bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(L‐alanine): Specific heat measurements at low temperatures (1.8–20°K) and one‐dimensionality
Authors: Finegold Leonard , Cude Jesse L.
Published: December 2004

Low‐temperature specific heat measurements have been made on random poly(L‐alanine) (Pilot). The effective one‐dimensional (intra‐molecular polymeric) Debye temperature is 323°K, and the corresponding three‐dimensional temperature is 54°K. An anomaly, similar to that seen in polyethylene and other high polymers, is observed. The method will be a useful tool for the study of low‐frequency vibrations in polypeptides.
Conformational equilibria in a synthetic copolypeptide
Authors: Gratzer W. B. , Beaven G. H.
Published: December 2004

A synthetic copolymer of L‐glutamic acid and L‐tyrosine (23:1) with molecular weight 17,000 was examined conformationally as a function of pH, using circular dichroism, difference spectrophotometry, fluorescence, potentiometic titration, and high‐resolution nuclear magnetic resonance (220 MHz). A water‐dioxan mixture (2:1) was used to avoid complications due to aggregation (which was shown by infrared spectroscopy to lead to the formation of β‐structures). In the α‐helical form the tyrosine residues generate a sizeable negative Cotton effect in the near ultraviolet; this is a consequence of perturbation of the chromophores by the helix, and not of tyrosine‐tyrosine interactions, which are known to give rise in the right‐handed α‐helical state to positive Cotton effects. The pH profile of this Cotton effect is different from that of the peptide Cotton effects, which reflect the helix‐random coil equilibrium. The data are interpreted in terms of preferential breakdown of the α‐helix in the neighborhood of the tyrosine residues. An ultraviolet difference spectrum in the tyrosine absorption bands is generated at the low pH extreme of the conformational transition, the absorbance change being largely complete at a pH at which the other optical parameters have only begun to change. A possible explanation is the formation of a hydrogen bond between the phenolic hydroxyl and a carboxylate, the pK of which is lowered by the hydrogen bonding. An alternative explanation is the freezing of side‐chain rotations at a pH below the onset of the helix‐random coil transition, when the degree of side chain ionization approaches zero. Some support for the latter scheme comes from the splitting of side‐chain methylene proton resonances, indicating partial immobilization, as well as small changes in chemical shift of tyrosine ring protons in the pH (or pD) region in which the difference spectrum appears.
Myoglobin as a test case in the construction of space‐filling models of proteins using dihedral angles
Authors: Yankeelov John A. , Coggins John R.
Published: December 2004

A method for construction of space‐filling models of proteins of improved accuracy was developed from the dihedral angle technique proposed by Hauschka and Segal (P. V. Hauschka and D. M. Segal, Biopolymers, 4, 1051, 1966). Tools were designed to facilitate the marking of accurate reference lines on component atoms and a simple method for cementing the fixed angles was devised. The torsion angle method was extended to include all side chains. The improved technique was used to assemble a model of sperm whale metmyoglobin from the x‐ray data.
Preferential and absolute interactions of solvent components with proteins in mixed solvent systems
Authors: Inoue Hideo , Timasheff Serge N.
Published: December 2004

An equation is derived relating total and preferential interactions of solvent components with macromolecules in a three‐component system. Application of this equation to literature data shows that binding of non‐polar solvents to proteins parallels the unfolding of the latter. This observation is discussed in terms of local inter‐residue and residue‐solvent interactions.
The Interaction of Na Ions with Synthetic Polynucleotides
Authors: Archer B. G. , Craney C. L. , Krakauer H.
Published: December 2004

The interaction of Na+ with poly A, poly U, poly A·poly U, and Poly A·2 poly U has been investigated by means of potentiometry, by means of potentiometry, by means of a linked‐function analysis of its effect on the binding of Mg++ ions, and of K+ by means of an analysis of its effect on the sedimentation coefficients of the polymers. The last method was found to be inapplicable. The results of the other two methods were found to be consistent, except in the case of poly A where the existence of base stacking, influenced by the binding of Mg++, significantly affects the linked‐function analysis. The results are also consistent with the effects of the concentration of Na+ ions on the thermally induced conformational transitions of poly A·poly U and poly A·2 poly U, and with the extents of “binding” of Na+ to DNA measured by equilibrium and by transport methods. The interaction of Na+ with polynucleotides appears to be physically quite specific, although its thermodynamic basis is not clear.

The extent of binding of Na+, Ψ, was found to be independent of the total Na+ concentration but a quadratic function of the extent of Mg++ binding, θ. In the absence of Mg++, Ψ = 0.35–0.38 for poly U, 0.40 for poly A, 0.59 for poly A·poly U, and 0.66 for poly A·2 poly U.
Thermal denaturation of nucleohistones—effects of formaldehyde reaction
Authors: Li Hsueh Jei
Published: December 2004

Thermal denaturation of native or partially dehistonized nucleohistones shows two melting bands at 66 and 81° in 2.5 × 10−4 M EDTA, pH 8.0. These correspond to the melting of DNA segments bound by the less basic and the more basic half‐molecules of histones, respectively. These two melting bands combine into a broad melting band from around 70 to 85° when these nucleohistones are pre‐treated with formaldehyde. A formaldehyde reaction which fixes histones on DNA by covalent bonds account for the effect. Formaldehyde fixation also increases the melting temperature of some free DNA segments from around 42 to around 55°. This is interpreted as a result of closed or rigid boundaries between free DNA and formaldehyde‐reacted histone‐bound DNA segments. MgCl2 dissociates histones from DNA more effectively and leaves longer free DNA segments than does NaCl. Thermal denaturation of a formaldehyde‐reacted nucleoprotein thus provides an effective tool for comparing the relative size of free DNA regions on nucleoproteins. The effect of reversible binding of ligands on helix‐coil transition of DNA is descussed and found not adequate for thermal denaturation of nucleohistones.
Crystallite Features of Valonia cellulose by Electron Diffraction and Dark‐Field Electron Microscopy
Authors: Bourret A. , Chanzy H. , Lazaro R.
Published: December 2004

Individual cellulose crystallites from the cell wall of Valonia ventricosa have been studied by electron diffraction and observed by dark‐field electron microscopy. These two techniques reveal that the crystalline zones which run along the fibrils are above 1000 Å in length without any longitudinal periodicity. The width of the crystallites covers the width of the microfibrils and ranges from 140 to 180Å without persistent 35 Å subunits. In several instances, the crystalline zones terminate in the manner of a fork with two arms of 30 to 40 Å in width.
Linear relaxation analysis of the mechanochemical transformation of collagen fibers
Authors: Yannas I. V. , Olson D. A.
Published: December 2004

The isometric tensile stress generation observed when collagen fibers are immersed in aqueous solutions of lithium bromide ranging in molar concentration up to 7 was studied at 23°C. The reverse process, namely, isometric stress relaxation of the fiber occurring by subsequent immersion in distilled water, was also studied. We find that the data in the region of LiBr concentration up to about 2.5 moles/liter are adequately represented by a superposition integral

where σ(t) is the time‐dependent stress generated by the collagen fiber held at fixed length, c(t) is the history of LiBr molar concentration, and K(t) is the isometric contractility function, expressed as stress per unit salt concentration. We conclude that, within a limited range of salt concentration, a collagen fiber in a LiBr bath behaves as if it were a linear, time‐invariant system defined mechanochemically by a single function K(t) which depends on the structural characteristics of the fiber while being independent of salt concentration. An analysis is presented of isometric mechanochemical data obtained under conditions of equilibrium by other workers who studied the behavior of collagen fibers in aqueous solutions either of urea, LiBr, or KCNS. The analysis shows that these independent (equilibrium) data confirm the linarity of the relation between isometric contractile stress and salt concentration on which our superposition integral representation is based. We also find that the asymptotic (infinite‐time) value of the isometric stress is linearly related to the chemical potential of the salt as well, in agreement with the equilibrium thermodynamic treatment of mechanochemical processes by Katchalsky and Oplatka.
On the application of polyelectrolyte “limiting laws” to the helix‐coil transition of DNA. I. Excess univalent cations
Authors: Manning Gerald S.
Published: December 2004

A general theory of polyelectrolyte solutions is here used to calculate the differences in Gibbs free energy, enthalpy, and entropy between the coil and helix forms of DNA at any temperature and salt concentration. The salt has univalent cations and is assumed present in excess over the base concentration. The results are restricted to sufficiently dilute solutions. It is shown that the salt concentrations effect is entirely entropic in origin. When applied to the melting temperature, the calculations yield a relation between the enthalpy difference at the melting temperature and the slope of the plot of melting temperature vs. the logarithm of the salt concentration. In accord with observation, both the Gibbs free energy difference at any fixed temperature and the melting temperature are predicted to be linear functions of the log of the salt concentration.

However, the theory is not in quantitative agreement with enthalpy data. Data on various colligative and transport properties of both helix and coil forms are reviewed in the text and in Appendix B, and good agreement is found with theory for both forms. No attempt is made to explain why the theory is quantitative for these properties but not for heat measurements.

Finally, in Appendix A, an approximate calculation is made of the free energy contributions due to ionic effects not associated with the salt concentration.
PPP calculations of the circular dichroism spectra of some dinucleoside phosphates
Authors: Bailey Margaret L.
Published: December 2004

Circular dichriosm (CD) spectra have been calculated for serveral dinucleoside phosphates using a variant of the Pariser‐Parr‐Pople π‐electron molecular orbital method. This method does not require the prior knowledge of the experimental absorption spectra of transition moments of the bases forming the dinucleoside phosphates. Calculated spectra were obtained in good agreement with experimental spectra for four dinucleoside phosphates, ApA, UpU, GpA, and UpA, and reasonable agreement was obtained for ApG and ApU. The effect of changing conformation on the CD spectrum was studied for ApA, UpU, UpA, and ApU; the spectra of UpU, UpA, and ApU were sensitive to small change in conformation, whereas ApA was insensitive over the range of conformation studied. Further studies await detailed knowledge of the structure of dinucleoside phosphates in solution.
The circular dichroism of aromatic polypeptides: Theoretical studies of poly‐L‐phenylalanine and some para‐substituted derivatives
Authors: Woody Robert W.
Published: December 2004

We have calculated rotational strengths and circular dichroism (CD) curves for sidechain and backbone transitions in poly‐L‐Phenylalanine (PLP), POLY‐p‐amino‐L‐phenylalanine (PPALP), poly‐p‐chloro‐L‐phenylalanine (PPCLP), poly‐o‐acetyl‐L‐tyrosine (POALT), and poly‐p‐nitro‐L‐phenylanine (PPNLP), using methods applied previously to poly‐L‐tyrosine (PLT). Comparison of the theoretical CD curves with available experimental data for PLP and PPALP indicate that these polypeptides form right‐handed helices with side‐chain conformations similar to that of PLT. For PPNLP, where experimental data are also available, no conformational assignment could be made, as none of the calculated curves gave good agreement with experiment. Possible reasons for this lack of agreement are discussed. For the other two polypeptides, PPCLP and POALT, although no experimental data are yet available, the calculated curves indicate that an unambiguous assignment should be possible. For the conformations (RA and LA) in which the side chains are packed more loosely, there are strong similarities in the calculated CD curves of a particular conformation, regardless of the para substituent. In the tighter R1 and L1 conformations, few generalizations can be drawn, each derivative having a distinctive pattern. In PLP, PPCLP, and POALT, where the side‐chain La band is in the 200–210 nm region, the L1 conformation exhibits a negative nπ* rotational strength, opposite to that expected for a left‐handed helix. One must therefore be cautious about assigning the helix sense of aromatic polypeptides on the basis of the sign of the nπ* CD band. Side‐chain nπ* transitions present in POALT and PPNLP were found to have small rotational strength.
Optical and conformational properties of the 7‐(beta‐D‐ribofuranosyl) purines
Authors: Miles Daniel W. , Inskeep Warren H. , Townsend Leroy B. , Eyring Henry
Published: December 2004

The optical and conformational properties of certain 7‐ribosyl purines have been studied using several experimental and theoretical methods. The CD, MCD, and absorption spectra of the 7‐ribosyl purines and their cations have been determined experimentally with some solvent effects being noted. Theoretically we have used the SCF‐CI and CNDO molecular orbital calculations to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the ribose moiety; the optical activity was determined by the dipole coupling and electricmagnetic coupling equations; and the conformational energy calculations are included as a basis for excluding highly improbable conformations. On the basis of these calculations, we concluded that the oxy derivatives and the amino derivatives are predominately in the “extreme anti” conformation and “standard anti” conformation, respectively. However, the conclusions are tentative since at the present time the band assignments are not unequivocal. At least one n‐π* transition has been identified in the spectra which is not notably sensitive to pH and solvent effects. Several implications of this observation are discussed.
Structural Changes in t‐RNA from Changes in the Raman Scattering Intensities
Authors: Small Enoch W. , Brown Kenneth G. , Peticolas W. L.
Published: December 2004

Laser Raman spectra of a mixture of yeast t‐RNA's are examined as a function of temperature and after total alkaline hydrolysis to mononucleotides; the data are interpreted on the basis of extensive preliminary studies previously reported from this laboratory on the Raman spectral properties of numerous synthetic model compounds. Since the Raman intensities observed are extremely sensitive to conformational changes in the nucleic acid, much useful structural information can be obtained.
The molecular parameters of monomeric and acid‐soluble collagens. Low shear gradient viscosity and electric birefringence
Authors: Ananthanarayanan S. , Veis A.
Published: December 2004

The molecular parameters of pronase‐treated acid‐soluble bovine skin collagen (P‐ASC) were determined from low‐shear gradient viscosity, electric birefringence, and electron microscopic data in order to determine the shear gradient range in which viscosity studies yield data which can be correctly interpreted by use of the various hydrodynamic equations for prolate ellipsoids of revolution. The P‐ASC solutions could be characterized by a single relaxation process in electric briefringence with rotary diffusion coefficient θ of 810 sec−1 and a corresponding molecular length of 2850 Å. Viscosity data were found to be shear gradient dependent and only the extrapolated zero‐shear value [η]D = 0 could be used with the viscosity hydrodynamic equations to provide a correct value of molecular length. Intrinsic viscosities obtained at shear gradients >250 sec−1 are nearly 30% lower than the zero‐shear value. Untreated acid‐soluble collagen (ASC) solutions contain aggregates and these appear, from electric birefringence data, to be of endlinked character. ASC solutions show a much more marked shear gradient dependence than P‐ASC. For example, at D∼500sec−1,[η] = 22 dl/g, whereas the extrapolated zero‐shear value of[η] was found to be 44 dl/g. Thus, the shear gradient dependence of native collagen solutions is much more marked than previously assumed and, in contrast to the usual practice, only viscosities measured near zero shear can be interpreted in terms of molecular parameters for collagen solutions containing aggregates.
Kinetics of the helix‐coil transition in DNA
Authors: Record M. Thomas , Zimm Bruno H.
Published: December 2004

The kinetics of the helix‐coil transition have been investigated for T2 and T7 phage DNA in a formamide‐water‐salt mixed solvent using a slow temperature perturbation technique (applicable to kinetic processes with rate constants ⩽ 3 min−1). In this solvent degradation of the DNA is effectively suppressed. Complex kinetic curves are observed by absorbance and viscosity measurements for the response to denaturing perturbations in the transition region. Analysis of the decay curves indicates that the denaturation reaction in this time range can be treated as a first‐order reaction with a variable first‐order rate parameter, k, the derivative of the logarithm of the absorbance or viscosity change with respect to time. In the approach to denaturation equilibrium in the transition region, the rate parameter is determined only by the instantaneous extent of denaturation of the molecules. Near equilibrium, the rate parameter assumes a constant value characteristic of the equilibrium state. In this region, where the denaturation reaction proceeds as a simple first‐order process, both the decay of absorbance (reflected local conformational change) and the decay of solution viscosity (reflecting macromolecular conformational change) are characterized by the same constant value of k. In 83% formamide, 0.3M Na+, the rate parameter k for T2 DNA decreases from an extrapolated value of 2.0 min−1 at 0% denaturation to 0.11 min−1 at 90% denaturation. Rate parameters determined for T7 DNA at the same counterion concentration and fraction of denaturation are approximately five times as large as those cited for T2 DNA, indicating an inverse proportionality of rate constant to molecular length. On the other hand, simple first‐order kinetic responses with constant k are obtained for renaturing perturbations within the transition, indicating that the mechanism of rewinding differs, in most cases, from that of unwinding. Only in the limit of very small perturbations about a given equilibrium position are the rate constants k obtained from denaturing and renaturing perturbations equal. For perturbations of finite size, it appears possible that an intramolecular initiation or nucleation event may precede rewinding and limit the rate of this reaction. The rate parameters again are approximately inversely proportional to molecular weight. The one exception to the first‐power dependence on molecular weight appears when temperature jumps are made upward into the post‐transition region. Here the molecular‐weight dependence is second power, but complications arising from the different strand‐separation properties of T2 and T7 DNA's make interpretation difficult. The previously used model of friction‐limited unwinding appears to fit all the observations except for the molecular‐weight dependence.
On the kinetics of helix formation between complementary ribohomopolymes and deoxyribohomopolymers
Authors: Lee Cheng H. , Wetmur James G.
Published: December 2004

The rate of double helix formation by single‐stranded poly A plus poly dT, poly dA plus poly U, poly dA plus dT, poly G plus poly dC, poly dG plus poly C, and poly dG plus poly dC have been investigated and compared to rates of ribohomopolymer helix formation rates. After correction for molecular weight, comparisons of rate data at 30°C below the melting temperature of the double helix show that:

Rates of helix formation by all combinations of guanine plus cytosine homopolymers are the same.

The rate of helix formation for poly dA plus poly dT is three times faster than the rate for poly A plus poly U. Rates of formation of DNA‐RNA hybrid molecules are intermediate between these two rates, but closer to the poly dA plus poly dT rate.

The effect of temperature on the rate of helix formation is interpreted in terms of a steady‐state model for helix propagation. The results are consistent with a mechanism in which the formation of the second base pair is the rate‐determining step.
Extrinsic cotton effects of acridine orange bound to helical sodium desoxycholate
Authors: Zinner Klaus , Cilento Giuseppe
Published: December 2004

Acridine orange bound to helical sodium desoxycholate polymers shows several Cotton effects which in some cases stongly resemble the ones seen with glycosaminoglycans. The dye molecules are probably bound to the outside core of the helix through electrostatic interactions. The strong Cotton effect in the 540‐nm region arises from dye‐dye interactions. Subtle factors, including shaking, affect CD and ORD spectra of these complexes.
Optical anisotropy of polypeptide chains
Authors: Ingwall R. T. , Flory P. J.
Published: December 2004

Optical anisotropies γ2 of N‐t‐butylacetamide (tBA), N‐Methylacetamide (MA), and N, N‐dimethylacetamide (DMA) have been determined from the Rayleigh ratios for depolarzed scattering by dilute solutions of the amides in p‐dioxane. Traceless optical polarizability tensors \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for the amides are derived from these results in conjunction with the Kerr constant for tBA determined by LeGèvre and co‐workers. It is shown that the tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}i for the glycyle unit in a polypeptide chain may be identified with \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}MA. Methods for deriving corresponding tensors for other peptide units are indicated and the traceless polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for a polypeptide chain in any specified configuration is formulated.
Study of the interaction of polynucleotide chains with oligomers by means of chromatography
Authors: Bresler S. E. , Chernajenko V. M. , Saminski E. M.
Published: December 2004

A new method of measurement of the binding constant of oligonucleotides with complementary polynucleotide chains was developed using a gel filtration procedure. Data for complexing of poly U with triplets ApApA are presented and analyzed by means of a simple statistical theory of cooperative adsorption deduced by the Bethe‐Guggenheim method. The complexes are triple, they contain two polymer chains bound by oligomers. The energy of stacking is found equal to 1300 cal/mol in fair agreement with earlier data of Ts'o. The energy of binding of a single triplet to both complementary chains is equal to 14,000 cal/mol.
Dielectric properties of polyelectrolytes. III. Effect of divalent cations on dielectric increment of polyacids
Authors: Minakata Akira
Published: December 2004

Dielectric dispersion of polyacrylic acid (PAA) and polystyrene sulfonic acid (PSS) was measured in the presence of divalent cations. Effects of divalent ions were studied by neutralization with varying ratios of sodium hydroxide and divalent base concentration, addition of salts of divalent cations, and neutralization with divalent bases only. Two dispersion regions were observed in all cases, i.e., low‐frequency dispersion (102–104 Hz) and high‐frequency dispersion (105–106 Hz). The dielectric increment increases in the presence of sodium and alkaline earth metal ions together, but not with sodium and transition metal ions. This is due to the increment of low‐frequency dispersion and is attributable to the fluctuation of bound counterions which is explained by our theory previously reported.1 In the case of PAA neutralized with large fractions of divalent ions, or with divalent ions only, the increment is very small because of reduction of the fluctuation by interaction between bound ions at the neighboring sites and reduction of the effective length of polyion probably due to chelation by divalent ions. There are some differences among the effects of Mg++, Ca++, and Ba++ on dielectric increment which may result from affinity or chelating ability of these ions.
Far‐infrared spectra of sequential copolymers of amino acids with alkyl group side chains
Authors: Itoh Koichi , Katabuchi Hiroaki
Published: December 2004

Far‐infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L‐Ala‐L‐Ala‐Gly)n, (L‐Ala‐Gly)n, (L‐Ala‐Gly‐Gly)n, (L‐Val‐L‐Ala‐L‐Ala)n, and (L‐Val‐L‐Ala)n, have the antiparallel pleated sheet structures and that the backbone conformations of (L‐Val‐L‐Val‐L‐Ala)n and (L‐Val‐L‐Val‐Gly)n are the same as that of poly‐L‐valine. The far‐infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly‐L‐alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x‐ray powder‐diffraction patterns of these samples.
The hydrolysis of poly (L‐prolyl‐glycyl‐L‐prolyl) by bacterial collagenase
Authors: Harper Elvin , Berger Arieh , Katchalski Ephraim
Published: December 2004

Poly (L‐Prolyl‐Glycyl‐L‐Prolyl), a polymer which resembles collagen by physical and immunochemical criteria, has been shown to serve as a substrate for the highly specific bacterial collagenase obtained from Clostridium histolyticum. The postulated reaction products Gly Pro, Gly Pro Pro, and Pro Gly Pro Pro have been isolated. The enzyme has been employed as an analytical tool in elucidating the sequence of synthesized polymers of proline and glycine.
Effect of non‐complementary nucleotides on the rate of helix formation: Kinetics of formation of poly (I)·poly (C,I) and poly (I)·poly (C,U) complexes
Authors: Kallenbach Neville R. , Drost Stanley D.
Published: December 2004

Apparent second‐order rate constants for complex formation between poly (I) and poly (C) and copolymers of C containing non‐complementary I or U residues have been determined spectrophotometrically. The rate constants decrease as the concentration of either I or U in the C strands increases–the effect seems insensitive to the species of residue involved, when differences in the thermal stabilities of the poly (I) poly (C,I) and poly (I). poly (C,U) complexes are taken into account. These results suggest that low concentrations of relatively stable defects can alter the apparent kinetic “complexity” of polynucleotides as determined by hybridization methods (C0t analysis).
Model connective tissue system: The effect of proteoglycan on the diffusional behavior of small non‐electrolytes and microions
Authors: Preston B. N. , Snowden J. Mck.
Published: December 2004

The diffusional behavior of low‐molecular‐weight solutes through gel membranes containing polyanionic material has been studied as a model for connective tissue. A steady‐state isotopic flux measurement is used. Results indicate that the presence of solutions of “native” proteoglycans within a gelatin‐agarose matrix has negligible effects on the diffusion of non‐electrolytes but markedly affects the behavior of ionic species. The permeabilities of counter‐and coions are discussed in terms of a Donnan equilibrium. It is evident that not all the counterions of the polyionic salt can be regarded as mobile in terms of the Donnan effect. The polyelectrolyte theories of Katchalsky et al. are applied to the behavior of the gel membranes to explain this observation. These quantitative interpretations suggest that counterion fixation by the proteoglycans occurs.
Criteria for the crystallization of polysaccharides
Authors: Atkins E. D. T. , Wills H. H. , Mackie W.
Published: December 2004

The relationship between crystallization and the annealing process is well established in the synthetic polymer field. This relationship appears to have been somewhat neglected in studies on biopolymers. Results are presented to show the effect of both humidity and temperature in promoting structural changes in polysaccharide system. Three different polysaccharides have been used as examples of how crystallization may be speeded up by annealing at elevated temperatures.
Solution properties of synthetic polypeptides. XII. Enthalpy changes accompanying helix‐coil transition of polypeptide
Authors: Teramoto Akio , Norisuye Takashi
Published: December 2004

For helix‐coil transitions of polypeptide in binary mixtures consisting of helix‐forming solvent and coil solvent, the transition enthalpy ΔH(T,x) has been found to depend significantly on temperature (T) and solvent composition (x). For such systems, calorimetric measurements may yield some averages of ΔH(T,x) which are no longer amenable to direct comparison with ΔH itself. Theoretical equations relating calorimetric data to ΔH(T,x) are derived and tested favorably with experimental data. It is demonstrated that the transition enthaply from heat capacity measurements is approximately equal to ΔHcfm, while those from heat of dilution and heat of solution measurements are equal to ΔHc. Here ΔHc denotes the value of ΔH at the transition point and fm represents the maximum helical content attained in a thermally induced transition. The discrepancies among calorimetric data are also discussed.
Conformational studies on copolymers of L‐leusine and L‐leucine: Circular dichroism and potentiometric titration studies
Authors: Snell Christopher R. , Fasman Gerald D.
Published: December 2004

Conformational aspects of a series of copolymers of L‐Leucine and L‐leucine [poly‐(LysxLeuy)] containing 0 to 0.41 mole fraction L‐leucine have been studied by circular dichroism (CD) and potentiometric titration in 0.05M KF solution. CD studies on the α‐helical conformation showed a dependence of the magnitude of the CD ellipticity band at 222 nm on copolymer composition; the [θ]222 decreasing with higher leucine contents. This was interpreted as the result of an increase of the hydrophobicity of the environment of the amide group due to the presence of the leucyl residues. Values of the Zimm‐Rice parameter, σ, for the copolymers were obtained from the potentiometric titrations and used to fit theoretical curves to the experimental data. Using the variation of σ with polymer composition, a value of σ for the leucyl residue was estimated to be 6.3 × 10−2, assuming independence of σ on the amino acid sequence in the copolymer. The free energy change for the conversion of one mole residue from uncharged helix to uncharged coil, ΔGhc°, was also obtained from the titration data for each copolymer up to a leucine mole fraction of 0.16; a value of 385 cal mole−1 was estimated for ΔGhc° for a leucyl residue. These values for σ and ΔGhc° are compared with other values in the literature for various amino acid residues obtained from titration and melting curve data.
The approach to equilibrium in a buoyant‐density gradient
Authors: Schmid Carl W. , Hearst John E.
Published: December 2004

The theory for the approach to equilibrium in a buoyant‐density gradient is experimentally examined for the case of DNA in CsCl.
Coformational aspects of polypeptide structure XL. The synthesis of poly[(S)‐thiazolidine‐4‐carboxylic acid]
Authors: Goodman Murray , Su Kai‐Chiang
Published: December 2004

The synthesis of poly[(S)‐thiazolidine‐4‐carboxylic acid] is described. The polymer is obtained by the polymerization of the N‐carboxyanhydride of (S)‐thiazolidine‐4‐carboxylic acid in pyridine or nitrobenzene using triethylamine as an initiator. The amino acid is prepared by the condensation of cysteine and formaldehyde. N‐Acetyl‐(S)‐thiazolidine‐4‐carboxylic acid methyl ester is also prepared as a model compound by standard acetylation and esterification reactions.
Non‐empirical valence bond calculation of hydrogen bond energy in polypeptides
Authors: Takashima Shiro
Published: December 2004

An approximate ab‐initio valence bond calculation of hydrogen bond energy was carried out and the results are discussed. The total bond energy of a simplified NH…O structure is calculated for various NH and N…O distances and the potential energy profiles are obtained. The hydrogen bond energy, ie, the delocalization energy gained by the formation of one hydrogen bond is found to be 8.7–12.0 kcal/mole. The potential energy is characterized by a deep minimum at 1.6–1.8 a.u. from the nitrogen and the second trough is found to be considerably higher than the first.
High shear rate viscosity measurements with dilute solutions of bovine fibrinogen
Authors: Lederer Klaus , Schurz Josef
Published: December 2004

Viscosity measurements at a rate of shear between 104 and 5 X 105 sec−1 were carried out with solutions of bovine fibrinogen (c = 8.0–18.4 mg/ml). The degree of anisotropy of the fibrinogen molecule estimated from the data is less than expected for Hall and Slayter's molecular model of fibrinogen. A tentative interpretation is offered in terms of Köppel's model of fibrinogen.
Comparison of the UV flow dichroism spectra of TMV and several of its mutants
Authors: Gabler Raymond , Bendet Irwin
Published: December 2004

The dichroic ratio spectra of TMV and four of its mutants (YTAMV, GTAMV, HR, and CV4) were determined from 320 to 240 nm. Measurements were also made on particles of ATMV (TMV protein reconstituted with polyadenylic acid) and rods of repolymerized TMV, YTAMV and GTAMV protein, respectively. These cylindrical molecules were oriented in a flow gradient with their degree of orientation being determined from anisotropic light scattering measurements. Taking length distributions into account, the dichroic ratios were then extrapolated to values characteristic of perfect particle alignment.

Due to the large number of overlapping absorbing bands in the whole viruses, it is very difficult to separate out specific contributions to the total spectra. Since, however, the spectra for the whole viruses were similar, this would suggest an overall likeness in structure for all the virus particles studied. Because the repolymerized proteins did not have the four RNA chromophoric groups present, their spectra would be more sensitive to protein contributions to the total spectrum. Repolymerized rods of YTAMVP yielded results similar to those for TMVP, while the spectrum for repolymerized rods of GTAMVP was significantly different from that obtained for TMVP.

Dichroic ratio spectra of the nucleic acids, as they exist within the whole particles, were also calculated by subtracting protein absorptivities from their respective viral absorptivities. The spectra indicates similar results for the various nucleic acids in all the particles studied.
The Circular Dichroism of Complexes of 2,7‐Di‐tertiary‐Butyl Proflavine with DNA
Authors: Dalgleish D. G. , Feil M. C. , Peacocke A. R.
Published: December 2004

The binding isotherm of 2, 7‐di‐tert‐butyl proflavine on calf thymus DNA has been measured by dialysis equilibrium. The CD spectra of complexes of the dye and DNA have been measured, and the variation of the induced circular dichroism of the dye with the amount of dye bound (r) has been found. The results show that di‐tert‐butyl proflavine binds to DNA in a completely different manner from proflavine itself, since both the visible and ultraviolet CD spectra of complexes of the two dyes with DNA differ markedly. The conformation of the nucleic acid is not affected by the binding of di‐tert‐butyl proflavine. It is possible that these results may allow determination, by using CD spectroscopy, of whether molecules intercalate into DNA.
Raman studies of nucleic acids. VII. Poly A · poly U and poly G · Poly C
Authors: Lafleur L. , Rice J. , Thomas G. J.
Published: December 2004

Laser‐excited Raman spectra of the double‐helical complexes poly A·poly U and poly G·poly C are reported for 2H2O and H2O solutions. The spectra are discussed in relation to their use as quantitative reference spectra for determining the dependence of the Raman scattering of RNA on secondary structure. The Raman line at 815 cm−1, due to the phosphodiester group, exhibits the same intrinsic intensity in spectra of poly A·poly U and poly G·poly C and is thus dependent only upon the amount of ordering of the helix and not on the kinds of nucleotides involved. The hypochromic Raman lines in spectra of poly A·poly U are identified and their intensity changes are determined quantitatively over the temperature range 32–85°C. Comparison of the spectra in the 1500–1750 cm−1 region reveals that the Raman lines from carbonyl group vibrations of uracil are about sevenfold more intense than those of guanine and cytosine for both paired and unpaired states and will thus dominate the spectra of RNA. The Raman frequencies in this region are also compared with previously reported infrared frequencies and give evidence of being strongly perturbed by base‐stacking interactions in the helices.
Side chain interactions in aromatic dipeptides
Authors: Deber Charles M. , Joshua Henry
Published: December 2004

A study of the 100‐MHZ nuclear magnetic resonace spectra in D2O solution was made of a series of linear dipeptides of the types L‐phenylalanine‐L‐and‐D‐X, and L‐phenylalanine‐L‐and‐D‐Y, where X comprised a group of amino acid residues with polar side chains (X = glutamine, glutamic acid, arginine, and Nε‐acetyllysine) and Y comprised amino acid residues with purely aliphatic side chains (Y = α‐aminobutyric acid and norvaline). It was found that regardless of the side chain length, resonances due to the α‐methylene protons in the X and Y side chains of the L‐Phe‐D‐Y series consistently exhibited upfield shifts greater than any other protons in these side chains, when compared to the corresponding side chain resonances of the nonaromatic dipeptide series L‐Ala‐L‐X and L‐Ala‐L‐Y. The magnitudes of these shielding effects were consistently and considerably greater for the L‐Phe‐D‐X series than for the L‐Phe‐D‐Y series. An intramolecular complex–formed by association of armatic π‐electrons with the positive end of the dipole in the polar side chains—was proposed as one plausible interpretation of the enhanced shielding effects. An increase in temperature from 32 to 70–80° was sufficient to overcome the enhanced shielding attributable to the suggested complex.
Protein labeling by acetylation
Authors: Miller I. R. , Great H.
Published: December 2004

A method has been developed for labeling proteins by acetylation without appreciable loss in biological activity.
Adsorption of single‐stranded and double‐helical polynucleotides on the mercury electrode
Authors: Brabec V. , Paleček E.
Published: December 2004

The adsorption of single‐stranded polynucleotides and double‐helical DNA on the dropping mercury electrode has been studied with the aid of Breyer's alternating current (a.c.) polarography. Our results indicate that all three constituents of polynucleotides (residues of bases, sugar, and phosphoric acid) are involved in the adsorption. At neutral pH their participation in adsorption depends on the ionic strength, the potential of the electrode, and the conformation of the polynucleotide in the solution.

At an ionic strength of about 0.1, double‐helical DNA is adsorbed electrostatically on a positively charged electrode surface by inadequately masked negative charges of the phosphate groups. At a higher ionic srength (about 0.5), this electrostatic adsorption is no longer detectable by using a.c. polarography; under these conditions it is probable that native DNA is adsorbed around the potential of the electrocapillary maximum with the aid of sugar residues and a few bases. Single‐stranded polynucleotides, on the other hand, are primarily adsorbed by means of the bases.

Desorption of double‐helical DNA occurs around a potential of −1.2 V against SCE. At this potential, the helical regions of single‐stranded polynucleotides are also desorbed. Desorption of the disordered regions of single‐stranded polynucleotides occurs at more negative potentials. Adsorption and desorption of a small number of bases released from double‐helical DNA was evident in the a.c. polarograms only at elevated temperature, or at room temperature after degradation of DNA by sonication.
A V7 conformation of dimethyl sulfoxide‐amylose complex
Authors: Simpson T. D. , Dintzis F. R. , Taylor N. W.
Published: December 2004

X‐ray investigation of a crystalline complex between dimethyl sulfoxide (DMSO) and amylose indicates a sevenfold helical structure having an orthogonal unit cell: a = 30.23 Å, b = 28.18 Å, and C = 7.91 Å (helix axis). This helical amylose results from precipitation of amylose in DMSO solutions under suitably dry conditions using toluene as a precipitating agent. Analyses show a molar ratio of 0.95:2:0.4:0.08 for DMSO, amylose glucose units, water, and toluene, respectively. DMSO and amylose combine in at least two crystalline conformations, sixfold and sevenfold helices. The amount of water present influences the resulting conformation. The existence of the sevenfold helical solid indicates that the amylose sevenfold helix has greater stability than previously recognized by conformational energy calculations. In general, potential energy calculations cannot be correct that ignore the influence of guest molecules and their effects upon the maltose residue conformation and that lead to a sixfold helix as the most probable structure.
Fine structure of DNA melting curves
Authors: Lyubchenko Yu. L. , Frank–Kamenetskii M. D. , Volgodskii A. V. , Lazurkin Yu. S. , Gause G. G.
Published: December 2004

Theoretical calculations predict that the differential melting curves for random polynucleotide sequences having lengths up to several tens of thousands of base pairs have a clear‐cut fine structure. This structure appears in the form of multiple narrow peaks 0.3–0.4°C wide on the bell shaped main curve. The differential melting curves have different shapes for different specific sequences. The theory also predicts the disappearance of the fine structure when the length of the sequence increases and when circular, covalently closed DNA is considered instead of the open structure. The predictions of the theory were confirmed by the measurements of differential melting curves for open and covalently closed circular forms of DNA for PM2 phage (N = 104 base pairs) and also for other phage DNA's of different length: T7 (N = 3.8 × 104); SD (N = 9.2 × 104); T2 (N = 17 × 104). It was shown that the effect of fine structure results mainly from the cooperative melting out of DNA regions 300–500 base pairs long.
Conformation of the cyclic tetrapeptide dihydrochlamydocin. Iabu‐L‐Phe‐D‐Pro‐LX, and experimental values for 3 → 1 intramolecular hydrogen bonds by X‐ray diffraction
Authors: Flippen Judith L. , Karle Isabella L.
Published: December 2004

Chlamydocin, Iabu‐L‐Phe‐D‐Pro‐LX, is a naturally occurring cyclic tetrapeptide that exhibits high cytostatic activity. The conformation of the peptide ring, as well as the stereo configuration in the vicinity of the epoxide ring, have been established by a single‐crystal X‐ray study of dihydrochlamydocin: C28H40N4O6·H2O. It crystallizes in the monoclinic space group P21 with a = 12.616(6) Å, b = 12.355(6) Å, c = 9.442(5) Å, and β = 99.5(1)°. The structure was solved by the symbolic addition procedure for phase determination followed by the tangent formula method of phase refinement. This structure represents the first cyclic tetrapeptide in which all four peptide units have been found in the trans conformation; however, each peptide unit is significantly nonplanar with ω angles deviating by 14–24° from the ideal value of 180°. This molecule contains two intramolecular 3 → 1 hydrogen bonds and experimentally determined parameters for these seven‐membered turns are presented.
Fluctuations of an α‐helix
Authors: Gō Mitiko , Gō Nobuhiro
Published: December 2004

Fluctuations in backbone dihedral angles in the α‐helical conformation of homopolypeptides are studied based on an assumption that the conformational energy function of a polypeptide consisting of n amino‐acid residues can be approximated by a 2n‐dimensional parabola around the minimum point in the range of fluctuations. A formula is derived that relates 〈ΔθiΔθj〉, the mean value of the product of deviations of dihedral angles ϕi and ψi (collectively designated by θi) from their energy minimum values, with a matrix inverse to the second derivative matrix F,n of the conformational energy function at the minimum point. A method of calculating the inverse matrix Fn−1 explicitly is given. The method is applied to calculating 〈ΔθiΔθj〉 for the α‐helices of poly(L‐alanine) and polyglycine. The autocorrelations 〈(Δϕi)2〉 and 〈(Δψi)2〉 at 300°K are found to be about 66 deg2 and 49 deg2, respectively, for poly(L‐alanine), and 84 deg2 and 116 deg2, respectively, for polyglycine. The length of correlations of fluctuations along the chain is found for both polypeptides to be about eight residues long.
Coenzyme models. IV. Effect of polymer micelles on rate and equilibrium of addition of cyanide ion to N‐substituted 3‐carboxamidopyridinium ions
Authors: Shinkai Seiji , Kunitake Toyoki
Published: December 2004

The water‐soluble poly(1‐vinyl‐2‐ethylimidazole) quaternized with ethyl bromide and lauryl bromide was prepared; lauryl group content, 8.8 mol% (L‐9), 28.9 mol% (L‐29), and 40.9 mol% (L‐41). The λmax value of methyl orange near 460 nm shifted to shorter wavelengths (417–433 nm) in the aqueous solution of L‐29 and L‐41, and the intrinsic viscosity of L‐29 was more than ten times smaller than that of L‐9. The rate and equilibrium constants (kƒ and K) for addition of cyanide ion to the N‐substituted 3‐carboxamidopyridinium ions were studied at 30°C, where N‐substituents employed were n‐propyl, n‐hexyl, benzyl, 2,6‐dichlorobenzyl, and n‐lauryl. The kinetic parameters for n‐lauryl‐3‐carboxamidopyridinium were markedly increased in the presence of L‐29 and L‐41 and with increasing polymer concentrations (84‐fold for kƒ and 7800‐fold for K), especially at low ionic strength, whereas L‐9 decelerated the addition reaction. These distinct behaviors mean that L‐29 and L‐41 are classified as micellelike polymers and L‐9 as a polyelectrolytelike polymer. However, L‐29 depressed the rate of the forward reaction for benzyl‐3‐carboxamidopyridinium, acting like a simple polyelectrolyte. Therefore, the polymer micelle can provide both the microenvironments characteristic of polyelectrolytes and micelles, depending on the hydrophobicity of substrates.