bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and characterization of an ionizable polyhexapeptide collagen model
Authors: Sigler Gerald F. , McMillin Carl R. , Walton Alan G. 
Published: December 2004

AbstractPoly(Lys(HBr)‐Gly‐Pro‐Pro‐Gly‐Pro) has been synthesized and studied by circular dichroism (CD) spectroscopy. It is apparently the first polyhexapeptide collagen model reported with an ionizable side chain. The monomer (ε‐(p‐nitrobenzyloxycarbonyl)‐Lys‐Gly‐Pro‐Pro‐Gly‐Pro‐p‐nitrophenyl‐ester) was prepared by a stepwise strategy employing active esters. Polymerization in N,N‐dimethyl formamide, followed by removal of the Lys side chain protection with HBr/acetic acid, gave a polydisperse product. Fractionation was accomplished by gel filtration chromatography. The polydisperse material had a molecular weight (Mr = 5–17,000). High molecular weight fractions from triple helices under concentrated conditions at 2°C. The triple helical structure gives a CD pattern very similar to that of collagen and its triple helical analogs. However, unlike collagen, the polyhexapeptide undergoes spontaneous dissociation at temperatures substantially below the melting temperature from a triple helical form to single chains. This process is promoted at low concentrations, high temperature, neutral pH, and low molecular weight, and is apparently due, in large part, to unfavorable ionic side‐chain interactions. In addition to this relatively slow “ionic” dissociation the triple helical polypeptide may be thermally dissociated in a manner similar to collagen. The thermal denaturation is a relatively fast process compared with ionic dissociation.A high molecular weight fraction (3 × Mr = 48,000) was found to melt at 42°C at neutral pH but increased to 54°C at pH 12 where the lysyl side chains are predominantly deprotonated. Furthermore, reconstitution of triple helices appeared to be more readily achieved at high pH. Thus it is concluded that ionic repulsion between side chains causes destabilization of the triple helix and hinders reconstitution.
Étude thermodynamique de la transition hélice–pelote statistique en solvants mixtes de différents esters de l'acide poly(L‐glutamique)
Authors: Daoust Hubert , Choquette Michel , Hoduc Nga 
Published: December 2004

AbstractHelix–coil transition of poly(γ‐methyl‐L‐glutamate), poly(γ‐ethyl‐L‐glutamate), and poly(γ‐benzyl‐L‐glutamate) has been studied in mixed solvents by calorimetry, polarimetry, and viscometry. The experimental data have allowed the evaluation of solvation enthalpy Δhb, equilibrium constant K for hydrogen bond formation between the active solvent component and CO and NH groups, and the cooperativity parameter σ. The conformational transition of polypeptides in solution in a mixed solvent containing enough active solvent to maintain the coiled conformation has been produced by dilution with the helix‐supporting solvent for the measurements of enthalpy of transition Δhs. The average value for Δhs is 3550 ± 300 J/mol and is practically independent of the nature of the side chain for the dichloroacetic acid‐ethylene dichloride solvent pair at 25°C. A noticeable concentration effect exists in the case of poly(γ‐benzyl‐L‐glutamate). The helical conformation is less stable for poly(γ‐ethyl‐L‐glutamate), and this is explained by a steric effect hindering the access of dichloroacetic acid to side chains. Constant K has been calculated using polarimetric data and also from values of Δhs obtained at different temperatures using the Bixon and Lifson theory on the one hand and that of Sayama and coworkers on the other hand. Values of σ for poly(γ‐ethyl‐L‐glutamate) have been calculated according to both theories mentioned, and the results show that the two sets of values are quite similar. The constant σ depends on the nature of the active solvent, on temperature, and on the binary‐solvent composition. These conclusions are confirmed by viscometric results. Values of Δhb calculated from constant K are 5230 J/mol when Bixon and Lifson theory is used and 5569 J/mol when the theory at Sayama and coworkers is used. In both cases the value for Δhb is much lower than that of an intramolecular hydrogen bond. Experimental results suggest that the solvation mechanism would proceed in a manner so that mechanisms described in both theories are involved.
Specificity in the interaction between poly(L‐glutamate) and iron (III) complex ions in aqueous solution
Authors: Branca M. , Marini M. E. , Pispisa B. 
Published: December 2004

AbstractThe binding process between sodium poly(L‐glutamate) and trans‐2,2′,2″,2‴‐tetrapyridyl‐Fe(III) complex ions in aqueous solution at pH around 7 has been studied by means of equilibrium dialysis and optical measurements. The binding isotherm indicates the occurrence of a cooperative process, whereby bound molecules facilitate the association of additional molecules. According to circular dichroism (CD) data, this effect is coupled with that which sees a conformational change in the charged polypeptide upon progessive binding of complex counterions. All these features are discussed in the light of the structural characteristics of the interacting species. A stereochemical model of the association “complex” is proposed.
Fluorescence of proteins in aqueous neutral salt solutions. I. Influence of anions
Authors: Altekar Wijaya 
Published: December 2004

AbstractThe effects of anions of neutral salts on the fluorescence emission of six proteins as well as on tryptophan and tyrosine were studied in relation to the structure of proteins. Most anions are good quenchers of tryptophyl and tyrosyl fluorescence, free or in proteins. The results with tryptophan and tyrosine indicate involvement of a collisional quenching mechanism due to agreement with Stern–Volmer law. The deactivation of fluorescence probably occurs because of the transition from singlet state to triplet state. Lehrer's modification of Stern–Volmer law was applied to proteins. The effective quenching constants ([KQ]eff) and the fraction of fluorescence available ([fa]eff) to the quencher are also calculated.In contrast to its effect on tryptophan, CH3COO− quenches tyrosyl fluorescence and ClO4− does not. The effects on fluorescence of ribonuclease and free tyrosine are similar and without any changes in emission maximum. The anions are divided into three groups based on the effect they have on tryptophan‐containing proteins. (1) NO3−, NO2−, Br−, and I− have high [KQ]eff values and readily quench tryptophyl fluorescence of proteins causing a shift of emission maximum to a shorter wavelength. This change is due to the specific quenching of “exposed” tryptophan residues which are accessible to quenchers and the observed residual fluorescence is from the “buried” tryptophyls. (2) ClO4− and SCN− also quench fluorescence of tryptophan in proteins and have lower ([KQ]eff) values. In their presence the fluorescence maximum is shifted to a longer wavelength, which indicates the unfolding of a protein with [(fa)eff] = 1. (3) Cl−, CH3COO−, and SO4 do not have a direct effect on the fluorescence of tryptophan. Besides the “direct” effects, “indirect” effects on fluorophors in protein are also seen, pointing out that the neutral salts can interact in more than one manner with proteins. The effectiveness of anions in quenching fluorescence of proteins follows similar sequences which almost resemble the Hofmeister series, viz., SO4=, CH3COO− ≃ Cl− < ClO4− < SCN− < Br− < I− < NO3− < NO2−.
A general method for evaluation of diffusion constants, dilute‐solution viscoelasticity, and the dielectric property of a rigid macromolecule with an arbitrary configuration. I
Authors: Nakajima Haruhiko , Wada Yasaku 
Published: December 2004

AbstractAs the first part of the study on relaxational behavior of rigid macromolecules in solution, a general method for evaluating diffusion constants of a rigid macromolecule with an arbitrary configuration in a viscous solvent is presented. The evaluation is made by modeling the molecule with a rigid assembly of Stokes spheres. The diffusion constants are expressed by a 6 × 6 matrix which consists of translational, rotational, and cross constants, each being a 3 × 3 submatrix. Procedures of numerical calculation are presented for a given configuration of the molecule, together with some exemplifying results for the rigid rod, rigid sphere, and myosin molecule. The results for the rod and the sphere are compared with analytical results.
Binding of azide ion to methemoglobin at elevated temperatures and the reality of the “compensation” temperature
Authors: Anusiem A. C. I. , Ogunmola G. B. , Beetlestone J. G. 
Published: December 2004

AbstractWe have studied the binding of azide ion to ferrihemoglobin at elevated temperatures. Up to a temperature of 45°C there is no difference in the ligand binding behavior of hemoglobin when compared with the results obtained at lower temperatures. The compensation temperature Tc of 290.6 ± 5.3°K, obtained in this study within the temperature range 303–318°K, confirms that the compensation pattern obtained by Lumry and Rajender is not dependent on the temperature range of the experiment but an intrinsic property of the protein conformation.
Theory of DNA melting curves
Authors: Fixman Marshall , Freire Juan J. 
Published: December 2004

AbstractExact algorithms for the calculation of melting curves of heterogeneous DNA with N base pairs apparently require computer time proportional to N2. However, it is shown that a decomposition of the loop entropy factor into a sum of I exponential functions (1) gives an extremely accurate approximation to the loop entropy factor for small values of I and (2) makes the computer time for the exact algorithms proportional to I·N. In effect, exact results for melting curves and lengths of helix or coil stretches are obtained with computer time comparable to that required for the Frank‐Kamenetskii approximation. The remarkable accuracy of the latter for the fraction of helical content (errors of 0.01–0.05) is confirmed, but appreciably larger errors are found for the lengths of helix or coil stretches (typical errors of 30–100%).
Characterization of group C meningococcal polysaccharide by light‐scattering spectroscopy. III. Determination of molecular weight, radius of gyration, and translational diffusional coefficient
Authors: Tsunashima Y. , Moro K. , Chu B. , Liu T. Y. 
Published: December 2004

AbstractGroup‐specific polysaccharides isolated by means of a cetavlon procedure are immunogenic in man and induce protective immunity against meningococcal meningitis. Minute quantities of the polymers in solution can act as vaccines. We now report the first characterization of a fractionated (C‐1) group C polysaccharide in 0.4KM KCl and 0.05M sodium acetate by means of light‐scattering spectroscopy. Independent measurements of refractive index increments, absolute scattered intensities, angular scattering intensities and line widths as a function of scattering angles and delay times at different concentrations using incident wavelengths of 632.8 nm from a He–Ne laser and of 488 nm from an argon–ion laser yield information on aggregation properties, molecular weight (Mr), radius of gyration 〈r0g〉1/2z, translational diffusion coefficient 〈D〉0z, and second virial coefficients A2 and B2 of C‐1 polysaccharide.At relatively high ionic strength (0.04M KCl + 0.05M sodium acetate), we obtain for the C‐1 polysaccharide in solution Mr = 5.15 × 105, 〈r2g〉1/2z = 345 Å, A2 = 1.25 × 10−4 ml/g, 〈D〉 = 1.16 × 10−7 cm2/sec with a corresponding Stokes radius of 240 Å and B2 = 4.4 ml/g. A2 and B2 are the second virial coefficients from intensity‐ and diffusion‐coefficient measurements. The C‐1 polysaccharide aggregates in solution and behaves hydrodynamically like random coils. Viscosity and sedimentation studies further confirm our conclusions that the fractioned C‐1 polysaccharide aggregates in solution and EDTA can partially break up those aggregates. However, the system remains polydisperse even after adding an excess amount of EDTA. The weight‐average molecular weight of the C‐1 polysaccharide in solution depends upon ionic strength and exhibits a minimum at ∼0.2M KCl. Finally, viscosity, light‐scattering, and sedimentation results all show that the aggregated macromolecular system behaves like random‐coiled polymers with no measurable shape factors.
Collagen fibrils and elastic fibers in rat‐tail tendon: An electron microscopic investigation
Authors: Parry D. A. D. , Craig A. S. 
Published: December 2004

AbstractEarlier studies by the authors showed that the collagen fibrils in rat‐tail tendon have a bi‐modal distribution of fibril diameters from a time shortly after birth through to the onset of maturity at about 3–4 months. Present work has extended those observations for rats up to the age of 2 years. Histograms of the fibril diameter distributions for mature tail tendon and direct electron microscope observations show that the fibrils break down as the tendon ages. Further work on the constant diameter subfibrils of diameter 140 Å described previously, has confirmed that these are part of the elastic fibers present in tendon at all ages. It has been shown that there is relatively little variation in the collagen fibril diameter distribution as a function of the position of the specimen in the tail, and as the measured percentage of the area taken by the collagen fibrils present at any particular point. Estimation of the fibrillar collagen content of rat‐tail tendon as a function of age indicates that it increases steadily from birth and reaches a maximum at the onset of maturity, beyond which the fibrillar collagen content appears to remain constant.
Conformational studies on the pyridoxal Schiff bases of polypeptides
Authors: Dentini M. , Perretti G. , Savino M. , De Santis P. , Verdini A. S. 
Published: December 2004

AbstractThe pyridoxal Schiff bases of the polypeptides poly(L‐lysine), poly(L‐ornithine), and poly(L‐α,γ‐diaminobutyric acid) were prepared and investigated in water/methanol by CD spectra and equilibrium dialysis experiments. Only the poly(L‐α,γ‐diaminobutyric acid) derivative is characterized by a relevant optical activity similar to that found in pyridoxal enzymes. The stereospecific interactions between the pyridoxylideneimine group and the polypeptide chain prevent the hydrolysis reaction of the aldimine bond.
Conformation of amylose in water. I. Light‐scattering and sedimentation‐equilibrium measurements
Authors: Kodama M. , Noda H. , Kamata T. 
Published: December 2004

AbstractThe conformation of amylose in aqueous solution has been found to be dependent on its molecular weight. When the molecular weight of amylose is outside of the so‐called “dissolving gap” described by Burchard (6500<Mr<160,000) it behaves as a random coil, whereas when its molecular weight is within the “dissolving gap,” it easily aggregates forming a rigid coil which is the B‐type (retrograded) amylose. The conformation of this rigid coil is suggested to be a double helix.
Infrared spectra and structure of synthetic polytripeptides
Authors: Lazarev Yu. A. , Lazareva A. V. , Shibnev V. A. , Esipova N. G. 
Published: December 2004

AbstractA number of polytripeptides related to collagen, namely, (Gly‐Pro‐Pro)n, (Gly‐Pro‐Hyp)n, (Gly‐Hyp‐Hyp)n, (Gly‐Pro‐Ala)n, (Gly‐Pro‐Leu)n, (Gly‐Pro‐Gly)n,(Gly‐Ala‐Pro)n, (Gly‐Ala‐Hyp)n, (Ala‐Pro‐Pro)n, and (Ala‐Hyp‐Hyp)n were investigated by the method of ir spectroscopy and hydrogen‐deuterium kinetics. Strength and order of interpeptide hydrogen bonds of the polytripeptides in a triple‐helical conformation were found to depend on the amino acid composition and residue sequence in the triplets. Correlation of X‐ray diffraction and spectroscopic data for (Gly‐Pro‐Hyp)n showed that the increase of the helix parameter in the process of dehydration is accompanied with the weakening of interpeptide hydrogen bonds. Influences of bound water on the length and order of interchain hydrogen bonding was also examined. It was shown that the incorporation of water molecules into the triple helix depends on the amino acid composition and residue sequence. Synthetic models and native collagens were compared.
Optical properties and viscosity of hyaluronic acid in mixed solvents: Evidence of conformational transition
Authors: Park J. W. , Chakrabarti B. 
Published: December 2004

AbstractCircular dichroism, optical rotatory dispersion, and viscosity of hyaluronic acid at various solvents compositions, concentrations, and pH values have been studied. The data show a large change in the molecular properties in organic/water solvents such as ethanol, p‐dioxane, or acetonitrile/water at pH ⩽ pKa. At this pH range of aqueous solution, hyaluronic acid shows a CD minimum near 210 nm whereas in the presence of organic solvent it exhibits a strong negative dichroism (below 200 nm) and a positive band near 226 nm. It undergoes a sharp, cooperative transition with respect to pH and solvent. The observed CD features are assigned to the π‐π* and n‐π* transitions of the amide and carboxyl chromophores. The ORD results show a gradual blue shift of trough at 220 nm with increasing magnitude of rotation when the organic solvents and hydrogen ion concentrations are increased. A one‐term Drude's equation was used to analyze the ORD data, and the result show a variation of dispersion parameters with different solvents in accordance with the observed CD changes. The intrinsic viscosity of hyaluronic acid in mixed solvent at pH 2.6 is lower than that of aqueous solution. All the observed property changes of hyaluronic acid are reversed on addition of foramide in mixed solvents indicating that the hydrogen bonds are involved in this transition. The observed spectroscopic and hydrodynamic features are attributed to a conformational change of hyaluronic acid in a mixed solvent involving intramolecular hydrogen bonding between the acetamido and carboxyl groups. The possible conformational state of hyaluronic acid in solution under various conditions is discussed in terms of the reported helical structure of hyaluronic acid from x‐ray diffraction studies.
Shape of the conformational energy surface near the global minimum and low‐frequency vibrations in the native conformation of globular proteins
Authors: Gō Nobuhiro 
Published: December 2004

AbstractBased on the assumption that the conformational energy surface of a protein molecule can be approximated near the global minimum point by a multidimensional parabola, conformational fluctuations in the native state are discussed. In this approximation the conformational fluctuations can be viewed as excitations of coupled harmonic oscillations of dihedral angles. For the purpose of estimating the range of frequencies vibrations, globular proteins are assumed to made of homogeneous continuous elastic material. The number of vibrational modes in such an elastic body, with the wavelength no less than the characteristic length of an amino acid residue, are estimated roughly to be three times the number of amino acid residues in a protein, which is slightly less than the number of variable dihedral angles in a protein. Their frequencies, when converted to the wavenumber of corresponding light, are found to range from 1.8 × 10 cm−1 to 2.1 × 102cm−1 for a protein with the diameter d = 40 Å, when Young's E = 1011 dyne/cm2 is assumed. A significant fraction of the coupled vibrations of dihedral angles in real globular proteins are collective ones, i.e., those involving the whole protein molecules. Based on these results, it concluded that the depth of the global minimum s at least 150 Kcal/mol.
Hydrodynamic properties of macromolecular complexes. IV. Intrinsic viscosity theory, with applications to once‐broken rods and multisubunit proteins
Authors: De La Torre José Garcia , Bloomfield Victor A. 
Published: December 2004

AbstractWe have extended our previous theories of the translational and rotational frictional properties of multisubunit complexes to calculate the intrinsic viscosity of such structures. Our theory is similar to those recently construced by McCammon and Deutch, and by Nakajima and Wada, in that it uses a modified hydrodynamic interaction tensor and solves the system of simultaneous interaction equations by digital computation rather than by successive approximations. However, there are some differences in the formulation and averaging of these equations. Extensive numerical comparison is made between this theory and others that are available—associated with the names of Hearst and Tagami, Abdel‐Khalik and Bird, and Tsuda—using as a basis exact results for prolate ellipsoids of revolution. For large axial ratios, only our theory asymptotically approaches the correct limit; but for small axial ratios, only the Tsuda “shell‐model” theory is adequate, because the other theories neglect the preponderant influence of the sphere located at the center of rotation. Intrinsic viscosities, translational frictional coefficients, and Scheraga‐Mandelkern β parameters, are tabulated for a large number of polygonal and polyhedral subunit structures, with up to eight elements, using both our theory and Tsuda's. Particular application is made to hemerythrin and aspartate transcarbamylase. Finally, the viscosities and friction coefficients o once‐broken rods are calculated and compared with an approximate theory by Wilenski.
Oxidation of dihydronicotinamide adenine dinucleotide by a flavin derivative of polyethylenimine
Authors: Spetnagel Wayne J. , Klotz Irving M. 
Published: December 2004

AbstractA modified Polyethylenimine has been prepared that has riboflavin attached to it, as well as hydrophobic groups. The catalytic efficiency toward oxidation of6 dihydronicotinamide adenine dinucleotide (NADH) by this flavopolymer is more than 100‐fold greater than observed with small‐molecular riboflavin. The products of the reaction in aerobic solution have been established to be the oxidized nicotinamide NAD+ and hydrogen peroxide. The kinetics fit a Michaelis‐Menten mechanism. Thus, the versatility of modified polyethylenimines as catalysts has been extended from hydrolyses and decarboxylations to oxidation‐reduction reactions also.
Poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid). II. Catalysis of p‐nitrophenyl acetate hydrolysis
Authors: Goren H. Joseph , Fletcher Thea , Fridkin Mati , Katchalsi‐Katzir Ephraim 
Published: December 2004

AbstractThe hydrolysis of p‐nitrophenyl acetate is catalyzed by imidazole, free in solution or as the side chain in poly(His‐Ala‐Glu). This is based on the observations that the reaction is first order in ester and first order in nonprotonated imidazole. Catalysis of p‐nitrophenyl acetate hydrolysis is dependent on solvent conditions. The effect of low concentrations of ethanol, dioxane, and trifluoroethanol were investigated. As the concentration of organic solvent is increased, the second‐order rate constant for imidazole catalysis decreases. The decrease, however, is greater for imidazole than for poly(His‐Ala‐Glu). In 2% trifluoroethanol/water solution, free imidazole has twice the catalytic activity of polymeric imidazole, while in 40% trifluoroethanol/water they have equal activity. Since under the latter solvent conditions poly(His‐Ala‐Glu) is partially α‐helical, the relative improvement in polymeric–imidazole catalysis may be attributed to imidazole hydrogen‐bonded to a carboxylate ion. With this assumption the carboxylate–imidazole hydrogen‐bonded system has been calculated to have three times the base catalytic activity of imidazole.