA. With increasing degree of polymerization the stability of the secondary structure of poly(N‐methyl‐L‐alanine) increased. This was confirmed by circular dichroism spectra. However, the degree of asymmetric selection did not increase as the stability of the secondary structure of poly(N‐methyl‐L‐alanine) increased. These findings indicate that the interaction of a growing polypeptide in an ordered structure with NCA molecules prior to the reaction does not lead to an asymmetric selection, and that the mechanism of the asymmetric selection by poly(N‐methyl‐L‐alanine) should be different from those proposed so far.
Nmr studies of poly‐γ‐benzyl‐L‐glutamate in trifluoroacetic/deuterochloroform solutions: Temperature dependence
Authors: Brosio E. , Delfini M. , De Paolis A. , Paci M. , Conti F. 
Published: December 2004

AbstractThe helix–random‐coil transition process for poly‐γ‐benzyl‐L‐glutamate (PBG) in solvent mixtures trifluoroacetic acid/deuterochloroform (TFA/CDCl3) at different temperatures has been studied by nmr. The chemical shift behavior of the α‐CH resonances of the peptide chain and of the TFA carboxylic protons is reported.
The formation of the triple helix in a mixed solution of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n′. A model of molecular size recognition
Authors: Suezaki Yukio , Gō Nobuhiro 
Published: December 2004

AbstractA theoretical analysis is given of the triple‐helix–random‐coil transition in a mixed solution of poly(Pro‐Pro‐Gly)n with two different but defined degrees of polymerization n and n′. Because of the highly cooperative nature of this helix–coil transition, each polypeptide chain tends to form a triple helix with other polypeptide chains with the same degree of polymerization (size recognition). Occurrence of triple helices consisting of polypeptide chains with different degrees of polymerization (error in recognition) is studied in detail as a function of the cooperativity, and n and n′. Implication of this analysis for molecular recognition in general is discussed.
Synthesis of a novel fluorescent polyriboadenylic acid analog by polynucleotide phosphorylase
Authors: Tsou K. C. , Yip K. F. 
Published: December 2004

AbstractPoly(1,N6‐etheno‐2‐aza‐adenylic acid) [poly(2‐aza‐εA)] was synthesized from 1,N6‐etheno‐2‐aza‐adenosine 5′‐diphosphate (2‐aza‐εADP) and Escherichia coli polynucleotide phosphorylase. The values Km = 1.02 mM, V = 1.06 μmol hr−1 enzyme unit−1 were found for the polymerization reaction. In contrast to polyadenylic acid, this novel fluorescent polymer has a random structure in solution. The application of the 2‐aza‐εADP for localization of polynucleotide phosphorylase was also described.
Solution properties of synthetic polypeptides. XVII. Stability of the α‐helical conformation of poly(γ‐benzyl L‐glutamate) in helicogenic solvents
Authors: Matsumoto Tadao , Teramoto Akio 
Published: December 2004

AbstractThe Zimm–Bragg parameters s and σ were determined for poly(γ‐benzyl L‐glutamate) (PBLG) in m‐cresol and in dimethylformamide (DMF) from ORD data as a function of molecular weight. It was found that, within the temperature range between 10 and 55°C and on the average, s = 1.61 ± 0.1 and √σ = 0.04 ± 0.01 in m‐cresol and s = 1.65 ± 0.05 and √σ = 0.045 ± 0.015 in DMF. The values of s in m‐cresol decreased with increasing temperature, while the values of σ in the same solvent increased. This result for s suggests that PBLG in m‐cresol will undergo a thermal helix–coil transition of normal type. The parameters in DMF showed no appreciable trend to vary with temperature. Aside from the difference between the two solvents, our results are consistent with existing data for various conformation‐dependent properties such as light‐scattering radius, intrinsic viscosity, and dipole moment, each indicating that the polypeptide chain has some flexibility in helicogenic solvents.
Conformations of cyclic 2′,3′‐nucleotides and 2′,3′‐cyclic‐5′‐diphosphates. Interrelation between the phase angle of pseudorotation of the sugar and the torsions about the glycosyl C(1′)–N and the backbone C(4′)C(5′) bonds
Authors: Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractSemiempirical potential energy calculations have been carried out for cyclic 2′,3′‐nucleotides and their 5′‐phosphorylated derivatives, which are the intermediates in the hydrolysis of RNA. Calculations have been performed for both purine and pyrimidine bases for the observed O(1′)‐endo, O(1′)‐exo and the unpuckered planar sugar ring conformations. It is found that the mode of sugar pucker largely determines the preferred conformations of these molecules. For cyclic 2′,3′‐nucleotides themselves, the O(1′)‐endo sugars show a preference for the syn glycosyl conformation while the O(1′)‐exo sugars exclusively favor the anti conformation regardless of whether the base is a purine or pyrimidine. For the unpuckered planar sugar, the syn conformation is favored for purines and anti for pyrimidines. Both the gauche (+) (60°) and trans (180°) conformations about the C(4′)C(5′) bond are favored for O(1′)‐endo sugars, while the gauche (−) (300°) and trans (180°) are favored for O(1′)‐exo sugars. On the contrary, the 5′‐phosphorylated cyclic 2′,3′‐nucleotides of both purines and pyrimidines show a preference for the anti‐gauche (+) conformational combination about the glycosyl and C(4′)C(5′) bonds for the O(1′)‐endo sugars and the anti‐trans combination for the O(1′)‐exo sugars. The correlation between the phase angle of the sugar ring and the favored torsions about the glycosyl and the backbone C(4′)C(5′) bonds as one traverses along the pseudorotational pathway of the sugar ring is examined.
Conformation of histidine model peptides. I. Conformational energy calculations for L‐alanyl‐L‐histidine diketopiperazine
Authors: Grebow Peter E. , Hooker Thomas M. 
Published: December 2004

AbstractSemiempirical conformational energy calculations were carried out for the cyclic dipeptide L‐alanyl‐L‐histidine diketopiperazine. The results indicate that electrostatic effects are probably significant in determining the conformation assumed by this molecule. When the imidazole group is in its uncharged state the most stable conformations of the molecule are those with the imidazole ring folded over the diketopiperazine ring (χ1 = 60°). Upon protonation of the imidazole group the folded conformation may be destabilized relative to conformations characterized by χ1 positions near 180°.
The physical properties and molecular structure of Ligamentum Nuchae elastin
Authors: Mukherjee Debi P. , Hoffman Allan S. , Franzblau Carl 
Published: December 2004

AbstractThe swelling and equilibrium stress–strain behavior of elastin in formamide and in its aqueous solution shows a “loosening” effect on the structure of elastin. The nature of the changes are irreversible even after the solvent has been leached out. The possible reason for such structural changes may relate to hydrophobic bonding and hydrogen bonding. Enzymatic studies on the hydrolysis of formamide treated and untreated elastin confirm these same observations.
Raman studies of the crystalline, solution, and alkaline‐denatured states of β‐lactoglobulin
Authors: Frushour B. G. , Koenig J. L. 
Published: December 2004

AbstractThe Raman spectra of β‐lactoglobulin in the crystalline, freeze‐dried, and solution states are compared. The spectra of the freeze‐dried and crystalline proteins were practically identical. The conformationally sensitive amide III line appearing at 1242 cm−1 increased in intensity 30% upon dissolution of the protein in water which is interpreted as a conformational change in the disordered chains of the protein. This result appears to be a phenomenon for globular proteins containing a large disordered chain fraction.The alkaline denaturation of β‐lactoglobulin was studied. When the pH was increased from 6.0 to 11.0, the amide III line shifted from 1242 to 1246 cm−1, broadened, and decreased in intensity. This is consistent with the conversion of β‐sheet regions in β‐lactoglobulin to the disordered conformation, as has been proposed by other investigators. At pH 13.5 the amide III shifts to 1257 cm−1 characteristic of a completely disordered protein, indicating that any remaining “core” of β‐sheet has been randomized.Several changes in the intensities of the tyrosine and tryptophan vibrations accompany the denaturation. As the pH is increased from 6.0 (native state) to 11.0 (denatured state) the intensity ratio of two tyrosine ring vibrations, I855 cm−1/I830 cm−1, decreases from 1.0:0.9 to 1.0:1.3. The same ratio for a copolymer consisting of 95% glutamic acid and 5% tyrosine at pH 7.0, where the polymer forms a random coil exposing the tyrosine to the aqueous environment, is 1.0:0.62. This ratio more closely resembles that corresponding to β‐lactoglobulin at pH 6.0 (native state) than pH 11.0 (denatured state) suggesting that the average tyrosine in the denatured state may be in a more hydrophobic environment than in the native state. A time‐dependent polymerization of the denatured protein reported by other investigators and observed by us may account for the change in the tyrosine environment.A tryptophan vibration appearing at 833 cm−1 in the spectrum of the native state becomes weak as the pH is increased to 11.0. The intensity of this line may also reflect the local environment of the tryptophan residue.
Studies on deoxyribonucleoprotein structure. Small‐angle X‐ray scattering in solutions of various ionic strengths
Authors: Aleksanyan V. I. , Vorob'ev V. I. , Fedorov B. A. 
Published: December 2004

AbstractThe cross‐sectional radius of gyration of the deoxyribonucleoprotein (DNP) threads was measured by small‐angle X‐ray scattering in a wide range of ionic strengths (from 0.0005 to 2 M NaCl). For DNP in a solution of low ionic strength, this value is 30 Å. The increase of ionic strength results in partial deproteinization of DNP, while the cross‐sectional radius of gyration varies from 25 Å for DNP in 0.7 M NaCl to 10 Å for DNP in 2 M NaCl. It is suggested that gradual deproteinization by the increase of NaCl concentration causes conformational changes, which are associated with the alteration of the DNP superstructure. The data are interpreted on the basis of the superhelical model of DNA packing in DNP; however, the coexistence of superhelical and unfolded regions in the DNP structure is also a possibility.
Gel formation from solutions of single‐chain gelatin
Authors: Finer E. G. , Franks F. , Phillips M. C. , Suggett A. 
Published: December 2004

AbstractThe changes in conformation undergone by α‐gelatin molecules on quenching aqueous solutions to below the temperature at which they can gel have been monitored by nuclear magnetic resonance and dielectric relaxation techniques. The relative rates of these conformational transitions are compared with changes in rheological properties. The nmr spectral intensity changes for 0.2 and 0.5% w/v α‐gelatin solutions correspond to a unimolecular process with k ∼ 10−2 min−1 at 15°C; this process occurs independently of whether or not the solution is concentrated enough to form a gel. The process involves a slow intramolecular nucleation step, followed by a rapid conformational change of the whole molecule from random coil to a rigid stage. Comparison with other data suggests that the transition gives rise to a triple collagen‐like helix. In dilute solution (but above the critical concentration for gel formation, e.g., 0.5% w/v), the gelatin process follows the formation of the rigid molecular species. It probably involves the formation of junction zones consisting of three polypeptide chains in a collagen‐like triple‐helical conformation. These junctions may form, at low concentrations, from a reorganization of previously formed, intramolecular, triple helices. Solutions below a concentration of about 0.4% w/v α‐gelatin cannot gel by this mechanism, and only form viscous liquids.
Synthesis of poly(L‐Tyr‐L‐Glu‐L‐Ala‐Gly) and poly(L‐Glu‐L‐Lys‐L‐Ala) and their circular dichroism spectra in aqueous solution
Authors: Zeiger Allen R. , Lai Chang‐Hai , Maurer Paul H. 
Published: December 2004

AbstractTwo sequential polypeptides, poly(O‐benzyl‐L‐Tyr‐γ‐benzyl‐L‐Glu‐L‐Ala‐Gly) and poly(ε‐benzyloxycarbonyl‐L‐Lys‐L‐Glu‐L‐Ala), were synthesized, the former by the pentachlorophenyl ester of the tetrapeptide monomer and the latter by the azide of the tripeptide monomer. After deprotection and dialysis, poly(L‐Tyr‐L‐Glu‐L‐Ala‐Gly) was obtained in 71% yield and had a molecular weight of 53,000. The circular dichroism spectra (CD) of the polymer at pH's 7.2, 10.5, and 11.8 and of oligomers and of the monomer at pH 7.2 indicated that the polymer exists in an α‐helical conformation.After deprotection, poly(L‐Lys‐L‐Glu‐L‐Ala) was obtained in 37% yield and had a molecular weight of 3000. The CD spectra of the polymer at pH 7.2 and 2.8, and of the monomer at pH 7.2, indicated that the polymer is in a randomly coiled configuration.
Potentiometric studies of hydrophobic effect on ion binding of ionic dextran derivatives
Authors: Gekko Kunihiko , Noguchi Hajime 
Published: December 2004

AbstractIn order to clarify the effect of degree of substitution of ionic and hydrophobic group on the polyelectrolytic behavior of polysaccharides, potentiometric titration and activity measurement of counterions were made for carboxymethyldextran (Cm‐dextran) having various degrees of substituted carboxyl group and for carboxymethylbenzyldextran (Cm‐Bzl‐dextran) containing various degrees of substituted benzyl group. From the shape of titration curve, no conformational change was observed for both Cm‐dextran and Cm‐Bzl‐dextran. The pK0 value of Cm‐dextran was independent of the degree of the degree of substituted carboxy group. However, the pK0 of Cm‐Bzl‐dextran increased with an increasing degree of substituted benzyl group. The suppression of dissociation of a carboxyl group, caused by the surrounding hydrophobic groups, was discussed mainly in terms of the change of water structure around such groups. From the results of activity measurement for counterions of these dextran derivatives, we proposed the possibility of ion selectivity based on the hydrophobicity.
Conversion of fibrinogen to fibrin. The correlation between clotting kinetics and morphology of fibrin polymerized in different solvent media
Authors: Conio G. , Trefiletti V. , Troglia C. , Patrone E. 
Published: December 2004

AbstractThe morphology of fibrin strongly depends on solvent medium, as shown by clotting experiments carried out in the presence of different salts. The clots were characterized by electron microscopy and spectrophotometric methods; the kinetics of gelation were determined.In the presence of electrolytes which strongly delay clotting, the strands are thin and few branching points are observed; opposite morphological changes are induced by salts which act as accelerating agents. On the basis of this correlation, and of previous data on the structure of fibrin, a kinetic model of the self‐assembly process is outlined. It accounts well for the observed solvent effects on the morphology of the network.An important result emerging from our experiments is that the fibers undergo branching prior to gelation. Branching points arise from the defective growth of the fibers; a simple explanation of the occurrence of branching may be obtained by our self‐assembly model.
Ferric complexes of acetoacetyl derivatives of poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid). I. Preparation and absorption properties in solution
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Bacchion G. , Peggion E. 
Published: December 2004

AbstractPoly(Nε‐acetoacetyl‐L‐lysine), poly(Nδ‐acetoacetyl‐L‐ornithine) and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid) form colored complexes with ferric ions in water/dioxane solutions. These complexes are soluble at pH values lower than 2.8 and show their maximum absorption at 257 nm in the uv and at 478 nm in the visible region; whereas the ferric complex of the model compound n‐hexylacetoacetamide exhibits absorptions centered at 258 and 536 nm, respectively. It is shown that in the complex of the model compound one metal ion is bound per acetoacetamide group, while in the complexes of the three polymers two β‐ketoamides side chains are bound per ferric ion under the same solvent, pH, concentration, and ionic strength conditions. The binding constants of ferric ions to the three polymers, and the formation constant of the ferric complex of the model compound are also evaluated.
Intensity fluctuation spectroscopy of deoxyribonucleic acid (DNA). I. Temperature profile of bacteriophage N1‐DNA
Authors: Schmidt R. L. , Boyle J. A. , Mayo John A. 
Published: December 2004

AbstractIntensity‐fluctuation laser‐light‐scattering spectroscopy has been used to characterize the temperature dependence of the translational diffusion coefficient through the helix–coil region for the DNA isolated from bacteriophage N1. The diffusion coefficient does not change smoothly, but exhibits fine structure detail similar to that seen in the uv absorption hyperchromicity. These changes are related to the heterogeneous distribution of bases along the N1‐DNA chain.
Theory of protein molecule self‐organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments
Authors: Finkelstein A. V. , Ptitsyn O. B. , Kozitsyn S. A. 
Published: December 2004

AbstractConstants of the helix–coil transition for all natural amino acid residues are evaluated on the basis of thermodynamic parameters obtained in paper I of this series. The specific effects at the termini of the helices are also considered as well as the parameters controlling the formation of β‐bends in the unfolded protein chain. Evaluated s constants of the helix–coil transition agree with the experimental data on helix–coil transitions of synthetic polypeptides in water. Only a very qualitative correlation exists between s constants (both experimental and theoretical) and the occurrence of corresponding residues in internal turns of α‐helices in globular proteins: residues with s > 1 occur in helices as a rule more often than residues with s < 1. At the same time a direct correlation is demonstrated between theoretical parameters of residue incorporation into α‐helical termini and β‐bends in an unfolded polypeptide chain and the occurrence of residues in corresponding positions of the globular protein secondary structures.
Transient electric birefringence of T‐even bacteriophages. III. T2L and T6 with retracted fibers compared with T4B
Authors: Boontje W. , Greve J. , Blok Joh. 
Published: December 2004

AbstractMeasurements of birefringence are used to study electro‐optical and hydrodynamical properties of the bacteriophages T2 and T6 under conditions in which the fibers are folded back along the tail.The rotational diffusion coefficients corrected to 25°C and water viscosity (D25,w) are 325 ± 12 sec−1 and 322 ± 12 sec−1, respectively. These values differ significantly from those reported for T4(D25,w = 280 ± 9 sec−1). This might be due to a difference in configuration. It could be shown that the orientation of T‐even bacteriophage particles in the electric field is largely due to a permanent dipole moment. This dipole moment can be calculated from the measurements and appeared to be dependent on ionic strength. At low ionic strength (pH 6) the dipole moments of T2 and T6 approach the values 4.1 × 10−25 C·m (1.24 × 105 D) and 6.6 × 10−25 C·m (2.0 × 105 D), respectively, which is much larger than the value of 0.8 × 10−25 C·m (0.24 × 105 D) found for T4. An increase in ionic strength decreases the permanent dipole moment. This effect can be described by a Debye–Hückel model of the screening of surface charges by counterions in the case of T4 and T6. For T2 the picture is more complicated, as an increase in buffer concentration causes a change in configuration.
Cyclic peptides. XVIII. 13C spin‐lattice relaxation times of (X‐pro‐Y)2 cyclic hexapeptides
Authors: Niu C.‐H. , Pease L. G. , Blout E. R. 
Published: December 2004

Abstract13C spin‐lattice relaxation times (T1's) of four cyclic hexapeptides of sequence, (X‐L‐Pro‐Y)2, are reported. The T1's of the protonated carbons, which undergo dipolar relaxation, are interpreted qualitatively in terms of the overall tumbling motion of the molecule and in terms of internal motion. It is found that three of the cyclic hexapeptides, those which adopt all‐trans β‐conformers, tumble isotropically and appear to lack internal motion in the peptide backbone. The method of Torchia and Lyerla was applied to these compounds in order to compare the mobility of the proline rings. The results show that the sequence and particular type of β‐turn present affect the internal motion of the Pro ring. Data on a fourth cyclic hexapeptide, which occurs in a conformation with two‐cis X‐Pro bonds, suggests that internal motion of the backbone contributes an additional frequency component to the motion of the Y residue α‐carbons. A consideration of the mobility of the proline rings in the conformer with two‐cis peptide bonds revealed that they are significantly more rigid in the two‐cis structure than in the all‐trans.