bluuebunny/crossref_metadata_2025 huggingface dataset:
Helix‐coil transition of poly(L‐glutamic acid) in N‐methylacetamide
Authors: Harry John B. , Franzen James S.
Published: May 2005

The folding of randomly coiled poly(L‐glutamic acid) to the helical state has been studied in N‐methylacetamide by titration methods. Since this solvent would be expected to form amide‐peptide group hydrogen bonds with the unfolded form of the polymer, to a first approximation no helix stabilization could come from intrapolymer hydrogen bonds. The titration data, collected from 30 to 70°C yield the following values per residue for the thermodynamic parameters governing the coil‐helix reaction for the uncharged polymer: ΔG30°C°, −1. 9 ± 0.1 kcal; Δ H°, 0 ± 0.1 kcal; ΔS30°C°, 6.3 ± 0.6 eu. In N‐methyl acetamide, the helix is an order of magnitude more stable than in water, and this stabilization appears to be entirely the result of the entropy gained by solvent molecules which are released from the polymer upon folding.
Electron microscopy of poly (O‐acetyl hydroxy‐L‐proline) crystals
Authors: Andries J. C. , Walton A. G.
Published: May 2005

Single crystals of POAHP II were grown from acetic anhydride, a solvent in which POAHP I is thought to be stable. The single crystals gave an electron diffraction pattern which specified a hexagonal unit cell and the lateral spacing between molecular chains (11.4 Å). There is reasonable indication that molecular chain folding occurs in the POAHP single crystals. Epitaxial crystallization of POAHP II has been observed in the [100] and [320] directions on NaCl, [110] direction on KCl, and [100] direction on KI. Evidence indicates that the molecular axis is normal to the long axis of the POAHP needles and parallel to the substrate surface.
Stereochemistry of nucleic acids and polynucleotides. V. Conformational energy of a ribose‐phosphale unit
Authors: Lakshminarayanan A. V. , Sasisekharan V.
Published: May 2005

The potential energy calculations on the sugar‐phosphate unit for different puckerings of the sugar are reported in this paper. The results obtained here essentially confirm our earlier predictions made by using criteria of contact distances (hard‐sphere potential) and are also supported by observed conformation in crystal structures. The minimum energy conformations of the sugar phosphate unit, along with the preferred orientations of the base with respect to the sugar given in the previous paper, determine the probable conformations of the monomer unit of a polynucleotide (or nucleic acid) chain.
Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate
Authors: Sasisekharan V. , Lakshminarayanan A. V.
Published: May 2005

As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles ϕ and ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche–gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.
Chain conformation of copoly(γ‐methyl D, L‐glutamate)
Authors: Musuda Yukio , Miyazawa Tatsuo , Goodman Murray
Published: May 2005

Copolymers of γ‐methyl D‐ and L‐glutamates with various D/L ratios were prepared. Infrared absorption spectra of solid films were measured and sums of right‐ and left‐handed helix contents were determined from intensities of amide V bands. Farultraviolet absorption spectra and optical rotatory dispersion of these copolymers in solutions are used to ascertain their helical character. Chain conformations of DL‐copolypeptides are discussed.
Theoretical model for the equilibrium behavior of DNA superhelices
Authors: Laiken Nora
Published: May 2005

A statistical‐mechanical model for superhelical DNA is presented. The partition function for a DNA superhelix is written by using a combinatorial approach in order to allow for the known relation between the number of superhelical twists and the states of the base pairs in the double helix. While the theory allows any factors which might contribute to the free energy of superhelical twisting to be included in the statistical weights of the superhelical twists, only the reduction in configurational entropy is considered in this paper. Similarities between an imperfectly matched DNA double helix and a DNA superhelix are used in the derivation of expressions for the entropy of superhelical DNA. Although the partition function is presented in a general form, permitting many equilibrium properties of DNA superhelices to be treated, the application considered in this paper is the calculation of helix–coil transition curves. Several experimentally observed features of such transitions are predicted. For example, the curves are bimodal, with an early and a late transition relative to that of a nicked molecule. The results are very sensitive to the volume within which two parts of the double helix must meet when forming a superhelical twist. The free energy of superhelix formation is calculated, and the results are compared with those obtained from the data of Bauer and Vinograd for ethidium bromide intercalation. In the present model, the free energy increases less sharply with an increase in the number of superhelical twists than observed experimentally, indicating that factors other than configurational entropy probably make important contributions to the free energy of superhelix formation.
Flexibility of tropocollagen from sedimentation and viscosity
Authors: Utiyama Hiroyasu , Sakato Kuniaki , Ikehara Kenji , Setsuiye Takashi , Kurata Michio
Published: May 2005

Sedimentation constant and intrinsic viscosity were measured on purified tropocollagens extracted from earthworm‐cuticle and lathyritic ratskin. A cartesian diver viscometer was used to make viscosity measurements at small shear stress and to avoid the effects of surface forces. By comparing the experimental data with the hydrodynamic theories of wormlike‐coil of Ullman a value of 1300 Å has been assigned for the persistence length of these tropocollagens. Other factors which may affect the estimate are discussed.
Study of dielectric behavior of DNA in shear gradient
Authors: Takashima Shiro
Published: May 2005

The dielectric behavior of the DNA molecule is investigated in the presence of mechanical force as well as the electrical field. In the present experiment, the direction of the electrical field is perpendicular to that of the mechanical force. The dipole moment of polar molecules manifest itself as dielectric increment at low frequencies or as the conductance increment at high frequencies. These two quantities are closely related to each other by Eq. (1) in the text. Because of the difficulty due to electrode polarization at low frequencies, no useful information was obtained by investigating the dielectric increment in the present system. Therefore, the effect of shear gradient was studied by measuring the conductance increment at high frequencies with various velocity gradients. The conductance increment decreased when the shear was applied perpendicular to the electrical field. The conductance change is converted into the unit of dielectric constant; it was found that the dielectric increment of DNA solution decreases by as much as 85 percent. From these observations, it is concluded that the direction of the dipole moment in DNA is longitudinal rather than transverse. The same experiment was repeated with the random coil DNA and no anisotropy in the dielectric increment was observed.
The effect of acridine orange on the structure of ribosomes
Authors: Tal Moshe , Rotem Haim , Alfasi Matya , Berg Robert A.
Published: May 2005

Exposure of Escherichia coli MRE‐600 ribosomes to acridine orange (AO) at low ionic strength (1mM Tris‐acetate pH 7.4) results in quantitative binding of the dye. Under our experimental conditions about a few hundred dye molecules can be bound to any one of the 30, 50, or 70‐S particles. AO causes the 30 and the 50‐S subunits to form ribosomal aggregates of approximate sedimentation constants of 70 and 100‐S.
Synthèse et Caractérisation des Trois Premiers Oligomermères de l'Acide α‐L‐Glutamique. I
Authors: Rinaudo M. , Domard A. , Spach G.
Published: May 2005

In the present work, the synthesis of the three primary oligomers of α‐L‐glutamic acid is described; the general formula is the following:
magnified image

The choice of protective groups at the both ends of the chain allows for the good solubility in the water and the liberation of free carboxyl groups on the side chain. Thus, models are obtained for the study of thermodynamic properties of solutions and especially of the interactions between polyanions and cations. The prepared products are characterized by different techniques such as mass spectrometry potentiometry, tonometry, and thin‐layer chromatography. The results are in agreement and lead to the conclusions that the molecules have the general formula of [I] and are stereoregular.
Isokinetic relationships for the effect of inorganic phosphate adn protons on the deoxygenation rate of human hemoglobin
Authors: Salhany J. Mitchell
Published: May 2005

The rate of hemoglobin deoxygenation is measured as a function of inorganic phosphate concentration, pH, and temperature. Isokinetic relationships (enthalpy‐entropy compensation) are searched for by applying the method of O. Exner and, for comparative purposes, the conventional method of plotting the energy of activation (E*) versus the natural log of the pre‐exponentional factor of the Arrhenious equation (In A). Both plots indicate compensation between the activation parameters. However, unlike the conventional plot, the Exner treatment is able to distinguish between two types of compensation. Furthermore, when extrapolated rate constants based on all the data in an Exner plot are transposed into E* vs. In A plots, so‐called “turn‐around” behavior is predicted for the effect of increasing phosphate concentration at constant pH. Such “turn‐around” behavior in E* vs. In A plots has been observed experimentally by Beetlestone and co‐workers for anion binding to human hemoglobin as a functin of pH. Lastly, the compensation temperatures obtained from these data all fall within the Vaslow‐Doherty compensation range (250–350°K) which is thought to indicate that the solvent, water, is involved in the reaction mechanism. Thus, Exner plots appear to further resolve isokinetic temperatures of the Vaslow‐Doherty type. Differences in the electrostriction of solvent in the activated state is suggested as one possible physical source for the Vaslow‐Doherty type compensation observed in this work.
Nuclear magnetic resonance study on the model compounds for poly(N‐alkylglycine)s
Authors: Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu
Published: May 2005

Cis‐trans isomerism was investigated with N‐acetyl and N‐propionyl, N‐alkylglycine dimethylamides as model compounds for poly(N‐alkylglycine dimethlamides as model compounds for (N‐alkylglycine)s using n.m.r. spectroscopy. The population of the cis isomer measured in benzene and methylene chloride solutions did not show any marked dependence on the bulkiness of N‐alkyl substituents. This contrasts with polyN‐alkylglycine)s, whose cis isomer population increased with the introduction of bulky N‐alkyl groups. Kinetics of the Cis‐trans isomerization was also investigated with N‐acetyldimethylamides of sacrosine, N‐n‐propylglycine, and N‐isopropylglycine in tetrachloroethane solution. The δG‡ values for Cis‐trans isomerization in these amides were 18 ∼ 19 kcal/mole, which were virtually the same as that of polysacrosine.
The distant shielding effect in trinucleoside diposphates
Authors: Kan Lou S. , Barrett J. C. , Ts'O P. O. P.
Published: May 2005

A comparative study on the proton magnetic resonance of the dinucleoside monophosphates TpT, dApT, TpdA, the trinucleoside diphosphates dApTpT, TpTpdA, and poly T has been made. The purpose of this investigation was to establish whether in a trimer the proton chemical shifts of one terminal residue are influenced by the magnetic anistropy of the other terminal residue. The conformation of the trimers was first studied and shown to the similar to that of the corresponding dimer, except that of the percentage of the lefthanded conformers in the population of the trimers is probably lower than in the population of the dimers. The methylprotons, H‐6, and H‐1′ of the 3′‐terminal T residue in TpTpdA (or the 5′‐terminal T residue in dApTpT) are found to be more upfield than the same protons on the dimer TpT up to a magnitude of about 0.1 ppm. The shielding of these protons of the terminal T(s) in these trimers is even larger than those corresponding protons in the poly(T) at the same condition. From these results, it is concluded that a distant shielding effect is exerted by the 5′‐terminal. A residue (or by the 3′‐terminal A residue) on the other terminal residue in the trimers studied.
Destabilization of secondary structure in polyadenylic acid by formaldehyde
Authors: Stevens Charles L.
Published: May 2005

Results of circular dichroism and ultraviolet absorption measurements of poly A in neutral aqueous formaldehyde solution are presented, which show that the hydroxymethylated residues retain the ability to stack, but the stacking tendency is diminished. The midpoint of the thermal denaturation profile falls from about 38°C to about 18°C on complete hydroxymethylation. Hydroxymethylation, however, appears to have only a small effect on the apparent standard enthalpy and entropy of stacking, both of which become slightly more negative. When present at concentrations greater than about 2 g/100 ml, formaldehyde has a further and somewhat more dramatic denaturing effect on poly A. This ability is probably related to the chemical similarity of aqueous formaldehyde (methylene glycol) and ethylene glycol, which is known to be an effective denaturant for nucleic acids. In the presence of 20 g/100 ml formaldehyde, a very broad thermally induced transition of poly A is observed through the loss of ultraviolet hypochromism. Only the low‐temperature part of the transition is observed; it appears to be completed only at temperatures well over 100°C where the hypochromism with respect to adenosine has largely disappeared. The transition cannot be identified with the unstacking reaction usually observed through thermal denaturation experiments in the absence of formaldehyde, although the associated structure may be related in some way. The molecular nature of the structure associated with the transition is not known.
Study of the self‐diffusion coefficients of cations in the presence of an acidic polysaccharide
Authors: Magdelenat Henri , Turq Pierre , Chemla Marius
Published: May 2005

Self‐diffusion coefficient measurements have been applied to the study of Na+, Ca++, and Sr++ in the presence of a linear acidic polysaccharide extracted from cartilage, i.e., chondroitin sulfate. A series of experimental determinations was made with and without supporting electrolytes, and an analysis of experiments involving the separation of the electrostatic interaction terms by an extension of Manning's theory produced results showing the preponderant nature of these electrostatic terms. The specificity of each type of ion or the influence of the pH can be considered merely as higher order corrections with respect to the preceding interactions. Counterion concentration ranges and pH ranges were determined, where either the alkaline‐earth counterions become free and hence move with their normal diffusion rate, or these cations are associated with the polyelectrolyte molecule, thus giving a diffusion coefficient similar to that of the macromolecule, or the apparent diffusion coefficients vary between these two extreme diffusion rates as a function of the association equilibria. This variation can be expressed as a function of the linear charge density parameter ξ related to the structure of the polyelectrolyte, the value of which was determined and found in good agreement with published values.
Synthesis and properties of alternating poly(Lys‐Phe) and comparison with the random copolymer poly(Lys51, Phe49)
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G.
Published: May 2005

The alternating copolypeptide poly(Lys‐Phe) was obtained by synthesis and polymerization of the respective tetrapeptide. Conformation and conformational transitions in aqueous solutions and in water–organic solvent mixtures were determined and compared with those of the random copolymer poly(Lys51,Phe49) by circular dichroism measurements. The alternating copolymer reveals a very strong tendency to adopt the β structure, which is accomplished by raising the pH or by adding sodium perchlorate or methanol. Partial α‐helical conformation, however, is obtained in the presence of 10–20% of the strong helix‐forming solvent hexafluoroisopropanol. The random copolymer reveals a much weaker preference for the β structure. It assumes the α helix in mixtures of water with hexafluoroisopropanol and also in those with methanol. As was already reported by Peggion et al. and confirmed by the present work, the addition of sodium perchlorate also leads to the helix conformation [(1972) Biopolymers 11, 633], whereas β structure is obtained by raising the pH [(1970) Macromolecules 3, 194]. These studies reveal the significance of affinities determined by near neighbor interactions in polypeptides.
Infrared studies of stereoregularity of copoly(γ‐benzyl‐D,L‐glutamate) by the polymerization of the N‐carboxylic anhydride
Authors: Akaike Toshihiro , Inoue Shohei , Itoh Koichi
Published: May 2005

The D and L copolymerizations of γ‐benzyl glutamate N‐carboxylic anhydride (NCA) were carried out by two different initiators, n‐butylamine and sodium methoxide. The stereoregularity of the polymer was examined by infrared spectroscopy in the region 700–200 cm−1. A remarkable difference was found between the polymers obtained by these initiators in the region 450–400 cm−1. In the polymer obtained with sodium methoxide as initiator, the 409‐cm−1 peak assigned to local α‐helical conformation was not greatly affected by the amount of the L‐form, but in the polymer obtained by n‐butylamine this peak was much affected by the variation of L‐content. This indicates that the stereo‐selectivity of the polymerization in the sodium methoxide initiated system is higher than that in the n‐butylamine initiated system.
Hydrodynamic properties of a new plasma expander: Polyhydroxyethylaspartamide
Authors: Antoni G. , Neri P. , Pedersen T. G. , Ottesen M.
Published: May 2005

The intrinsic viscosity and molecular weight of several samples of polyhydroxyethylaspartamide with differing degrees of polymerization were determined and related, according to the Mark‐Howink equation. The a exponent is consistent with a random‐coil structure. The average unperturbed dimensions of the polymer, the dimensions in water, and the water–polymer interaction parameter were calculated according to Flory and Fox. The interaction of the polymer with water may explain its good efficacy as a plasma expander, as has previously been demonstrated in biological experiments. The behavior of the molecule in 6 M guanidine hydrochloride solution was also studied: this solvent has a very slight effect on the configuration of the polymer, in contrast with its normal effect on proteins.
Critical chain length for helix formation in L‐methionine oligopeptides
Authors: Becker Jeffrey M. , Naider Fred
Published: May 2005

The circular dichroism of a series of L‐methionine oligopeptides [BOC‐(Met)n‐OMe] was examined in trifluoroethanol and hexafluoroacetone sesquihydrate. The results indicate that the trimer through the hexamer exists predominantly in disordered conformations in these solvents. An abrupt change in the CD pattern at the heptamer in trifluoroethanol suggests that L‐methionine oligopeptides begin forming helices at this chain length.
Microcalorimetric investigation of dilute and concentrated solutions and films of the polydeoxynucleotide poly[d(A‐T)·d(A‐T)]
Authors: Andronikashvili E. L. , Mgeladze G. N. , Monaselidze J. R. , Lezius A. G.
Published: May 2005

Microcalorimetric heat capacity measurements on dilute and concentrated solutions and films of poly[d(A‐T)·d(A‐T)] in 2 M sodium chloride have been carried out. Values for enthalpy, entropy, and temperature of the helix–coil transition have been found to depend on the polymer concentration, and to have maxima near 20% (w/w) of polymer. The results are discussed in terms of polynucleotide hydration as one of the structure stabilizing factors.
Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA
Authors: Chang Chiang‐Tung , Hain Timothy C. , Hutton James R. , Wetmur James G.
Published: May 2005

The effect of solvent viscosity on DNA renaturation rates has been investigated as a function of temperature for a number of solvent systems. The results are all consistent with a microscopic viscosity limitation of the rate determining step. Rates of renaturation in perchlorate and quaternary ammonium salt solutions are also discussed. Increasing the macroscopic viscosity with dissolved neutral or anionic polymers increases, rather than decreases, renaturation rates due to the excluded volume of the dissolved polymers.
Probability of internal unwinding in the triple helix of collagen
Authors: Schwarz Martin , Poland Douglas
Published: May 2005

Helix probability profiles are calculated for collagen models that take into account specific sequence and unwinding from the ends, by internal loops and by chain dissociation, using parameters from a previous study and the technique of the previous paper.2 An analysis is made of the occurrence of imino acids in known collagen sequences and no significant difference is found from random occurrence. Studies of model sequences generated by random placement of the imino acids show no tendency for collagen to unwind via internal loops even when one end is covalently linked and a loop is permanently nucleated at that end.
Studies on poly(L‐lysine50, L‐tyrosine50)–DNA interaction
Authors: Santella Regina M. , Li Hsueh Jei
Published: May 2005

Interaction between poly(Lys50, Tyr50) and DNA has been studied by absorption, circular dichroism (CD), and fluorescence spectroscopy and thermal denaturation in 0.001M Tris, pH 6.8. The binding of this copolypeptide to DNA results in an absorbance enhancement and fluorescence quenching on tyrosine. There is also an increase in the tyrosine CD at 230 nm. The CD of DNA above 250 nm is slightly shifted to the longer wavelength which is qualitatively similar to, but quantitatively much smaller than, that induced by polylysine binding. At physiological pH the poly(Lys50, Tyr50)–DNA complex is soluble until there is one lysine and one tyrosine per nucleotide in the complex. The same ratio of amino acid residues to nucleotide has also been observed in copolypeptide‐bound regions of the complex. The addition of more poly(Lys50, Tyr50) to DNA yields a constant melting temperature, Tm′, for bound base pairs at 90°C which is close to that of polylysine‐bound DNA under the same condition. The melting temperature, Tm, of free base pairs at about 60°C on the other hand, is increased by 10°C as more copolypeptide is bound to DNA. As the temperature is raised, both absorption and CD spectra of the complexes with high coverage are changed, suggesting structural alteration, perhaps deprotonation, on bound tyrosine. The results in this report also suggest that intercalation of tyrosine in DNA is unlikely to be the mode of binding.
Synthesis and conformational properties of polypeptides containing long aliphatic side chains. Poly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine)
Authors: Shibaev Valery , Palumbo Manlio , Peggion Evaristo
Published: May 2005

Poly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine) were synthesized both by polymerization of Nε‐pelargonyl and Nε‐stearyl‐L‐lysine NCA and by acylation of poly(L‐lysine) with pelargonyl and stearyl chloride. This second route has proven to be very useful, since completely acylated polymers are obtained in almost quantitative yield, whereas the usual scheme of preparation of ε protected poly(L‐lysine) cannot easily be applied due to solubility problems.

Poly(Nεpelargonyl and stearyl‐L‐lysine) are soluble in alcohols containing linear aliphatic chains such as n‐butanol and n‐octanol and in mixtures of these alcohols with hydrocarbons such as n‐hexane and n‐heptane. Both polymers show an α‐helical conformation in the above solvents, which can be disrupted upon addition of sulfuric acid. Also in the solid state, poly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine) show X‐ray diffraction patterns typical of order structure.
Histone‐induced conformational changes in DNA as probed by quasi‐elastic light scattering
Authors: Wun K. L. , Prins W.
Published: May 2005

Quasi‐elastic light scattering as measured by intensity fluctuation (self‐beat) spectroscopy in the time domain can be profitably used to follow both the translational diffusion D and the dominant internal flexing mode τint of DNA and its complexes with various histones in aqueous salt solutions. Without histones, DNA is found to have D = 1.6 × 10−8 cm2/sec and τint ≅ 5 × 10−4 sec in 0.8 M NaCl, 2 M urea at 20°C. Total histone as well as fraction F2A induce supercoiling (D = 2.6 × 10−8 cm2/sec, τint ≅ 2.8 × 10−4 sec) whereas fraction F1 induces uncoiling (D = 1.0 × 10−8 cm2/sec, τint ≅ 9.4 × 10−4 sec). Upon increasing the salt concentration to 1.5 M the DNA–histone complex dissociates (D = 1.8 × 10−8 cm2/sec). Upon decreasing the salt concentration to far below 0.8 M, the DNA–histone complex eventually precipitates as a chromatin gel.
Structure of guanylyl‐3′,5′‐cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P21
Authors: Hingerty B. , Subramanian E. , Stellman S. D. , Broyde S. B. , Sato T. , Langridge R.
Published: May 2005

The structural features of calcium guanosine‐3′,5′‐cytidine monophosphate (GpC) have been elucidated by X‐ray diffraction analysis. The molecule was crystallized in space group P21 with cell constants of a = 21.224 Å, b = 34.207 Å, c = 9.327 Å, and β = 90.527°, Z = 8. The hydration of the crystal is 21% by weight with 72 water molecules in the unit cell. The four GpC molecules in the asymmetric unit occur as two Watson‐Crick hydrogen‐bonded dimers related by a pseudo‐C face centering. Each dimer consists of two independent GpC molecules whose bases are hydrogen bonded to each other in the traditional Watson‐Crick fashion. Each dimer possesses a pseudo twofold axis broken by a calcium ion and associated solvent.

The four molecules are conformationally similar to helical RNA, but are not identical to it or to each other. Instead, values of conformational angles reflect the intrinsic flexibility of the molecule within the range of basic helical conformations. All eight bases are anti, sugars are all C3′‐endo, and the C4′‐C5′ bond rotations are gauche‐gauche. The R factor is 12.6% for 2918 observed reflections at 1.2‐Å resolution.
Interpretation of hypochromic and hyperchromic intensity changes in the Raman spectra of polypeptides and polynucleotides undergoing transition
Authors: Painter P. C. , Koenig J. L.
Published: May 2005

The hyperchromic and hypochromic changes in the intensity of the amide‐I and amide‐III lines of polypeptides and certain ring vibrations of the bases of polynucleotides are shown to be related to similar changes in the lower energy uv absorption bands. The selection rules strictly limit the pairs of excited electronic states that can contribute to the elements of the polarizability matrix. An energy‐dependent term in this equation weights the contribution of the pairs of electronic transitions in favor of those involving the lower energy transitions. For both polypeptides and polynucleotides, there is a large hypochromic inensity change in the first π → π* exciton band upon the coil‐to‐helix transition. Through the selection rules, certain conformationally sensitive Raman lines are shown to derive their intensity predominantly from this band and hence also display hypochromism. Again, through an application of the selection rules, certain Raman lines can be demonstrated to depend predominantly for their intensity upon the n → π* transition, and consequently have the opposite hyperchromic intensity change upon the same conformational transition.
Racemization in the synthesis of polytripeptide models of collagen
Authors: Rapaka Rao S. , Bhatnagar R. S. , Nitecki D. E.
Published: May 2005

Racemization in the synthesis of tripeptide intermediates and their polymers was investigated, using L‐amino acid oxidase. Stepwise investigation of peptide intermediates showed no racemization during peptide coupling steps or deprotection of benzyl esters by hydrogenolysis. Saponification of one of the methyl esters produced some racemization. Preparation of active esters from N‐protected tripeptide acids containing optically active C‐terminal amino acid, with one exception, produced racemization. The fractionated polymers were found to contain less racemized amino acids than the crude products or starting monomeric tripeptides, indicating that the racemized sequences gave rise to lower molecular‐weight oligomers. The sequences investigated were ‐Pro‐Pro‐Ala‐, ‐Ala‐Pro‐Pro‐, ‐Val‐Pro‐Pro‐, ‐Pro‐Pro‐Leu‐, ‐Pro‐Gly‐Leu‐, ‐Pro‐Gly‐Phe‐, ‐Pro‐Gly‐Val‐, ‐Gly‐Val‐Pro‐, ‐Phe‐Pro‐Gly‐, ‐Leu‐Pro‐Gly‐, and Ile‐Pro‐Gly‐.
Nonlinear electric properties of DNA solutions
Authors: Marion C. , Bernengo J. C. , Hanss M.
Published: May 2005

DNA solutions are shown to present a nonlinear electric behavior. This property is measured through the third harmonic current intensity, which appears when the solution is placed in a sinusoidal electric field of moderately high strength (about 100 V·cm−1).

The influence of different parameters has been examined: fundamental frequency, field strength, concentration, molecular weight, and conformation. By progressive sonication, it is shown that the harmonic current is linearly proportional to the DNA molecular weight, but under an Mr of approximately 106, the nonlinear electrical property decreases sharply and its spectrum shows a drastic change.

It is thought that the harmonic current is not related to an orientational phenomenon; an explanation based on the electrical deformation of the molecule is suggested.
Nuclear spin‐relaxation studies of hydrated elastin
Authors: Ellis G. E. , Packer K. J.
Published: May 2005

The nuclear magnetic spin‐lattice and transverse relaxation processes for the 1H and 2D nuclei in purified elastin (ligamentum nuchae), exchanged and hydrated with excess D2O, have been studied in the temperature range 276°–340°K. The 2D relaxation results clearly show the presence of D2O (1) external to the bulk elastin sample, (2) in spaces within the bulk elastin, and (3) as an integral part of the protein on a molecular level. It is shown from these measurements that the protein on a molecular level. It is shown from these measurements that the water content of the protein itself changes from ∼0.8 g D2O/g dry elastin at ∼280°K to ∼0.2 g D2O/g dry elastin at ∼335°K, a decrease of 400%. The D2O content of the interfiber spaces decreases by less than 20% over the same temperature range. This fact throws considerable doubt on the validity of the values of β, the thermal expansion coefficient of elastin, used by other workers in discussion of the elastic mechanism in elastin. The elastin proton transverse relaxation shows the presence of three regions in elastin having different degrees of molecular mobility. These are assigned to protons associated with the crosslinks, a fairly mobile, hydrophobic, and low‐water‐content region, and a more mobile higher water‐content region. The temperature variation of the relative proportions of these three regions is explained in terms of a hypothetical temperature‐composition phase diagram in which the two mobile regions are represented as two partially miscible phases with different negative temperature coefficients of ‘solubility’ in water. The implications of these observations for current views of the nature of elastin are assessed. It is concluded that the spin‐relaxation results are consistent with a multiphase structural model for elastin.

An approximate sorption isotherm for the water/elastin system is reported and shows the relatively weak nature of the water/elastin interaction.
Konformationsuntersuchungen an oligoalanin, substanz P und der myoglobinsequenz (66–73) der zirkulardichroismus von polyäthylenglykolgebundenen peptiden
Authors: Mutter M. , Mutter H. , Uhmann R. , Bayer E.
Published: May 2005

The conformation of polyethylene glycol‐bound peptides, synthesized by the liquid‐phase method, was investigated. This marcromolecular C‐terminal protecting group is transparent in the visible and the ultraviolet range to 190 nm and solubilizes peptides in many different solvents. The CD spectra of the polymer‐bound myoglobin sequence 66–73 and of the biologically active undecapeptide “substance P” were measured in each step of the synthesis. In both examples the formation of a secondary structure during the growth of the peptide chain was found.

In the hydrophobic octapeptide containing the myoglobin sequence 66–73, the influence of either the blocked or the free N‐terminal amino group on the conformation was observed. The blocked octapeptide in trifluoroethanol showed a higher degree of α‐helix contribution than in its free state.

The conformation of the polyethylene glycol‐bound nona‐ and decaalanine in trifluoroethanol and water was determined. The peptide with a free amino end group has β‐conformation in trifluoroethanol as well as in water. The corresponding N‐Boc‐protected derivatives show helical structure. The amino end group has a decisive influence on the formation of β‐structure.

The method of CD investigation of polymer‐bound peptide sequences during the peptide synthesis in solution enables one to determine the influence of protecting groups and the chain end of a peptide on its conformation. It is also possible to study the relationship between the secondary structure, the chain length, and the kinetic of the coupling reaction in different solvents. Since the crystallization method for the liquid‐phase peptide synthesis allows one to synthesize peptides in very short time, a new method of studying peptide conformations is opened.
Influence of D and L amino‐acid residues on the conformation of peptides in solution: A carbon‐13 nuclear magnetic resonance study of cyclo(prolyl‐leucyl)
Authors: Deslauriers Roxanne , Grzonka Z. , Walter Roderich
Published: May 2005

The 13C chemical shifts and spin‐lattice relaxation times are reported for cyclo(L‐Pro‐L‐Leu) and cyclo(L‐Pro‐D‐Leu). The chemical shifts of the D and L leucyl residues in the cyclic peptides differ from each other by 1.8 and 3.6 parts per million for the α and β carbons, respectively. The α‐carbons of the prolyl residues differ by 1.0 ppm as a consequence of proximity to a D or an L leucyl residue. The 13C spin‐lattic relaxation time(T1) of the prolyl residues, but not the leucyl residues, in both compounds are indicative of difference in conformational equilibria within the pyrrolidine ring in the L‐L isomer as compared to the L‐D isomer. Anisotropic overall molecular reorientation is not responsible for the differences observed in the T1 values. The differences in T1 values and chemical shifts between cyclo(L‐Pro‐L‐Leu) and cyclo(L‐Pro‐D‐Leu) appear to result from a difference in conformations of the two diketopiperazine rings.
Dinucleoside monophosphates. I. Optical properties and conformation in solution with one base charged
Authors: Topal Michael D. , Warshaw Myron M.
Published: May 2005

A least squares analysis of the titration properties of several dinucleoside monophosphates enables calculation of the pK's for protonation. These pK's are used to resolve the spectral properties of dinucleoside monophosphates with one base charged from the apparent spectral properties of a dinucleoside monophosphate in aqueous solution. This method is applied to dinucleoside monophosphates containing adenosine and/or cytidine. Results of CD, nmr, and CD‐temperature dependence measurements are presented. The results indicate that singly protonated dimers of these nucleosides stack as do their unprotonated analogs. It is suggested that this is true for all dimers with one base charged.
Calorimetric measurement of enthalpy change in the isothermal helix–coil transition of poly(L‐ornithine) in aqueous solution
Authors: Fu Yi‐Chang , Van Wart Harold E. , Scheraga Harold A.
Published: May 2005

The enthalpy change associated with the isothermal pH‐induced uncharged coil‐to‐helix transition ΔHh° in poly(L‐ornithine) in 0.1 N KCl has been determnined calorimetrically to be −1530 ± 210 and −1270 ± 530 cal/mol at 10° and 25°C, respectively. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔHh°, the observed calorimetric heat was corrected for the heat of breaking the sample cell, the heat of dilution of HCl, the heat of neutralization of the OH− ion, and the heat of ionization of the δ‐amino group in the random coil. The latter was obtained from similar calorimetric measurements on poly(D,L‐ornithine). Since it was discovered that poly(L‐ornithine) undergoes chain cleavage at high pH, the calorimetric measurements were carried out under conditions where no degradation occurred. From the thermally induced uncharged helix–coil transition curve for poly(L‐ornithine) at pH 11.68 in 0.1 N KCl in the 0°–40°C region, the transition temperature Ttr and the quantity (∂θh/∂T)Ttr have been obtained. From these values, together with the measured values of ΔHh°, the changes in the standard free energy ΔGh° and entropy ΔGh°, associated with the uncharged coil‐to‐helix transition at 10°C have been calculated to be −33 cal/mol and −5.3 cal/mol deg, respectively. The value of the Zimm–Bragg helix–coil stability constant σ has been calculated to be 1.4 × 10−2 and the value of s calculated to be 1.06 at 10°C, and between 0.60 and 0.92 at 25°C.
[4‐Amino‐D‐phenylalanine6]luliberin. A biologically active abalog of the luteinizing hormone‐releasing factor suitable for affinity labeling
Authors: Sakarellos Constantinos , Donzel Bernard , Goodman Murray
Published: May 2005

The syntheis of [4‐amino‐D‐phenylalanine6]luliberin by the solid‐phase method is described. The analog was found to be ten times more potent than luliberin. Some possibilities for the easy derivatization of the 4‐amino‐phenylalanyl residue into addinity labels suitable for the study of hormone‐receptor interations are considered. The preparation of Nα‐t‐butyloxycarbonyl‐4‐(benzyloxycarbonylamino)‐D‐phenylalanine, one of the key intermediates used in the synthesis of this luliberin analog, is also reported.
The application of polyelectrolyte limiting laws to the helix–coil transition of DNA. VI. The numerical value of the axial phosphate spacing for the coil form
Authors: Manning Gerald S.
Published: May 2005

It is concluded on the basis of comparison of polyelectrolyte theory with published data that the mean phosphate spacing b along the contour axis of an unfolded polynucleotide single strand is in the range 3–4 Å (polyelectrolyte parameter ξ ≈ 2), regardless of temperature, base composition, or extent of stacking. This result is consistent with the low‐angle X‐ray scattering measurements of Gulik, Inoue, and Luzzati on poly(C). No conclusion may be drawn from this value of b concerning the structure of the chain skeleton or the spatial arrangement of the bases other than that the chain is far from an all‐trans local conformation (for which b would be about 6–7 Å, the length of a nucleotide unit). The structural implications, or lack thereof, are discussed in detail in the following paper.
Polymerization of optical isomers of phenylalanine N‐carboxyanhydride by various secondary amines
Authors: Hashimoto Yutaka , Aoyama Akimasa , Imanishi Yukio , Higashimura Toshinobu
Published: May 2005

In the polymerization of phenylalanine NCA initiated by some secondary amines, the two enatimorphs of phenylalanine NCA were polymerized with the same rate, which was almost twice as high, as that found for the racemic mixture. This stereoselectivity was observed only when the polymerization was initiated by secondary amines which are sterically crowded and reluctant to undergo a nucleophilic addition to NCA. Poly(DL‐phenylalanine) produced in the stereoselective polymerization had a higher molecular weight than that produced in nonstereoselective polymerization. These findings point to the possibility that the stereoselectivity arises only in those polymerizations which are propagated by the activated monomers and not in the propagation involving the terminal amine of the growing polymer. A possible mechanism for the stereoselective polymerization is proposed and examined.
Circular dichroism calculations for double‐stranded polynucleotides of repeating sequence
Authors: Cech Carol L. , Tinoco Ignacio
Published: May 2005

Optical property calculations are presented for poly(A·U), poly[(A‐U)·(A‐U)], poly(G·C), and poly[(G‐C)·(G‐C)] in RNA, B‐DNA, and C‐DNA conformations. An all‐order classical coupled oscillator polarizability theory was used, and an effective dielectric constant of 2 was assumed. The calculated CD spectra were found to be sensitive to both geometry and sequence. Agreement with the measured CD spectra of poly(A·U), poly(G·C), and poly(dG·dC) is very good. Calculations for other sequences and geometries are less satisfactory and are particularly poor for poly[(G‐C)·(G‐C)] in RNA geometry and poly(A·T) in B‐DNA geometry. Attempts to improve agreement with measured spectra by varying monomer properties have been only partially successful for these calculations, but they illustrate the types of changes that may prove to be necessary. Calculations using other published X‐ray coordinates for certain deoxypolynucleotides of simple sequence, some of which are quite different from B‐DNA coordinates, did not result in better agreement with measured spectra. Finally, the dependence of the calculated CD on chain length is examined. Results show that non‐nearest neighbor interactions can be important when runs of 3 or more identical base pairs appear in a given sequence.
Inapplicability of “Scatchard‐type” analysis to highly cooperative binding systems
Authors: Schmitz Kenneth S.
Published: May 2005

There are several studies of small molecule binding by biopolymers which use “Scatchard‐type” plots to determine the intrinsic binding constant (k) and pairwise interaction energy between bound sites (S). “Scatchard‐type” refers to the plot ln (r/m(n – r)) versus r in this text whereas “Scatchard plot” conventionally refers to the plot r/m versus r. The quantities r, n, and m are, respectively, the average bound ligand/site, ligand/site at saturation, and concentration of free ligand. Although these plots result from approximate solutions to the problem of binding small molecules on a general three‐dimensional lattice, they are often used to represent binding isotherms in linear systems for which the solutions are known exactly. A critical examination regarding the applicability of “Scatchard‐type” analysis to systems with a large number of binding sites is presented herein.

Both experimental and simulated binding data are analyzed by “Scatchard‐type” and exact nearest neighbor plots (θ versus ln m, where θ = r/n). Numerical determination of k and S for the two theoretical approaches differ greatly in highly cooperative systems although their theoretical equivalence (interconversion) is demonstrated. A modified Scatchard theory, which correctly counts the degenerate energy states, is presented which reconciles this discrepancy. The “Scatchard‐type” plot for the modified theory in the highly cooperative limit is mathematically equivalent to the form ln (r/n – r) + p, where p contains all the molecular information and locates the r/n = 1/2 point. Contrary to the original theory, the r dependence in the “Scatchard‐type” representation is devoid of molecular interpretation and is characterized by curvature in the low and high‐binding regions with a (maximum) slope of 4 at r/n = 1/2. The modified theory is shown to reproduce accurately the poly(cytidylic acid)‐guanosine data of Sarocchi et al. and to account for the maxima exhibited in the conventional Scatchard plots.
Quantitative electron microscope observations of the collagen fibrils in rat‐tail tendon
Authors: Parry D. A. D. , Craig A. S.
Published: May 2005

An electron microscope study of collagen fibrils from fixed tail tendons of rats has revealed that from some time shortly after birth until maturity, the fibril diameters have a bimodal distribution. The “two” types of fibril are indistinguishable in both transverse and longitudinal section. Unfixed specimens of eight‐week‐old‐tail tendon showed a similar bimodal distribution of diameters though the positions of the peak values compared to fixed specimens of an eight‐week‐old‐tail tendon were shifted upwards by about 30%. It has also been shown quantitatively that the polar collagen fibrils are directed randomly “up” and “down” with respect to their neighbors. Whilst it has been suggested by others that anastomosis is a feature of collagen structure, the results presented here do not support this hypothesis. Fibrillar units ∼ 140 Å in diameter have been observed and the possibilities that these are elastic fibers or the breakdown products of collagen fibrils have been considered.
The organization and repair of DNA in the mammalian chromosome. III. Determination of the molecular weight of a mammalian native DNA
Authors: Lange Christopher S. , Liberman Daniel F. , Clark Roger W. , Ferguson Pamm , Sheck Lorraine E.
Published: May 2005

The necessary conditions for a unique solution of the sedimentation vs DNA molecular weight equations are considered and applied to the native DNA of the L5178Y mouse leukemia cell. A brief review and critique of the literature of sedimentation anomalies is given to demonstrate that such anomalies are not present in the data reported here. It is shown that the chromosomal DNA of L5178Y cells comes in uniform packages of 1.0 (0.5–2.0) × 1010 daltons. All pieces are of an identical size which corresponds to the DNA content of about 1/13 the average chromatid. Both the size estimate and the number of such molecules/cell are confirmed by viscoelastometry. This DNA is shown to be free of radioactively demonstrable protein and/or lipid contaminants and of the same isopycnic density as T4 DNA. Variance analysis is applied to determine the precision of all measurements and to pinpoint major sources of error. A relationship between [η] and M is derived for native DNA in 1.0M NaCl. A necessary conclusion from these data is that mammalian chromosome models requiring degrees of polynemy greater than 16‐neme (in G1) are incorrect (to the extent that the L5178Y cell is typical of mammalian cells).