bluuebunny/crossref_metadata_2025 huggingface dataset:
Infinite‐dilution viscoelastic properties of poly‐γ‐benzyl‐L‐glutamate in helicogenic solvents
Authors: Warren Thomas C. , Schrag John L. , Ferry John D.
Published: December 2004

The storage and loss shear moduli, G, and G˝, have been measured for solutions of three samples of poly‐γ‐benzyl‐L‐glutamate with molecular weights from 16 to 57 × 104, by use of the Birnboim‐Schrag multiple‐lumped resonator. The frequency range was 106 to 6060 Hz, the concentration range 0.0015–0.005 g/ml, and the temperature 25°C. Two helicogenic solvents with widely different viscosities, dimethylformamide and m‐cresol, were used to provide a broader effective frequency range. The intrinsic moduli, extrapolated to infinite dilution, were compared with the predictions of the theory of Ullman for rigid rods; agreement was rather good at the lowest frequencies, but unsatisfactory at high frequencies. The data over the entire frequency range of three of logarithmic decades could be described closely by a relaxation spectrum consisting of one terminal relaxation time separated by a gap from a sequence of relaxtion times spaced as in the Zimm theory. The terminal time agrees approximately with that calculated for end‐over‐end rotation of a rigid rod. The additional relaxation mechanisms are tentatively attributed to modes of flexural deformation of the helix.
Synthesis of two sequential polypeptides by dispersion in benzene and their circular dichroism spectra in aqueous solution: Poly(L‐Glu‐L‐Lys‐L‐Ala‐Gly) and Poly(L‐Ala‐D‐Glu‐L‐Lys‐D‐Ala‐Gly)
Authors: Zeiger Allen R. , Lange Armand , Maurer Paul H.
Published: December 2004

The monomers γ‐benzylglutamyl‐ε‐benzyloxycarbonyl‐lysylalanylglycine pentachlorophenyl ester and alanyl‐γ‐benzyl‐D‐glutamyl‐ε‐benzyloxycarbonyllysyl‐D‐alanyl‐glycine pentachlorophenyl ester, were polymerized in dilute solutions of dimethylform‐amide (DMF) or as dispersions in the same volume of benzene. After deprotection with hydrogen bromide, the products were either chromatographed on Sephadex G‐50 or dialyzed. The polymers derived from the polymerization in benzene were considerably larger than those from DMF. The results in benzene indicated that high monomer to solvent ratios are not necessary for the production of high‐molecular‐weight sequential polypeptides. Circular dichroism spectra of the polymers and monomers at neutral and acid pH indicated that poly(L‐Glu‐L‐Lys‐L‐Ala‐Gly) exists in a random coil configuration and poly(L‐Ala‐D‐Glu‐L‐Lys‐D‐Ala‐Gly) exists in a β conformation.
Electric birefringence of poly‐L‐lysine hydrobromide in methanol–water mixtures and helix–coil transition induced by high electric fields
Authors: Kikuchi Kazuo , Yoshioka Koshiro
Published: December 2004

The electric birefringence of poly‐L‐lysine hydrobromide in methanol–water mixtures has been measured at 25 °C over a wide range of field strengths by use of the rectangular pulse technique. An abrupt change in the specific Kerr constant was observed between 87 and 90 vol % methanol, corresponding to the solvent‐induced helix–coil transition. The specific Kerr constant increased rapidly with dilution in the random coil form, and more slowly in the helical conformation. The field strength dependence of the bire fringence at various concentrations, for both the helical and coil conformations, can be described by a common orientation function, which resembles the theoretical one for the case of permanent dipole moment orientation. This is interpreted in terms of the saturation of ion–atmosphere polarization. The optical anisotropy for the helical conformation was much larger than that for the coil form.

Anomalous birefringence signals were observed above a critical field strength (about 5 kV/cm) in 90 vol % methanol. The birefringence passed through a maximum and began to decrease slowly before the pulse terminated, reaching a steady‐state value. This steady‐state value was closer to that of the coil in the coil in the limit of very high fields. The results indicate that a transition from the charged helix to the charged coil is induced by high electric fields in the transition region. This effect can be explained on the basis of the polarization mechanism proposed by Neumann and Katchalasky.
The effect of temperature and salt concentration on the circular dichroism exhibited by unionized derivatives of L‐alanine in aqueous solution
Authors: Mattice Wayne L.
Published: December 2004

The circular dichroism of Ac–Ala–NHMe, cyclo(–Ala–Ala–), Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe has been measured in water and in aqueous salt solutions as a function of temperature. Only cyclo(–Ala–Ala–) exhibits circular dichroism which is independent of temperature. Each of the linear derivatives of L‐alanine exhibits a positive circular dichroism in the range 208–218 nm at 15°C in water. Heating reduces the intensity of the positive circular dichroism, and only Ac–Ala–OMe retains positive circular dichroism at 75°C in water. Isothermal addition of salts produces changes in the circular dichroism of linear derivatives of L‐alanine which resemble those seen on heating. The relative effectiveness of the salts tested, at a concentration of 4M, is LiCl ⩽ KCl = NaCl < MgCl2 ⩽ CaCl2 ⩽ NaClO4. The circular dichroism of cyclo(–Ala–Ala–) is also affected by the salts. Extrapolation of the results obtained with Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe to a long polypeptide with a –CH2R side chain in the L‐configuration leads to the conclusion that this polypeptide should exhibit a temperature‐dependent salt‐sensitive positive circular dichroism between 208 and 218 nm when it exists as a statstical coil.
The effects of cations and diamines on the viscosity of T2 DNA
Authors: Baxter‐Gabbard Karen , Fraser Dean
Published: December 2004

The viscosity of the DNA of T2 bacteriophage has been studied with the aim of understanding the folding of the DNA in the phage head. Thus the results of previous workers have been extended into a range of concentrations and mixtures of cations and polyamines simulating the conditions obtaining in actual phage heads. Difficulties in obtaining reproducible results with DNA in 0.001M NaCl have been attributed to the presence of traces of protein, perhaps nulease(s), that can be eliminated by hot‐phenol extraction of the DNA. The results have been negative in the sense that the minimum viscosity obtained (120–140 dl/g) indicates a molecule that is far from tightly folded and in that viscosities in this range can be obtained with a simple mixture of Na+ and Mg++. No specificity of the diamines putrescine and spermidine is seen; they are simply surrogate cations.
Effect of protonation on electronic structure of guanosine and 5′‐guanosine monophosphate and on glycosidic (CN) bond rotations
Authors: Jordan Frank
Published: December 2004

Semiempirical molecular orbital studies were performed on 5′‐guanosine monophosphate in its various states of base and phosphate ionization (employing the extended Hückel method) and on guanosine protonated on N‐3 and on N‐7 (employing CNDO/2). Semiempirical potential energy calculations (Lennard–Jones and Coulombic) failed to pinpoint the reasons for the recent experimental suggestion that guanine protonation increases the syn population in 2′‐ and 3′‐guanosine monophosphates. Changes in electron densities upon base protonation are much in evidence and are a very sensitive function of the site of base protonation assumed. It is suggested that the CNDO/2‐type calculations when combined with 13C and 15N pH‐dependent chemical shifts can lead to assignment of the site of protonation in the DNA bases.
A theory of complex multiple equilibria. The effect of polyU concentration on the binding of deoxyadenosine
Authors: Han Helen , Schurr J. Michael
Published: December 2004

A grand‐partition function method employed previously for the study of cooperative binding of nucleosides to polynucleotides is generalized to include the effect of changes in the polymer concentration, as well as the effect of changes in the nucleoside concentration. This method is applied to compute isotherms for the binding of deoxyadenosine by polyuridylic acid at various total concentrations of polyuridylic acid. It is found that these isotherms are extremely insensitive to the polymer concentration, as commonly assumed heretofore, and as demonstrated experimentally (to some degree) by Davies and Davidson. However, the conclusion inferred by Davies and Davidson that the complexes must be unimolecular in polyuridylic acid is now seen to be clearly unwarranted, though it remains still a viable possibility, until data over a much wider range of polyuridylic acid concentrations become available.
Raman spectroscopic study of mechanically deformed poly‐L‐alanine
Authors: Frushour Bruce G. , Koenig J. L.
Published: December 2004

Raman spectroscopy has been used in investigating the conformational transitions of poly‐L‐alanine (PLA) induced by mechanical deformation. We see evidence of the alpha‐helical, antiparallel beta‐sheet, and a disordered conformation in PLA. The disordered conformation has not been discussed in previous infrared and X‐ray diffraction investigations and may have local order similar to the left‐handed 31 poly glycine helix. The amide III mode in the Raman spectrum of PLA is more sensitive than the amide I and II modes to changes in secondary structure of the polypeptide chain. Several lines below 1200 cm−1 are conformationally sensitive and may generally be useful in the analysis of Raman spectra of proteins. A line at 909 cm−1 decreases in intensity after deformation of PLA. In general only weak scattering is observed around 900 cm−1 in the Raman spectra of antiparallel beta‐sheet polypeptides.

The Raman spectra of the amide N–H deuterated PLA and poly‐L‐leucine (PLL) in the alpha‐helical conformation and poly‐L‐valine (PLV) in the beta‐sheet conformation are presented. Splitting is observed in the amide III mode of PLV and the components of this mode are assigned. The Raman spectrum of an alpha‐helical random copolymer of L‐leucine and L‐glutamic acid is shown to be consistent with the spectra of other alphahelical polypeptides.
Sedimentation coefficient and intrinsic viscosity of semiflexible chains
Authors: Noda Ichiro
Published: December 2004

Published theoretical equations for the sedimentation coefficient and intrinsic viscosity of a semiflexible chain are compared, neglecting the excluded volume effect. The theories are extended to the case of a small excluded volume, by applying the perturbation theory, established for flexible chains, to a semiflexible chain. Using the derived equation, the experimental results for the sedimentation coefficient and intrinsic viscosity of DNA and cellulose trinitrate are analyzed.
Raman spectral studies of nucleic acids. XI. Conformations of yeast tRNAPhe and E. coli ribosomal RNA in aqueous solution and in the solid state
Authors: Chen M. C. , Thomas G. J.
Published: December 2004

Laser‐excited Raman spectra of tRNAPhe from yeast and of fractionated 16S and 23S rRNA from E. coli are reported for samples in aqueous solution and in the solid state. The Raman scattering spectrum of each RNA is not significantly altered by the change from an aqueous to a solid environment and displays the same characteristic frequencies and intensities associated with ordered polyribonucleotide structures. Unlike DNA, the backbone conformation of RNA thus appears to be largely insensitive to gross changes in the degree of hydration.

Raman scattering from the phosphate group vibrations of aqueous tRNAyeastPhe is qualitatively and quantitatively the same as obtained from previously studied tRNA's and is indicative of a highly ordered conformational structure in which some 85% of the nucleotide residues are in ordered configurations. The major differences observed between spectra of tRNA and rRNA are attributed to differences in base composition of these RNA's.
13C nmr study of the helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine
Authors: Di Blasi R. , Verdini A. S.
Published: December 2004

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.
The strand‐separation transition of T2 bacteriophage DNA
Authors: Elson Elliot L. , Record M. Thomas
Published: December 2004

Strand separation of T2 DNA has been investigated in a helix‐destabilizing solvent. Temperature‐shift experiments in which the conformation of the DNA is monitored by its viscosity, sedimentation behavior, and kinetics of helix formation show that a well‐defined strand‐separation transition follows the helix–coil transition usually observed by changes in absorbance. For T2 DNA, this strand‐separation transition is 70% as broad as the helix–coil transition, and is characterized by extremely slow kinetics of conformational change in the population. Strand separation requires the expansion of the two‐stranded coil observed at the end of the helix–coil transition. This expansion is apparently coupled with the disurption of the last remaining base pairs in the molecule. The expansion process increases the viscosity, and can be readily followed as a function of time and/or temperature. Subsequent separation of the expanded form into complementary strands results in a viscosity decrease, the net result of a reduction in hydrodynamic volume and the halving of the molecular weight. Only under conditions where the driving force for strand separation is large are these events at all synchronous in the population. When the kinetics of conformational change are complete in the strand‐separation transition, a mixture of expanded forms and separate strands is observed; the breadth of the transition reflects differences in stability with respect to strand separation among the molecules in the population. The transition exhibits hysteresis and is not a reversible equilibrium between double‐stranded and single‐stranded forms. It appears that renucleation is kinetically forbidden within the strand‐separation region.
Synthesis of some amino acids, sugars, and peptides in cold plasma abiotic synthesis of some high‐molecular‐weight proteid‐like structures (V)
Authors: Simionescu Cr. , Denes F. , Onac D. , Bloos G.
Published: December 2004

The synthesis of some high‐molecular‐weight protenoid structures in radiofrequency cold plasma conditions are discussed. The fractionation results of the raw product and the spectrum of free and protenoid‐bound amino acids are given. The uv analysis of these compounds is presented.

A protein‐forming mechanism that might have existed on the primitive earth is proposed.
The dynamic mechanical, dielectric, and melting behavior of reconstituted collagen
Authors: Nguyen An‐Lac , Vu Ban The , Wilkes Garth L.
Published: December 2004

The dielectric, dynamic mechanical, and melting (denaturation) behavior of reconstituted collagen has been investigated. Dynamic mechanical properties are reported for the range of temperature from −100 to 220°C. Dielectric properties are reported for the range of temperature from −120 to 90°C. Possible origins of dynamic mechanical and dielectric relaxations are discussed. Effect of moisture content on mechanical and dielectric behavior is also presented. The melting process of collagen immersed in diluents as well as that of dry collagen were studied by the techniques of hot‐stage polarizing microscopy, differential thermal analysis, thermal mechanical analysis, and small‐angle light scattering. It was concluded that the melting point of dry collagen is about 217°C.
Cooperative monomer binding by polynucleotides. Effect of multiple‐loop configurations on formation of triple‐stranded complexes
Authors: Schmitz Kenneth S.
Published: December 2004

Simulated binding curves for the reaction 2 polymer + monomer = triple‐stranded complex are presented, in which loop formation and sliding degeneracy of the polymer adsorption surface are considered. Exact calculations for a polymer chain length N of 11 units suggest that configurations of two or more loops have negligible effect on the isotherm when SW > 1, where S and W are exponential weighting factors for monomer–monomer S and polymer–polymer W nearest neighbor interactions. There is a pronounced effect, however, when SW ≪ 1. Limiting expressions (N ≫ 1, but finite) for the single‐loop configurations suggest these configurations are negligible at any degree of saturation θ if θ (1 − θ)2–k N3–k ≪ SW, where k is defined by the weighting factor (j + 1)−k for a ring of j units. This expression suggests that single monomer‐stack configurations are the only significant contributors to the grand partition function at the midpoint of the isotherm if N3–k ≪ SW. Furthermore, single‐loop configurations are negligible below θ = 0.5 but become dominant above the isotherm midpoint when SW ∼ 1 (random binding) if 2 < k < 3. For k > 3 and N → ∞, loop configurations have no effect in any region of the random binding isotherm usually analyzed experimentally (θ < 0.95). Equivalence of matrix and sequence generating methods is also demonstrated.
Theoretical analysis of conformations of Ac‐Gly‐L‐Ala‐Gly‐NHMe with intramolecular hydrogen bonds
Authors: Pletnev V. Z. , Kadymova F. A. , Popov E. M.
Published: December 2004

The hydrogen‐bonded structures of Ac‐Gly‐L‐Ala‐Gly‐NHMe have been studied by theoretical conformational analysis. The geometric parameters and energies of stable forms with various combinations of 3 → 1 and 4 → 1 type hydrogen bonds have been calculated. The stable conformations found can be used as canonical forms in the investigation of linear and cyclic peptide compounds with intramolecular hydrogen bonds.
Frequency dependence of the proton magnetic relaxation in aqueous solutions of haemoproteins
Authors: Lahajnar G. , Zupančič I. , Blinc R. , Pifat Greta , Maričić S.
Published: December 2004

The longitudinal proton magnetic relaxation times T1 were measured for ferri (met)‐and carbonmonoxy‐bovine haemoglobin and equine myoglobin in 0.1 M KH2PO4 aqueous solutions near pH 6 at 5°C and 35°C from 1.5‐ to 60‐MHz Larmor frequencies. It is concluded that the correlation time τC for the dipole–dipole interaction of electron and nuclear spins is in fact the electron (ferric) spin relaxation time τS being close to 1.5 × 10−10 sec for both metHb and metMb at 5°C. At 35°C the paramagnetic relaxation rates are not determined solely by the relaxation of protons exchanging from the haem pocket with bulk solvent. Hence, τC at 35°C cannot be calculated from the dispersion data obtained at this temperature. The relevance of this for the determination of interspin distances r is discussed.
Studies on the conformations and interactions of elastin. Proton magnetic resonance of the repeating tetramer
Authors: Urry D. W. , Ohnishi T.
Published: December 2004

Proton magnetic resonance studies at 220 MHz were carried out on synthetic polymers of the repeating tetrapeptide of elastin. Temperature dependence and solvent‐mixture dependence of peptide proton chemical shifts were determined for both linear polymers, N‐formyl‐(Val‐Pro‐Gly1‐Gly2)n‐Val OMe where n ≃ 8 and 40, and for cyclic polymers (Val‐Pro‐Gly1‐Gly2)n, where n = 3 and 4. The Gly2 NH was found to be solvent shielded. In addition, by studying the polymers Boc‐Val‐Pro‐Gly1‐Gly2‐OH, H‐Pro‐Gly1‐Gly2‐Val OMe, H(Pro‐Gly1‐Gly2‐Val)3OH, and others, it was demonstrated that the Val C–O immediately preceding the Gly2 NH in the sequence was required for solvent shielding. Also the Gly2 NH resonance is found at higher field than the Gly1 NH resonance. This provides the basis for proposing a β turn in which the Pro and Gly1 residues form the corners, i.e., residues i + 1 and i + 2, and in which the Gly2 NH, residue i + 3 hydrogen bonds to the carbonyl of residue i, the Val residue.

Studies on methanol–water solvent systems indicated retention of the β turn as a significant conformational feature. This suggests that the β turn occurs in the elastic fiber, which contains about 60% water but which utilizes association of hydrophobic groups as a primary force in fibrogenesis.
Pressure–temperature stability of DNA in neutral salt solutions
Authors: Hawley S. A. , Macleod R. M.
Published: December 2004

The effect of pressure on the melting temperature of DNA (Cl. perfringens) has been examined in several concentrations of neutral salt by measurement of uv absorbance. The results indicate that the apparent transition volume increases as the salt concentration, and hence the melting temperature, is raised, and suggest that the transition occurs without a change in volume at a Tm of 59°C. Additional experiments were conducted in an effort to determine whether transition behaviour can be found in other regions of pressure and temperature; no additional transition behaviour was observed in experiments conducted with temperatures as low as −21.85°C at 2000 atm and pressures in excess of 9000 atm at 58°C.
Structural studies of human placental dermatan sulfate during development using optical mixing spectroscopy
Authors: Jamieson Alexander M. , Lee Ting‐Yang , Schafer Irwin A.
Published: December 2004

Optical mixing spectroscopy is a recently developed technique which permits the measurement of diffusion coefficients and molecular weights of macromolecular species when only small amounts of material can be obtained for analyses. In this study, an approxmate empirical relationship between diffusion coefficient and viscosity‐average molecular weight was established for highly sulfated mucopolysaccharides. This relationship was then used to deduce the molecular weights of small quantities of highly purified dermatan sulfate extracted from human placenta at the full term (40 weeks) and at earlier stages of development (12–18 weeks). The effect of hyaluronidase digestion on molecular weight was then investigated as a probe for glucuronic acid substitutions in the dermatan sulfate. The molecular weights of dermatan sulfate were similar, 27,000–29,000, in the term and young placenta. Digestion with hyaluronidase produced a 50% reduction in molecular weight in the young placenta versus a 30% reduction in the term placenta, clearly demonstrating significant differences in the nature of glucuronic acid substitution at the two developmental stages studied.
Measurement of diffusion coefficients of meningococcal polysaccharide by optical mixing spectroscopy. I. A preliminary characterization on the aggregation of the Group C polysaccharide
Authors: Chen F. C. , Tscharnuter W. , Schmidt D. , Chu B. , Liu T. Y.
Published: December 2004

The angular distribution of scattered intensity and decay times of concentration fluctuations have been measured by means of digital photon counting and single‐clipped photon correlation for solutions of Group C meningococcal polysaccharides at 31°C. The z‐average diffusion coefficient 〈D〉z and its second moment 〈D2〉z have been determined from the time‐dependent correlation function using the cumulant expansion technique. Very low observed values of 〈D〉z and the tremendous width of the polydispersity index, which is the z‐average normalized variance, suggest a higher degree of aggregation than the monomer–dimer type self‐association at finite concentrations.
Contribution of side‐chain chromophores to the optical activity of proteins: Model compound studies. I. α‐Methyl‐L‐tyrosine
Authors: Goux Warren J. , Cooke Dennis B. , Rodriguez Raquel E. , Hooker Thomas M.
Published: December 2004

The optical rotatory power and the conformational energy of the amino acid α‐methyl‐L‐tyrosine has been calculated as a function of molecular conformation. Comparison of the results of these theoretical calculations with experimental circular dichroism data indicates that the conformational freedom of this molecule is highly restricted. The most heavily populated conformations appear to be those near χ1 = 60°, χ2 = 80°, Ψ = 175°, and χ1 = 300°, χ2 = 80°, Ψ = 5°. The χ1 = 180° conformations are not likely to be populated to a significant extent at ordinary temperatures.
Melting of DNA in ethanol–water solutions
Authors: Usatyi A. F. , Shlyakhtenko L. S.
Published: December 2004

The thermal denaturation curves of DNA have been investigated over a wide range of temperatures T and ethanol concentrations C by CD and uv absorption methods. The phase diagram of conformational DNA states has been constructed in T,C plane. The range of the A, B, and coiled forms of DNA was determined. The behavior of the DNA denaturation curve in the neighborhood of the triple point shows that the conformational transition B → A is realized by short parts of the DNA double helix. This is the reason for the coincidence of the melting temperatures of the A and B forms of DNA throughout the range of their coexistence.
Determination of the rate of renaturation of modified DNA by fluorescence depolarization
Authors: Miller Stephen J. , Wetmur James G.
Published: December 2004

Fluorescence depolarization was used to measure the rate of renaturation of T2 DNA, which had been modified by chloroacetaldehyde. Rates were measured on DNA samples with 5–15% of the base pairs modified and were found to agree with rates determined by DNA absorbance kinetics at 260 nm. The renaturation rate of a modified T2 DNA was unchanged in the presence of a ninefold abundance of unlabeled calf thymus DNA.
The effects of chain length on the secondary structure of oligoadenylates
Authors: Kroon Paulus A. , Kreishman George P. , Nelson James H. , Chan Sunney I.
Published: December 2004

The oligoadenylates (Ap)2–4A have been studied by proton magnetic resonance (pmr) spectroscopy. All the exterior base protons and a number of the interior base proton resonance have been assigned. The results of this work showed that the adenine bases in these oligoadenylates are intramolecularly stacked at 20°C with their bases oriented preferentially in the anti conformation about their respective glycosidic bonds. The oligomers were found to associate extensively even at concentrations of 0.02 M, primarily via “end‐to‐end” stacking. With increasing temperature, the oligomer bases destack, but it is argued that this unfolding process cannot be described in terms of a two‐state stacked versus unstacked model. Instead, the temperature dependences of the base proton chemical shifts support a base‐oscillation model. The relationship between this model and the two‐state model is discussed. Finally, on the basis of the chain‐length dependence of the proton chemical shifts of the various adenine bases, it was concluded that subtle variations in the secondary structure of these oligomers exist with increasing chain length. Evidence is presented to show that the effects of distant base shielding are considerably smaller than what was previously estimated. The observed departures from the “extended dimer” model are attributed to differences in the relative orientations of the bases with respect to their neighbors in the oligomer.
Conformational analysis of thyrotropin releasing factor by proton magnetic resonance spectroscopy
Authors: Montagut Martine , Lemanceau Bernard , Bellocq Anne‐Marie
Published: December 2004

The proton magnetic resonance spectrum of thyrotropin releasing factor (TRF) in solution in deuterium oxide and deuterated dimethylsulfoxide (DMSO–d6) has been analyzed. Two forms differing in cis–trans isomerism about the His‐Pro peptide bond are observed. From the temperature dependence of chemical shift of the amide protons, it is concluded that TRF in DMSO–d6 does not contain intramolecular hydrogen bonds. Measurement of NHCαH coupling constant provides an estimate of the histidine dihedral angle ϕ. Structural information about the histidine side‐chain is deduced from CαHCβH coupling constants and from the nonequivalence of the two prolyl δ‐protons. In DMSO–d6, there is evidence for a tautomeric equilibrium corresponding to an exchange of imidazole proton between the two nitrogen atoms N‐δ and N‐ε. In water, the N‐εH tautomer is found to be the predominant tautomeric form of the imidazole ring. These results in combination with energy calculation, vibrational analysis, and carbon nmr studies allow the determination of the conformationof TRF.
Ultrastructure of acid‐ and enzyme‐modified cross‐linked potato starch
Authors: Hollinger G. , Marchessault R. H.
Published: December 2004

Purified potato starch, cross‐linked with epichlorohydrin (65–5.4 anhydroglucose units per cross‐link) by an iterative method that preserved the native crystalline structure of the starch granule, was exposed to enzymic (B. subtilis α‐amylase at 50°C) and acidic (3 N HCl at 40°C) hydrolysis. The stability of the granules to digestion by enzymes, as measured by their weight loss after incubation with the enzyme solution, increased with the degree of cross‐linking; by contrast, the stability to acid attack decreased as a function of the degree of cross‐linking. The morphology of these samples was studied by scanning electron microscopy. A lamellar structure, which was most evident after enzyme treatment, was observed in samples that had a weight loss of greater than 50%. The results reflect differences in accessibility, which are interpreted in terms of a statistical model of the ultrastructure with correlated fluctuations in density in the radial direction.
Static and dynamic quenching of protein fluorescence. I. Bovine serum albumin
Authors: Feldman Isaac , Young Dolores , McGuire Robert
Published: December 2004

The fluorescence parameters, lifetime, relative quantum yield, maximum and mean wavelength, half‐width, and polarization, of bovine serum albumin (BSA) were measured at 15°C in aqueous solutions containing varying concentrations of different chemical perturbants, glycerol, Cu2+ ions, guanidine hydrochloride, and urea. By considering a quenching mechanism as being either dynamic or static, depending upon whether the quenching is or is not accompanied by a change in the fluorescence lifetime, we were able to correlate the changes produced in the various fluorescence parameters by the different chemical perturbants with changes in macromolecular structure as the concentration of perturbant was gradually increased. The addition of glycerol and of Cu2+ ions indicated that in aqueous BSA both tryptophan residues are below the surface of the macromolecule, out of contact with solvent water, and, as a consequence, they are statically quenched. “Ultra‐Pure” guanidine hydrochloride at 2.4 M or more caused a drastic conformation change, which resulted in the emergence of a visible tyrosine peak at 304 nm in the BSA fluorescence spectrum when either 260‐ or 270‐nm excitation was employed. With the same excitation, the enhancement of BSA tyrosine fluorescence by 6–8 M ultra‐pure urea produced only a shoulder near 304 nm in the BSA fluorescence spectrum. We have introduced the use of a new relative quantum yield for protein fluorescence, q′, referenced to the quantum yield of unquenched free tryptophan, which eliminates the quenching action of water from the reference.
Infinite‐dilution viscoelastic properties of tobacco mosaic virus
Authors: Nemoto Norio , Schrag John L. , Ferry John D. , Fulton Robert W.
Published: December 2004

The storage and loss shear moduli, G′ and G″, have been measured for dilute solutions of unaggregated and aggregated tobacco mosaic virus samples in glycerol–water mixtures, by the Birnboim–Schrag multiple‐lumped resonator modified for use with aqueous solvents. The frequency range was 100–5800 Hz, the concentration range 0.6–2.1 × 10−3 g/ml, and the temperatures 25.0° and 37.8°C. The number‐average and weight‐average molecular weights of the aggregated sample were estimated as 1.4 and 2.0 × 108, respectively, from electron microscopy. The extrapolated intrinsic moduli [G′] and [G″] were compared with the predictions of the Kirkwood–Auer theory for rigid rodlike molecules. For the unaggregated sample, the frequency dependence of [G′] and [G″] agreed well with the theory assuming the intrinsic viscosity to be 27 ml/g, though the asymptotic limit of [G′]M/RT at higher frequencies was slightly larger than the theoretical value of 3/5. For the aggregated sample, the data agreed with theory for rigid rods as modified to account for molecular‐weight distribution.
Investigation of the thermal unfolding of secondary and tertiary structure in E. coli tRNAfMet by high‐resolution nmr
Authors: Wong K. Lim , Wong Yeng P. , Kearns David R.
Published: December 2004

The high‐resolution (300 MHz) proton nmr spectrum of E. coli tRNAfMet has been examined in 0.17M NaCl, with and without Mg2+, and at various temperatures. In light of recent studies of other E. coli tRNA and fragments of tRNAfMet, some low field (11–15 ppm) resonances previously assigned to secondary structure base pairs are reassigned to a tertiary structure A14–S4U8 base pair and a protected uridine residue in the anticodon loop. These two resonances and other low field resonances which are assigned to secondary structure base pairs are used to monitor the thermal unfolding of the molecule. In the absence of Mg2+ the tertiary structure base pair is present only to ∼45°C, but in the presence of Mg2+ it remains until at least 70°C. Analysis of the temperature dependence of other low field resonances indicates that the melting of the dihydrouridine stem occurs more or less simultaneously with the loss of tertiary structure. The observation of the resonance from the A14–S4U8 base pair proves that tertiary structure is present in this molecule below 40°C, even in the absence of Mg2+.
Relaxation kinetics of the triple‐stranded helix ⇄ coil transition at short chain length. A model including the staggering of chains
Authors: Weidner H.
Published: December 2004

The relaxation kinetics of a staggering zipper model are presented, in which the formation of helical nuclei is regarded to be rate‐limiting and in which the sliding of strands along the helices is prohibited. Instead a realignment of staggered chains is only possible via complete uncoiling. While maintaining the third order of the initial reaction as in an all‐or‐none mechanism, the model predicts a large range of relaxation times, which contribute to the mean relaxation time according to the stability of the individual species and which are weakly coupled in the range of small amounts of helical content. The model can easily be compared to experimental results and agrees well with relaxation data obtained from a triple‐helical peptide fragment of collagen. It may be readily expanded to other multistranded helix ⇄ coil transitions with steady‐state formation of the individual species and it suggests that the fraying of the helix ends is hidden by the fast‐relaxation times due to the equilibration of the shortest helical species.
Variations thermiques, entre 1 et 300°K, de la chaleur specifique de la L‐alanine, tri(L‐alanine), et de la poly(L‐alanine) sous formes α et β
Authors: Daurel M. , Delhaes P. , Dupart E.
Published: December 2004

The heat capacities of L‐Alanine, tri(L‐alanine), and poly (L‐alanine) (α helicoidal form and β pleated sheet structure) have been measured between 1.5 and 300°K with a standard adiabatic calorimeter.

In the solid state, the heat capacity is in general dut to three parts which are additive in first‐order approximation. (1) The lattice vibrations or “acoustical modes” which are the largest at low temperatures. The low‐temperature lattice specific heat is proportional to T, T2, or T3 for an ideal one‐, two‐ or three‐dimensional solid, respectively. (2) The so‐called group vibrations or “optical modes” which, due to their high frequencies, usually take effect only at higher temperatures. (3) The defects and unharmonic effects.

The α‐amino acid and its trimer present a specific heat thermal variation characteristic of molecular solids which is correctly fitted with an empirical law proposed by Kitaigorodskii. This author assumes that, for such solids, the molecular lattice point has six degrees of freedom (three of translation and three of rotation). Thus the lattice contribution of the specific heat satisfies the Debye approximation in agreement with the doubling of the number of degrees of freedom per molecule (compared with atomic crystals).

The polypeptide behavior is, however, different. The specific heat for each form exhibits a thermal dependence connected with a strong vibrational anisotropy. The model proposed earlier by Tarasov accounts well for these results. In the case of the β form, we have observed the predicted three‐ and two‐dimensional behavior due to the intermolecular H bondings responsible for the sheet structure. For the α form we observed a one‐dimensional pattern at higher temperature, since each peptidic chain vibrates separately.

The comparison with other spectroscopic and theoretical investigations shows a large discrepancy. However, we have attemped to account for the “optical contribution” to the specific heat of poly(L‐alanine) by using a continuum of mean frequencies as suggested by Wunderlich. Vibrational frequency spectra are proposed to explain our results, but the overlapping of acoustical and optical branches in the case of the α form outlines the limits of macroscopic models. It is quite likely that the acoustical spectrum is greatly affected by the intramolecular H bonding.

At low temperature the specific heat is a physical property sensitive to the long‐range order of the macromolecule, and therefore further spectroscopic and theoretical investigations are necessary to explain correctly these experimental results.
Conformation of histidine model peptides. II. Spectroscopic properties of the imidazole chromophore
Authors: Grebow Peter E. , Hooker Thomas M.
Published: December 2004

Semi‐empirical molecular orbital calculations have been carried out for the free base and cationic forms of imidazole so as to obtain data which are required for the calculation of the chiroptical properties of molecules that contain this chromophoric group. The polarization, energy, and monopolar charge distribution are reported for the lowest energy electronic transitions. The absorption spectra for imidazole have been determined to 180 nm and circular dichroism spectra for L‐histidinol and L‐2‐amino‐1‐butanol have been measured.
Macromolecular binding
Authors: Schellman John A.
Published: December 2004

Formulas for the free energy of binding to a macromolecule are obtained by thermodynamic and statistical mechanical methods, and it is shown that the free energy of binding is intimately related with the binding polynomial and Wyman's binding potential. The expression for the free energy of binding is applied to a number of cases of ligand‐induced conformational changes, cooperativity, association reactions, etc.
Quantum‐mechanical study of the hypochromic effect in polynucleotides. Intra‐ and interstrand interaction contributions
Authors: Danilov V. I. , Volkov S. N.
Published: December 2004

The first uv absorption band hypochromism of poly(dA) · poly(dT), poly(dG) · poly(dC), poly(dA), poly(dT), poly(dG), and poly(dC) is calculated with the help of perturbation theory on the basis of monomer characteristics computed by the Pariser‐Parr‐Pople method taking into account all singly excited configurations. The theoretical results obtained are in good agreement with experimental values of hypochromism. The origin of the hypochromic effect in the double‐stranded polynucleotides is investigated. It is shown that intrastrand interactions between the bases make the main contribution to hypochromism (60–76%), while the contribution of the Watson–Crick‐pair formation is small (2–12%). The essential part of hypochromism (22–28%) is due to the interstrand interactions between the bases that are not coupled by hydrogen bonds. The discussion of the experimental data shows that the present theoretical investigation could serve as a basis for the correct treatment of experimental data.
Carbon‐13 and proton nmr studies of helix–coil transition of poly(γ‐benzyl‐L‐glutamate)
Authors: Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô
Published: December 2004

The helix–coil conformational transition undergone by poly(γ‐benzyl‐L‐glutamate) in solutions of trifluoroacetic acid and deuterated chloroform was studied by proton and carbon‐13 nmr. The results indicate that in the case of the solvent‐induced helix–coil transition, the side chain assumes a helical conformation before the backbone. In the thermally induced helix–coil transition, the results indicate the existence of an intermediate state, which is between the α‐helix and random coil and is free from intramolecular hydrogen bonding.
Levans. II. Light‐scattering and sedimentation data of Streptococcus salivarius levan in water
Authors: Stivala S. S. , Bahary W. S. , Long L. W. , Ehrlich J. , Newbrun E.
Published: December 2004

The molecular weights and radii of gyration of Streptococcus salivarius levan fractions were obtained from light‐scattering measurements in water. Sedimentation coefficients and partial specific volumes of the fractions were also obtained. Double logarithmic plots of [η] versus M̄w and S0 versus M̄w yielded slopes having values of 0.17 and 0.62, respectively. The data and various calculated parameters show that levan from Streptococcus salivarius is highly branched and behaves hydrodynamically as a compact particle of spherical symmetry.
Base pairing of adenine and uracil derivatives in the presence of water
Authors: D'Albis Anne , Wickens M. P. , Gratzer W. B.
Published: December 2004

The association of chloroform‐soluble derivatives of uracil and adenine has been examined in chloroform solution in the presence of dissolved water. Analysis by infrared spectroscopy shows that complex formation still occurs in these conditions, and that the extent of association is substantially unchanged by the presence of water. Evidence is presented for the coexistence of two kinds of base pair (involving, respectively, the C2 and C4 carbonyl groups of the pyrimidine) in the solutions, and for some displacement in their relative balance by the added water. The binding of water to the C2 and C4 carbonyl groups can be separately observed in both the free uracil derivative and its 1:1 complex with 9‐ethyladenine. Little or no competition has been found to occur between the formation of base pairs and binding of water to the bases, as judged by measurements of water solubility in chloroform solutions of the bases individually and in 1:1 mixtures. The evidence suggests that this phenomenon can be largely explained by the formation of double hydrogen bonds by the uracil carbonyl groups. Taken together with recent published observations, the results indicate that hydrogen bonding may make a much greater energetic contribution to conformational stability of biopolymers in aqueous solution that has been supposed.
Electrofocusing of heparin: Fractionation of heparin into 21 components distinguishable from other acidic mucopolysaccharides
Authors: McDuffie Norman M. , Dietrich Carl P. , Nader Helena B.
Published: December 2004

Twenty‐one fractions have been demonstrated in each of 15 different commercially available heparins subjected to electrofocusing. These fractions show a molecular‐weight range from 3000 to 37,500 with a constant interval between molecular weights. Degradation of each fraction by purified enzymes of Flavobacterium heparinum yielded identical end products, suggesting chemical identity. Only fractions with a molecular weight of 7000 and up had significant anticoagulant activities.

The phenomenon of electrofocusing of mucopolysaccharides is dependent upon pH, molecular weight, and ampholyte availability. Chemical composition of the mucopolysaccharide is also an essential factor since N‐ and O‐desulfation of heparin markedly changed the focalization pattern.

The pattern produced when heparin is subjected to electrofocusing is not duplicated by any other naturally occurring acidic mucopolysaccharide tested. Heparitin sulfate D shows some similarities to heparin and it is probable that heparitin sulfate D is a normal contaminant of heparin preparations (this assumption is supported by molecular‐weight and anticoagulant activity determinations).

The technique is specific and reproducible and unequivocally distinguishes heparin from other acid mucopolysaccharides.
Influence of the sugar configuration on the structure of DNA by conformational analysis of the deoxyribose‐phosphate unit
Authors: Cornillon Raphaël , Lespinasse Jean‐Noël , Broch Henri , Vasilescu Dane
Published: December 2004

The conformational analysis by the Extended Hückel Theory of the deoxyribose‐phosphate unit in the principal configurations of the sugar is discussed. The work is divided into three parts in order to determine the role of the different elements constituting such a unit. (1) The simultaneous study, for the four principal configurations of the sugar, of the possible ranges of the rotational parameters ψ and ϕ′ with P3 and P5 without their oxygen atoms. (2) The study of the influence of the oxygen atoms, situated on P3 and P5, on the rotations ψ and ϕ′ for the C3′endo and C2′endo sugar configurations. (3) The study of the influence of a nucleobase on the rotation ψ, and whether the oxygen atoms of the phosphate groups should be taken into account or not.

The results show the equivalences C3′endo ≃ C2′exo and C2′endo ≃ C3′exo; that the allowed angular ranges of our rotational parameters depend, in some degree on the chosen sugar configuration; and that the rotations ψ and ϕ′ appear as “quasi” independent. In addition, an energetic classification which, according to the Extended Hückel Theory, seems to show that the C2′endo sugar configuration is the most favored for our unit was established; it was shown that the introduction of the oxygen atoms has no influence on the rotation ψ, but on the contrary leads to a restriction of the possible range for the ϕ′ parameter; and it was determined that the influence of the adenine base fixed in its position of minimal energy (i.e., anti‐conformation) on the rotation ψ, as a function of the presence or absence of the oxygen atoms, is relatively limited.
Analyse conformationnelle de la N‐méthylamide de l'acide L‐pyroglutamique par diffusion Rayleigh depolarisée, spectroscopie de vibration et calcul de l'energie conformationnelle
Authors: Allard Michèle , Avignon Michel , Bellocq Anne‐Marie
Published: December 2004

Conformational analysis of N‐methylamide of pyroglutamic acid has been performed by theoretical energy calculations and experimental physical techniques, namely, laser Raman spectroscopy and depolarized Rayleigh scattering. The two theoretically predicted conformations are evidenced in crystalline state (ψ1 = +169°) and in aqueous solution (ψ1 ≃ −20°). This study confirms the interest of a careful vibrational analysis of peptides and N‐deuterated derivatives for providing an estimate of the dihedral angle ψ. The relationship between amide III frequency and ψ values is emphasized.
Refinement of the structure of β‐chitin
Authors: Gardner K. H. , Blackwell J.
Published: December 2004

The structure of β‐chitin has been refined by rigid‐body least‐squares methods, based on the intensity data for highly crystalline specimens from the pogonophore Oligobrachia ivanovi. The structure consists of an array of poly‐N‐acetyl‐D‐glucosamine chains all having the same sense, which are linked together in sheets by NH … OC hydrogen bonding of the amide groups. In addition to the O‐3′H … O‐5 intramolecular hydrogen bond, analogous to that in cellulose, the CH2OH side chain forms an intrasheet hydrogen bond to the carbonyl oxygen on the next chain. This structure shows considerably better agreement between observed and calculated intensities than that possessing an intersheet hydrogen bond, as had been proposed previously. The structure is consistent with the swelling properties of β‐chitin and can also be seen to be analogous to that of native cellulose.