bluuebunny/crossref_metadata_2025 huggingface dataset:
Etude par spectroscopie infrarouge de la transformation hélice–chaîne statistique des polypeptides. II. Etude de l'interaction de quelques polypeptides à chaînes latérales polaires avec l'acide trifluoracétique
Authors: Garrigou‐Lagrange P. Combelas et C. , Lascombe et. J.
Published: December 2004

The various polymer–acid solvation possibilities occuring in the helix–coil transition process of polypeptides with polar side chains were systematically analyzed by infrared spectroscopy. The following samples have been considered: poly‐γ‐benzyl‐L‐glutamate (PBLG), alternating poly‐γ‐benzyl‐D,L‐glutamate (PBD‐LG), and poly‐β‐benzyl‐L‐as‐partate (PBLA). The behavior of the amide A, I, II, and νCO ester absorptions of each polymer dissolved in trifluoroacetic acid–chloroform mixtures was studied in depth. The classical assumptions concerning the interaction between a polypeptide and a proton donor solvent are discussed. This interaction was previously proposed in a theoretical model of helix–coil transition.

For PBLG, the spectral characteristics of the cooperative transition are evidenced by the amide bands. These bands also show main chain–acid hydrogen bonding
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Quantitative analysis of phenomenon (I) was performed in order to localize the “binding sites” of the polymer. In agreement with the theory, only the complexation of peptide units belonging to random coil and terminal helical regions were observed. However, in contrast to the theory in which the association constants KCO and KNH of these residues are generally kept equal, the present results have shown that the main binding site is the carbonyl group (KNH ≃ 0 or « KCO).

The behavior of the polar side chains of these polypeptides were analyzed during the transition. Similarly to the peptide backbone, they bind the acid by hydrogen bonding
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Furthermore, this association is more important when the side chains are localized in the coiled regions than in the helical ones. This result suggests, by analogy with the main chain behavior, that the helix–coil transition theory should take into account two more association constants for polar side chains, namely k1 for the helical regions and k2 > k1 for the coiled ones.
Polytonic studies of reconstituted collagen fibers
Authors: Balmer R. T. , Soto R. J.
Published: December 2004

The tensile force‐contraction characteristics of cross‐linked reconstituted collagen fibers have been studied for 30 different water‐soluble reagents. The data were obtained via a “polytonic” loading technique, which was neither isometric nor isotonic. Certain data were found to fit a master curve, which did not depend strongly on the denaturant. For many denaturants the contractile force appeared to be a maximum at a denaturant concentration corresponding to all the solvent being consumed in denaturant hydration. Also, the maximum contractile force appeared to vary in the same manner as does the hydration number of the individual cations and anions in the solution (i.e., H > Li > Na > K, and I > Br > Cl > F). Several denaturants were found to be as effective as the well‐known LiBr and KSCN in contracting the collagen.
The elastic properties of elastin
Authors: Hoeve C. A. J. , Flory P. J.
Published: December 2004

The thermoelastic properties of elastin immersed in water or in aqueous solutions of alcohols closely resemble those of typical polymers in the rubber elastic state. The evolution of heat much in excess of the work performed on elastin when it is stretched while immersed in water at ca. 25°C is attributable to the exothermic heat of dilution by water absorbed into the polymer during elongation. The negative sign of the temperature coefficient of swelling is confirmatory of this explanation. A network of random chains within the elastin fibers, like that in a typical rubber, is clearly indicated. The elastic properties of elastin are not explicable in terms of a two‐phase model consisting of discrete globules of compact elastin molecules fused one to another by cross‐linkages, with diluent (water) filling the interstices.
Dispersion effect on turbidimetric size measurement
Authors: Cancellieri A. , Frontali C. , Gratton E.
Published: December 2004

If dispersion effects are not taken into account, the dimensions of particles in suspension estimated from spectrophotometric data (slope of the log OD versus log λ plot) are too low. By measuring dispersion curves for the medium and for the suspension, a consistent estimate of the size of latex particles of different diameter is obtained from the OD data.
Binding by derivatives of polyethylenimine: Effects of charge and structure of small molecules
Authors: Johnson Timothy W. , Klotz Irving M.
Published: December 2004

Apolar derivatives of polyethylenimine in aqueous solution have been shown previously to bind organic anions very strongly. These studies have been extended to other charged and noncharged small molecules, as well as to derivatives of polyethyl‐enimine with much reduced positive charge. From these investigations the effects of charge and of structure of the small molecules can be assessed.
Thermodynamic aspects of the gelatinization and swelling of crosslinked starch
Authors: Hollinger G. , Kuniak L. , Marchessault R. H. , Marchessault R. H.
Published: December 2004

Samples of epichlorohydrin crosslinked potato starch were prepared by using a high ratio of starch to water and alkali concentration below the gelatinization level. This yielded crosslinked samples that were partially crystalline, and where the number of crosslinks could be varied between 1 and 20 crosslinks per 100 anhydroglucose units. The degree of swelling varied regularly with degree of crosslinking, and the molecular weight between crosslinks Mc as derived from swelling data in a good swelling agent compared favorably with Mc derived from chemical analysis.

From the heat of gelatinization of the crosslinked starches, as observed in a differential scanning calorimeter, for gelatinization in glycerol, water, and dimethylsulfoxide, a model for the gel state of the crosslinked starch is proposed. It is concluded that the entropy of melting is the determining factor in establishing the temperature of gelatinization.
Superhelix density heterogeneity in closed circular intracellular PM2 DNA
Authors: Ostrander Daryl A. , Gray Horace B.
Published: December 2004

Covalently closed intracellular DNA obtained from Pseudomonas BAL 31 20 min after infection with PM2 phage has been shown to be heterogeneous in superhelix density. Analytical band sedimentation, in the presence of low concentrations of ethidium bromide, has been carried out on fractions centripetal and centrifugal to the mode of a single band of closed circular DNA in a preparative propidium iodide–CsCl buoyant density gradient. Different average sedimentation rates, as well as different band shapes, have been observed for upper and lower fractions centrifuged at a dye concentration near the minimum in s° versus ethidium bromide concentration titrations performed on DNA from proximate intermediate fractions. Similar differences, although not as pronounced, have been obtained at a dye concentration corresponding to a point in the steep region of the titrations. Differential band sedimentation experiments performed on the same fractions have confirmed these results.

Differential band sedimentation experiments on similarly fractionated mature PM2 I DNA (closed circular form) have shown slight differences in the relative sedimentation rates of upper and lower fractions at dye concentrations corresponding to the steep regions in the titrations. The same experiments, when performed on nicked circular DNA obtained from heating both the mature and intracellular fractions, showed no evidence of differences in sedimentation coefficients. Such results may indicate slight heterogeneity in the superhelix density of viral PM2 I DNA; however, the degree of this heterogeneity would be somewhat less than that of the intracellular DNA.

The possibility that superhelix density heterogeneity may arise from displacement loops, which have been found at low levels in intracellular PM2 DNA, has been subjected to experimental tests. Unless such structures are originally present and removed by the isolation procedure, this possibility may be rejected.
Synthesis and conformational study of poly(Nδ‐carbobenzoxy, Nδ‐benzyl‐L‐ornithine) and poly(Nδ‐benzyl‐L‐ornithine)
Authors: Yamamoto Hiroyuki , Hayakawa Tadao , Yang Jen Tsi
Published: December 2004

Poly(Nδ‐carbobenzoxy, Nδ‐benzyl‐L‐ornithine) (PCBLO) was prepared by the standard NCA method. PCBLO was converted into poly(Nδ‐benzyl‐L‐ornithine) (PBLO) through decarbobenzoxylation with hydrogen bromide. The monomer Nδ‐benzyl‐L‐ornithine was synthesized by reacting L‐ornithine with benzaldehyde, followed by hydrogenation. The conformation of the two polypeptides was studied by optical rotatory dispersion and circular dichroism. PCBLO forms a right‐handed helix in helix‐promoting solvents. In mixed solvents of chloroform and dichloroacetic acid (DCA) it undergoes a sharp helix–coil transition at 12% (v/v) DCA at 25°C, as compared with 36% for poly(Nδ‐carbobenzoxy‐L‐ornithine) (PCLO). Like PCLO, the helix–coil transition is “inverse,” that is, high temperature favors the helical form. PBLO is soluble in water at pH below 7 and has a “coiled” conformation. In 88% (v/v) 1‐propanol above pH (apparent) 9.6 it is completely helical. In 50% 1‐propanol the transition pH (apparent) is about 7.4; this compares with a pHtr of about 10 for poly‐L‐ornithine in the same solvent.
Side‐chain effect on conformation of ionizable polypeptides in aqueous solution
Authors: Murai Norio , Sugai Shintaro
Published: December 2004

In order to study the effect of side‐chain length on the conformation of polypeptides, conformational changes of various ionic polypeptides with various lengths of side chain, poly‐Nε‐glutaryl‐L‐lysine (PGL), poly‐Nδ‐glutaryl‐L‐ornithine (PGO), poly‐Nε‐succinyl‐L‐lysine (PSL), and poly‐Nδ‐succinyl‐L‐ornithine (PGO), were investigated by ORD, potentiometric titration, and dilatometric measurements in aqueous solution. The results of optical rotation and potentiometric titration measurements indicate strongly that the α‐helix stability increases in the sequence PSO < PSL ∼ PGO < PGL, which corresponds to increased side‐chain length. The volume change associated with the helix–coil transition also increased in the above sequence. This series of polymers seems to be more hydrophobic compared with poly‐L‐glutamic acid or poly‐L‐lysine, as suggested from the values of enthalpy and entropy changes for coil–helix transitions.
Solvent effects on the orientaion of naphthalene rings in the side chain of poly‐γ‐1‐naphthylmethyl‐L‐glutamate
Authors: Ueno Akihiko , Toda Fujio , Iwakura Yoshio
Published: December 2004

The orientation of naphthalene rings in the side chain of poly‐γ‐1‐naphthylmethyl‐L‐glutamate (PNLG) in mixed solvents of dichoroethane (DCE) and hexafluoroisopropanol (HFIP) has been studied together with its conformation by infrared, circular dichroism, and fluorescence spectra. The CD pattern of PNLG varies with the solvent composition while it maintains the α‐helical conformation. The fluorescence spectra of PNLG in solution show excimer emission of the naphthalene chromophores. The ratio of intensity of the excimer emission to that of the normal fluorescence decreases as the HFIP component in the solvent increases. It is suggested that the naphthalene rings in the side chain of α‐helical PNLG are more rigidly orientated in the solvents of higher HFIP ratio.
Conformational stability in dinucleoside phosphate crystals. Semiempirical potential energy calculations for uridylyl‐3′‐5′‐adenosine monophosphate (UpA) and guanylyl‐3′,5′‐cytidine monophosphate (GpC)
Authors: Broyde S. B. , Stellman S. D. , Hingerty B. , Langridge R.
Published: December 2004

Classical potential energy calculations were performed for the dinucleoside phosphates UpA and GpC. Two widely accessible low‐energy regions of conformation space were found for the ω′, ω pair. That of lowest energy contains conformations similar to helical RNA, with ω′ and ω in the vicinity of 300° and 280°, respectively. All five experimental observations of crystalline GpC, two of ApU, and the helical fragment of ApApA fall in this range. The second lowest region has ω′ and ω at about 20° and 80°, respectively, which is in the general region of one experimentally observed crystalline conformer of UpA, and the nonhelical region of ApApA.

It is concluded that GpC and ApU, which were crystallized as either sodium or calcium salts, are shielded from each other in the crystal by the water of hydration and are therefore free to adopt their predicted in vacuo minimum energy helical conformations. By contrast, crystalline UpA had only 1/2 water per molecule, and was forced into higher energy conformations in order to maximize intermolecular hydrogen bonding.
Structure of aggregates and helix–coil transition of polypeptides by dielectric measurements. II. Poly‐D,L‐phenylalanine and poly‐β‐benzyl‐L‐aspartate in chloroform–dichloroacetic acid mixtures
Authors: Marchal E.
Published: December 2004

The dielectric absorption of poly‐DL‐phenylalanine and poly‐γ‐benzyl‐L‐aspartate (PLAB) was measured in very dilute solutions to determine the type of molecular association and to locate the helix–coil transition. Both polypeptides were present as associated helices in chloroform. The mode of aggregation, which was determined by measuring the dipole moment and the critical frequency, did not depend on the polarity of the side chain but rather on that of the solvent.

In both polymers, the dissociation of the aggregates in chloroform was observed on addition of small amounts of dichloroacetic acid; further addition of the acid lead to the helix–coil transition.

No second region of dielectric absorption that might be related to the kinetics of the transition was found during the helix–coil transition of PBLA.
Molecular conformation of polysaccharides in solution. Changes in the optical rotation and in the elution pattern of gel filtration
Authors: Hirano Shigehiro , Kondo‐Ikeda Sumiyo
Published: December 2004

Molecular conformation of some polysaccharides in aqueous solution in evidenced by changes in the optical rotation and in the elution pattern of gel filtration. The changes in the specific rotation against that in water are expressed as a molar conformational value [K]: −495° for colominic acid in 1.0 N NaOH solution, and −180° for hyaluronate (HA), +85° for corneal keratin sulfate, and +234° for amylose in 8 M urea solution. The gel filtration of amylose and HA dissolved in 8 M urea solution shows elution patterns distinctly different from those dissolved in water. The phenomena are attributable to a molecular conformational transition of polysaccharide molecules in aqueous solution.
Calculations of the circular dichroism of double‐helical nucleic acids. I. Effects involving π → π* transitions
Authors: Studdert David S. , Davis Robert C.
Published: December 2004

The circular dichroism of double‐helical nucleic acids was calculated as a function of geometry using the theory of Tinoco and Johnson. This theory does not include contributions of near ultraviolet transitions that are not π → π* in nature. The calculated circular dichroism shows a strong dependence on the distance of base pairs from the helix axis and the tilt of the base pair. Smaller dependences are predicted for the propeller‐like twist of a base pair and for variation of the angular increment per base pair. Moderately good agreement between calculated and many experimentally observed spectra could be generated.
Calculation of the circular dichroism of double‐helical nucleic acids. III. Dependence of the results on the choice of wave functions for purines and pyrimidines
Authors: Studdert David S. , Davis Robert C.
Published: December 2004

The circular dichroism of double‐helical nucleic acids was calculated using three different sets of wave functions for the purine and pyrimidine chromophores. Different wave functions give qualitatively the same types of spectra. Quantitatively, the differences are very substantial. However, the dependence of calculated circular dichroism spectra on nucleic acid geometry and base composition is very similar for the three different sets of wave functions. Each set of wave functions could be used to reproduce some, but not all experimentally observed spectra. The geometries required to reproduce experimentally observed spectra consistently require double‐helical geometries similar to the B or C forms of DNA.
Collagenase induced changes in the circular dichroism spectrum of collagen
Authors: Chu F. H. , Lukton A.
Published: December 2004

The maximum at 220 nm in the circular dichroism spectrum of native collagen solution changed to a negative value after heat denaturation or collagenase hydrolysis. The enzyme induced rate of CD change at 220 nm was shown to be first order in collagen concentration. The specific rate constant k is actually a combined rate constant kfast and kslow in which the ratio kf/ks is 4.1. The initial rates were linear with respect to enzyme concentration, and the Km was found to be 5.5 × 10−7 M. The rate of ultraviolet hyperchromicity at 220 nm on collagen hydrolysis was determined. The kfast was the same as that obtained by CD. The kf/ks ratio was 4.6. Both methods may be readily used to assay for collagenase activity.
The effect of neutral salts on the conformational transition of poly‐α‐amino acids. I. Potentiometric titration and optical rotatory dispersion studies
Authors: Conio G. , Trefiletti V. , Bodria F. , Troglia C. , Patrone E.
Published: December 2004

The effect of salts on the coil‐to‐helix transition of poly‐α‐amino acids was investigated by optical rotatory dispersion and potentiometric titration techniques. Both charge‐dependent and charge‐independent contributions to the free energy were considered.

The free energy of formation ΔF° of the uncharged α‐helix from the uncharged random coil for poly‐L‐glutamic acid (PGA) decreases very rapidly in the limit of zero added salt concentration. This effect probably depends on the uncertainty affecting the choice of the extrapolation of the apparent pK for the random coil at low ionic strength. Above 0.1 M salt, where the free energy determination becomes meaningful, the anions and cations investigated do not affect the value of ΔF°, with the exception of Li+. Our data support the point of view that this cation binds to the peptide group.

A class of salts produces an increase of the helical content of poly‐L‐ornithine (PO) both at low and high degree of ionization. This effect appears to be anion dependent. It is shown that (1) no change of ΔF° is involved; (2) recent theories of polyelectrolyte solutions cannot account for our results. We suggest that a true site binding of the anions to the charged amino groups occurs. The role of electrostatic binding in determining the conformational stability of proteins in the presence of some anions is stressed, and a general treatment for the electrostatic binding equilibria is outlined.
Vibrational analysis and dispersion curves of poly‐L‐hydroxyproline chain
Authors: Srivastava R. B. , Gupta V. D.
Published: December 2004

Dispersion curves and frequency distribution for poly‐L‐hydroxyproline (PLHP) chain were obtained using Wilson's GF matrix method as modified by Higgs. These are compared with those of poly‐L‐proline II and polyglycine II, which also have three‐fold screw symmetry. Ring and skeletal modes characteristic of PLHP are identified and the assignments of observed infrared and Raman frequencies are reported. Urey‐Bradley force constants were evaluated.
A circular dichroism study of poly dG, poly dC, and poly dG:dC
Authors: Gray Donald M. , Bollum F. J.
Published: December 2004

We have measured the ultraviolet circular dichroism spectra of oligo d(pG)5, poly dN AcG, poly dI, poly dC, two samples of poly dG, and four samples containing double‐stranded poly dG:dC. We find that oligo d(pG)5 and poly dG exist in self‐complexed forms as well as in single‐stranded forms. Unlike the self‐complexed form of poly dG, the single‐stranded form of poly dG can hydrogen‐bond with single‐stranded poly dC. We present spectral data for double‐stranded poly dG:dC, which can be used to help characterize poly dG:dC preparations and which provide a basis for resolving discrepancies among other reported poly dG:dC spectra.
Reversible oxygenation of heme bound to polyvinylpyridine and polyvinylimidazole
Authors: Tsuchida Eishun , Honda Kenji , Sata Hiroshi
Published: December 2004

The interaction between heme bound to poly‐4‐vinylpyridine (PVP) or poly‐N‐vinyl‐2‐methylimidazole (PVMI) and molecular oxygen (O2) was studied. In this paper, the reactions of some types of heme with O2 in organic solvents, particularly in N,N‐dimethylformamide (DMF) were discussed. The free heme not bound to an axial base was easily oxidized irreversibly to hemin in DMF with bubbled O2. The hemochromogens complexed with pyridine, imidazole, or their polymeric derivatives such as PVP and PVMI bound O2 to one of the axial coordination sites. The characteristic absorption band assignable to the resulting oxygenated heme was observed at 402 nm. This absorption band could be changed back to the characteristic band of the reduced hemochromogen at 418 nm by removing O2 dissolved in the DMF solution by a vacuum or by a stream of nitrogen. Thus, the hemochromogens bound to the synthetic polymers were found to adsorb and desorb O2 reversible in DMF.

When the polymeric ligands were used, the equilibrium constants in the complexation of heme with these polymers were about 102 times as large as those of the corresponding monomeric ligands. The oxygenation rates and the capacities of O2 of the polymeric hemochromogens were larger than those of the monomeric hemochromogens. In addition, the oxygenation rate of the polymer complex was changeable owing to the conformational change of the polymeric ligand; this rate increased about ten times under the optimal condition.
Proton and phosphorus magnetic relaxation studies on the dynamic structure of single‐stranded polyriboadenylic acid
Authors: Akasaka Kazuyuki
Published: December 2004

Proton and phosphorus‐31 nuclear spin‐lattice relaxation times (T1) have been measured with the Fourier‐transform method at 100 and 40.5 MHz, respectively, on single‐stranded polyriboadenylic acid (poly(A)) in a neutral D2O solution in the temperature range of 14–82°C. T1 minimum is observed around 35–45°C for H(8), H(1′), and phosphorus resonances. Rotational correlation times have been deduced from the T1 data, which indicate that the sugar–phosphate backbone as well as the base–sugar segment is undergoing rapid internal motion of 10−8–10−10 sec range. The molecular motion of the sugar–phosphate backbone as deduced from the phosphorus relaxation is well‐characterized by a single activation enthalpy of 8.1 kal/mole for the whole temperature range of 14–82°C. Activation enthalpies of similar magnitude have been obtained for the motion of the adenine–ribose moiety from H(8) and H(1′) relaxation. The relative magnitude of T1 for H(8) and H(1′) infers that the poly(A) nucleotide exists on the average as anti in the single‐stranded form. The phosphorus T1 value is consistent with a conformation such that both C(4′)–C(5′) and C(4′)–C(3′) bonds are nearly trans to their connected O–P bonds.
Statistical thermodynamics of oligomer–polymer interactions
Authors: Delisi Charles
Published: December 2004

A new method for formulating partition functions for a system of particles interacting on a one‐dimensional lattice has recently been developed.3,4 In this paper the method is applied to oligomer–polymer systems. The details of the connection between this method and the matrix formulation are first established. The method is then used to find expressions for the partition function of an oligomer–polymer system when the oligomers have a distribution of lengths and an alternating sequence.
Conformational change of the triple‐helical structure. I. Synthesis of model peptides of collagen by the solid‐phase method
Authors: Sutoh Kazuo , Noda Haruhiko
Published: December 2004

As model peptides of collagen, (Pro‐Pro‐Gly)n (n = 10, 12, 14, and 15) and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n (2n + m = 15; m = 1, 3, and 5) were synthesized by the solid‐phase method. The final products were pure when checked by high‐voltage paper electrophoresis and by amino acid analysis. Elemental composition was also examined.
A statistical mechanical study of helix–coil transition in concentrated solutions of polypeptides and proteins
Authors: Maleev V. Ya. , Gasan A. I.
Published: December 2004

The helix–coil transition in polypeptides was studied by methods of statistical mechanics, taking account of interaction between “melted” amide groups through hydrogen bonds. The statistical sums are calculated in the explicit form for two limit cases: (1) the dilute solution when the main contribution is given by collisions of two particles; (2) “condensation” when contacting macromolecules form a united aggregate. In the first case the transition enthalpy was shown to decrease linearly when the concentration increases, while at the appropriate choice of theoretical parameters, melting temperature and range are almost independent of the concentration. In the second case the structural transition parameters were shown to be independent of the concentration (the saturation effect). These results agree with the experimental data on synthetic polypeptides reported by other authors and with data on some globular proteins (serum and egg albumin) reported in this paper.
Electrical properties of hydrated collagen. II. Semiconductor properties
Authors: Tomaselli Vincent P. , Shamos Morris H.
Published: December 2004

The dc conductivity of hydrated bovine Achilles' tendon collagen has been determined as a function of hydration over a limited temperature range. At ambient temperature the conductivity changes from 10−15 (Ω cm)−1 in the dry state to about 10−8 (Ω cm)−1 at ∼24% water content by weight. For all temperatures the conductivity increases exponentially with hydration obeying σ(h) = A exp (βh), where h is a measure of the hydration, A is independent of temperature, and the parameter β ∼ T−1. It is shown that the data may be described by an impurity‐type mechanism in which the effective activation energy for the process is dependent on temperature and hydration. Conduction is assumed to be electronic with the impurity (water) acting as a donor. In the solid state the effect of water on the conductivity is reversible indicating the absence of chemical alteration of the hydrated collagen.
Normal vibrations of cyclic tetraglycine
Authors: Randhawa H. S. , Reddy N. V. R. , Rao C. N. R.
Published: December 2004

Normal vibration analysis of cyclic tetraglycine has been carried out employing the Urey‐Bradley force field and the vibrational assignments are compared with those in related molecules.
Helix–coil transition in heterogeneous DNA
Authors: Fixman Marshall
Published: December 2004

The broadening of a helix–coil transition due to base pair heterogeneity is calculated on the basis of a cumulant perturbation expansion in the quasi‐grand ensemble. In this ensemble the fictitious, homogeneous chain, to which the perturbation is referred, automatically decreases its correlation length as the heterogeneity increases. This “renormalization” seems to stabilize the perturbation expansion, in view of the good agreement between the present results and the exact theory of a heterogeneous polypeptide helix–coil transition. For the DNA model in which ring entropy is included, the transitions is found to be extremely narrow for an infinite random chain with conventional parameters. A tentative reconciliation of this result with contradictory calculations of some other workers is offered on the basis of end effects, coarse graining, or approximation to the ring entropy. An application of the new method to DNA with a non‐random base pair distribution requires evaluation of the correlation function between molecular states (helix or coil), at different sites of the reference chain. The evaluation is reduced to quadrature, but numerical calculations have been made only for the random chain.
Physical properties of endonuclease S1 digestion products of DNA renaturation intermediates
Authors: Miller Stephen J. , Wetmur James G.
Published: December 2004

The growth of the weight‐average double‐strand length of renaturing sonicated DNA was investigated as a function of the degree of renaturation. Endonuclease S1 was used to digest single‐strand ends and gaps. The ratio of the average renatured length to the initial length was found to be 0.6 ± 0.1 early in the reaction and to approach 1.0 at infinite time, while the ratio of the average single‐strand length of native regions increased from 0.6 ± 0.1 to 0.8 ± 0.1 at infinite time. The ratio increases are nonlinear, with the greatest growth occuring around 50% renaturation. Relaxation times of double‐strand DNA were measured in low salt using alternating field electric birefringence and were found to increase to only 70% of the relaxation time of the initial DNA at infinite time. In the molecular‐weight range examined (150–320,000 daltons), relaxation times vary with the 2.3 ± 0.3 power of molecular weight.
Raman spectra of D and L amino acid copolymers. Poly‐DL‐alanine, poly‐DL‐leucine, and poly‐DL‐lysine
Authors: Frushour B. G. , Koenig J. L.
Published: December 2004

The Raman spectrum of poly‐DL‐alanine (PDLA) in the solid state is interpreted in terms of the disordered chain conformation, in analogy with the spectrum of mechanically deformed poly‐L‐alanine. The polymer is largely disordered with only a small α‐helical content in the solid state. When PDLA is dissolved in water, the spectra suggest that short α‐helical segments are formed upon dissolution. These helical regions might be stabilized by hydrophobic bonds between side‐chain methyl groups. Addition of methanol to the aqueous PDLA solutions results in a Raman spectrum resembling that of solid PDLA. This result suggests that the methanol disrupts the helical regions by breaking the hydrophobic bonds.

The Raman spectra of poly‐DL‐leucine (PDLL) and poly‐L‐leucine (PLL) are compared and only slight differences are observed in the amide I and III regions, indicating that PDLL does not have an appreciable disordered chain content. Significant differences are observed in the skeletal regions. The 931‐cm−1 lines in the PLL and PDLL spectra are assigned to residues in α‐helical segments of the preferred screw sense, i.e., L‐residues in right‐handed segments and D‐residues in left‐handed segments (in PDLL). On the other hand, the 890‐cm−1 line in the spectrum of PDLL is assigned to residues not in the preferred helical sence, i.e., L‐residues in left‐handed segments and D‐residues in right‐handed ones. The Raman spectra of poly‐DL‐lysine and poly‐L‐lysine in salt‐free water at pH 7.0 are compared. The Raman spectra of the two polymers are very similar. However, this does not negate the hypothesis of local order in poly‐L‐lysine because the distribution of the residues in poly‐DL‐lysine probably tends towards blocks, and the individual blocks may take up the 31 helix.
Characterization of rodlike DNA fragments
Authors: Thomas M. Record , Woodbury Charles P. , Inman Ross B.
Published: December 2004

Native calf thymus DNA was sheared by sonication in a viscous solvent to the molecular‐weight range from 3 × 104 to 3 × 105 daltons, and fractionated by gel chromatography. Number and weight average molecular weights (M̄n and M̄w) were determined for individual fractions by electron microscopy; the ratio M̄w/M̄n for the peak fraction is approximately 1.1. Sedimentation coefficients (s020,w) of these fractionated samples show an approximately linear dependence on the logarithm of the molecular weight M̄w. This behavior is that expected for rodlike molecules, and is in quantitative agreement with the theory of Yamakawa and Fujii [(1973) Macromolecules 6, 407–415] for the sedimentation coefficient of a wormlike chain with a persistence length of 625 Å, a diameter of 25 Å, and a mass per unit length of 195 daltons/Å. It appears that the wormlike coil model, without excluded volume, can represent the sedimentation behavior of DNA over the entire conformational range from rigid rod to flexible coil, using the above parameters.

Equilibrium melting curves were determined for various fractions in aqueous 2.4 M tetraethylammonium bromide. A substantial broadening of the transition and decrease of the melting temperature were observed with decreasing molecular weight. Empirical expressions have been obtained relating both the transition temperature and breadth in this solvent to molecular weight.
Raman spectroscopic study of the structure of antibodies
Authors: Painter Paul C. , Koenig J. L.
Published: December 2004

The Raman spectra of human IgG, IgM, and rabbit IgG in lyophilized form and solution are reported. The spectral results indicate that the predominant structure in these immunoglobulin proteins is the antiparallel β‐sheet. The Raman spectra have also been obtained of rabbit anti‐ovalbumin, and this antibody molecule precipitated with its respective antigen. The spectra reflect a conformational change on binding of antibody with antigen. The conformational change occurs in the direction of disordering.
Helix–coil transition of poly(γ‐benzyl‐L‐glutamate) in the dioxane–dichloroacetic acid mixture
Authors: Gupta A. K. , Dufour C. , Marchal E. , Benoit H.
Published: December 2004

The thermal helix–coil transition of four samples of poly(γ‐benzyl‐L‐glutamate) in the dioxane–dichloroacetic acid (DCA) mixture was studied by optical rotatory dispersion method. The transition occurred at very high DCA content (97.5% by weight) in this system. The transition parameters have been evaluated by two methods based on the theories of Zimm and Bragg and of Nagai. The values of the helix initiation parameter and of the enthalpy of transition were found to be (4.4 ± 0.4) × 10−5 and 340 cal/mole, respectively. The range of validity and equivalence of the two methods is discussed.
Condensed states of nucleic acids. II. Effects of molecular size, base composition, and presence of intercalating agents on the Ψ transition of DNA
Authors: Cheng Sheau‐Mei , Mohr Scott C.
Published: December 2004

Circular dichroism spectroscopy has been used to investigate the influence of DNA molecular size, base composition, and the presence of intercalating agents upon the Ψ transition of DNA brought about by high concentrations of poly(ethylene oxide) and salt (Lerman (1971) Proc. Natl. Acad. Sci. (U.S.) 68, 1886–1890). A molecular weight of 0.15–3.0 × 106 daltons yields maximum formation of Ψ‐DNA. Both the amplitude of the large negative CD band at 265 nm—a chief characteristic of the Ψ state—and the thermal stability of Ψ‐DNA increase linearly with increasing mole fraction of guanine plus cytosine in the DNA sample. Either ethidium or proflavine, at concentrations where approximately one dye is bound per 5–10 nucleotide residues, can prevent the transition completely. Striking similarities between the Ψ‐DNA produced by poly(ethylene oxide) + salt and the complexes formed between DNA and lysine‐rich histone f1 suggest the presence of similar nucleic acid–nucleic acid interactions in both types of condensed phase.
Estimation of amino acid residue side‐chain absorption in the infrared spectra of protein solutions in heavy water
Authors: Chirgadze Yu. N. , Fedorov O. V. , Trushina N. P.
Published: December 2004

The values of maximum frequencies, intensities, and other spectral parameters of the main absorption bands of amino acid residue side‐chain groups have been obtained in the 1500–1800‐cm−1 region for solutions in heavy water at pD 1–12. It is shown that absorption of residues of asparagine, glutamine, aspartic and glutamic acids, arginine, and tyrosine must be taken into account in quantitative studies of the infrared spectra of polypeptide and protein solutions in heavy water. Examples of separating out the amide I band for ribonuclease A in heavy water are given.
Influence of the sugar configuration on the structure of RNA by conformational analysis of the ribose‐phosphate unit
Authors: Broch H. , Cornillon R. , Lespinasse J. N. , Vasilescu D.
Published: December 2004

The conformation of the ribose‐phosphate unit for the four principal configurations of the sugar ring has been studied using the extended Hückel theory and the Lennard–Jones empirical potential. Initially, the oxygen atoms of the p3 and p5 groups were not taken into account. With this restriction, the energy of this residue with regard to the structure of RNA has been minimized for the rotational angles ψ and ϕ′.

The equivalence of the sugar puckering C2′endo ≃ C3′exo and C3′endo ≃ C2′exo has been confirmed. We find that the role of the sugar configuration is important and that there is a difference in the rotations around the bond C3′‐O3′ (ϕ′ angle) according to this configuration. The C3′endo sugar form seems to be energetically preferred for this residue of RNA.

The oxygen atoms and the electrostatic interactions were then introduced into the empirical potential. The variation of the energy when varying ϕ′ for different positions of the p5 group was studied for the main C3′endo and C2′endo configurations of the sugar; in this condition the ϕ′ rotation is considerably restricted but the allowed regions continue to differ according to the configuration of the sugar considered.
Neutron‐scattering spectroscopy of the α‐ and β‐ forms of poly‐L‐alanine. Motion of the methyl side chain
Authors: Drexel Winfried , Peticolas Warner L.
Published: December 2004

Detailed inelastic, incoherent neutron‐scattering (INS) spectra are presented for poly‐L‐alanine in both the α‐helical and β‐sheet form. Assignments are made from previous normal coordinate calculations. Of particular interest is the methyl torsion at 230 cm−1, which is the strongest peak in the spectrum and is independent of backbone conformation. The height of the potential barrier for methyl group rotation is calculated to be 14 kJ mol−1.
Studies on cyclic peptides. II. Synthesis of cyclic peptides containing sarcosine
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

Cyclic peptides containing sarcosine, cyclo‐(Pro‐Sar‐Gly)2, cyclo‐(Sar‐Sar‐Gly)2, cyclo‐(Sar4), and cyclo‐(Sar6) have been synthesized by the cyclization of the p‐nitrophenyl ester of linear peptides. The tert‐butoxycarbonyl group was used as the Nα‐protecting group, which was removed by acid. Benzyl ester was used to protect the C‐terminal. tert‐butoxycarbonylpeptide was obtained by the stepwise elongation of the peptide bond by the carbodiimide method. Deblocking and cyclization of the linear peptides gave the cyclic peptides.
A 13C spin‐lattice relaxation study of dipeptides containing glycine and proline: Mobility of the cyclic proline side chain
Authors: Fossel E. T. , Easwaran K. R. K. , Blout E. R.
Published: December 2004

Molecular dynamics of the cyclic dipeptides cyclo(Gly‐L‐Pro), cyclo‐(L‐Pro‐L‐Pro), and cyclo(L‐Pro‐D‐Pro) and the linear dipeptides L‐Pro‐Gly and cis and trans Gly‐L‐Pro were studied in neutral aqueous solution by 13C nuclear magnetic resonance. Spinlattice relaxation times (T1) were determined for each individual carbon atom. The correlation times, τ, were derived from a semiquantitative analysis of the T1 data. The correlation times of the proline ring carbons, β, γ, and δ suggest that the cyclic dipeptides have more restriction of conformational freedom in the proline ring than the linear dipeptides. This effect is most pronounced on the γ carbon.
Hill's equation applied to reconstituted contractile collagen
Authors: Balmer R. T. , Soto R. J.
Published: December 2004

A new type of automatic force‐displacement recording myograph has been developed to measure the contraction–relaxation characteristics of contractile systems. The device produces a polytonic (variable‐force) load and therefore provides a more realistic measurement than either isometric or isotonic apparatus. Measurements on collagen that was first well ground and then extruded into a reconstituted thin tape show contraction and relaxation behaviour that can be characterized by a slightly modified form of Hill's 1938 equation. The characteristic parameters of the Hill equation determined for the reconstituted collagen were remarkably similar to those of intact muscle tissue.
Ion–polyelectrolyte interactions. Comparison between Manning's electrostatic theory and the multiple equilibrium theory of Scatchard in the case of linear polyelectrolytes and bivalent counterions
Authors: Magdelenat Henri , Turq Pierre , Chemla Marius
Published: December 2004

Manning's and Scatchard's models for the description of ion–polyelectrolyte interactions are compared in the case of linear polyelectrolytes and bivalent counterions, where “condensation” of the counterions is known to occur for certain concentration ratios of the two species in solution. This comparison leads to the definition of certain conditions on Scatchard's parameters for a precise structural interpretation of Scatchard's plots to be valid. Experimental data obtained with both models are compared and found in good agreement under such conditions.
Nmr study of the structure of short‐chain peptides in solution
Authors: Gupta‐Bhaya Pinaki
Published: December 2004

The electron‐mediated spin–spin coupling constant J between the amide NH and the α‐CH protons in the dipeptide fragment CαCO(NHCαH)RC′ONHCα is dependent on the dihedral angle of rotation (Φ) around the NC bond. Measurement of J in a series of zwitterionic dipeptides H3N+CHR1CONHCHR2CO2− (which is conformationally similar to the dipeptide fragment) in TFA solution shows that J is independent of R1, but dependent on the steric bulk of R2. The data are interpreted in terms of a model that assumes that what we measure is an average value of Ja thermal average over all the possible rotamers. The groups R1 and R2 are, in most cases, sterically kept apart by the trans and planar amide bonds, and hence the independence of J of R1. This model is consistent with the theoretical calculations done on the dipeptide fragment. The effect of the structural characteristics of the side chains (e.g., the effect of lengthening and branching the side chains) on the J values in dipeptides is discussed in the light of the existing results of theoretical calculations.

Study of 〈J〉 values in tripeptides (C6H5CH2OCONHCHR1CONHCHR2CO2CH3, essentially three linked peptide units) shows that electrostatic interaction between the two amide bonds modifies the potential energy surface and the 〈J〉 value of a dipeptide subunit in the tripeptides. Also in some cases, direct steric interaction between the two side chains in the two adjacent dipeptide subunits in the tripeptide affects the potential energy surfaces of the individual dipeptide subunits and hence the 〈J〉 values. The influence of the structural characteristics of the side chains of individual amino acids on structure formation at or beyond the dipeptide level is discussed at various points.

The J(NHαCH) values of CH3CONHCHRCONH2 and CH3CONHCHRCO2CH3 with the same R are quite different for R = valine, leucine, phenylalanine, methionine, but equal for R = glycine. This, coupled with the fact that one of the carboxamide NH resonances has a chemical shift different from its counterpart in simple amides like CH3CONH2 and the other carboxamide NH has the same chemical shift as its counterpart in CH3CONH2, suggest the presence of a hydrogen bond in dipeptide CH3CONHCHRCONH2 with carboxamide NH as the donor. Theoretical evidence for two seven‐membered hydrogen‐bonded rings with the carboxamide NH as donor and the acetyl oxygen as acceptor is summarized. Our data cannot suggest the number of such hydrogen‐bonded rings, nor can they conclude the relative proportion of these rings in a particular dipeptide. A discussion of the difficulty of interpretation is presented and the data are discussed under certain simplifying assumptions.
On the various types of circular dichroism induced on acridine orange bound to poly(S‐carboxymethyl‐L‐cysteine)
Authors: Imae Toyoko , Ikeda Shoichi
Published: December 2004

Circular dichroism and absorption spectra are measured on mixed solutions of acridine orange and poly(S‐carboxymethyl‐L‐cysteine) at different pH and P/D mixing ratios. The observed circular dichroism spectra are classified into several types, mainly based on the number and sign of circular dichroic bands in the visible region. Three of them are associated with the absorption spectra characteristic of dimeric dye or higher aggregates of dye. Type I is observed with solutions, of which the pH is acid and P/D is higher than 4, and it has an unsymmetrical pair of positive and negative dichroic bands at 470 and 430 nm. This type is induced on the dye bound to the polymer in the β‐conformation. Types II and III are considered to be characteristic of randomly coiled polymers. Type II is exhibited by solutions of P/D higher than 1 at pH 5–7 and has two dichroic bands around the same wavelengths as Type I but with opposite signs and an additional positive band at 560 nm. Type III, shown by solutions of P/D 2–0.6 at pH 6–10.5, has three dichroic bands around the same wavelengths as Type II but with signs opposite to it. The other two types of circular dichroism, induced for the solutions of P/D less than 1 at slightly acid pH, are associated with the absorption spectra of monomeric dye and are observed with disordered or randomly coiled polymer. They have a pair of dichroic bands at 540 and 425 nm, and the signs of these bands are opposite to each other in these two types.
Basic polypeptides as histone models. Synthesis, conformation, and interaction with DNA of statistical copolymers (Lysx,Alay)n
Authors: S̆okrová S̆. , Šponar J. , Havránek M. , Sedláček B. , Bláha K.
Published: December 2004

Statistical copolymers (Lysx,Alay)n were synthesized by copolymerization of N‐carboxyanhydrides of L‐amino acids. The conformation of copolymers in aqueous solutions was investigated using circular dichroism (CD). Calculations based on the CD data showed that polymers (Lysx,Alay)n can exhibit a random conformation, an α‐helix, and a β‐structure in various ratios. CD spectra of complexes of copolymers with DNA prepared by gradual dialysis from a high ionic strength to 0.15 M NaCl can be correlated with the copolymer conformation in medium and high ionic strength. For copolymers forming an α‐helix and β‐structure, these spectra show resemblance with similar spectra of complexes of those histones that are able to exhibit ordered conformations.