bluuebunny/crossref_metadata_2025_split huggingface dataset:
Independence of length and temperature effects on the rate of helix formation between complementary ribopolymers
Authors: Lee Cheng H. , Wetmur James G. 
Published: December 2004

AbstractThe rate of double helix formation by single stranded Poly A plus Poly U, Poly I plus Poly C, Poly G plus Poly C, and T2 DNA has been investigated as a function of both the length of the reacting strands and temperature. The length dependence of the rate is found to be independent of temperature. All of the reactions studied show a rate approximately proportional to the square root of the length of the shorter of the complementary strands. At or about 30°C below the melting temperature the ribopolymers react with about the same rate. This rate is four to five times slower than DNA renaturation rates. The effect of temperature on ribopolymer reaction rates is interpreted in terms of a steady‐state model for helix propagation.
Dielectric dispersion of the α‐helix at the transition region to random coil
Authors: Wada Akiyoshi , Tanaka Toyoichi , Kihara Hiroshi 
Published: December 2004

AbstractDielectric studies have been carried out for the helix–coil transition of poly‐β‐benzyl‐L‐aspartate with m‐cresol as a solvent. The transition of the solute molecules has been sharply reflected as a characteristic change in the dielectric dispersion curves in changing temperature. Two polarizations, one having a low and the other a high critical frequency, have appeared. According to theoretical considerations of a model of a broken helix, the former is found to come from the orientation. of helical sequences and the latter from the chemical relaxation due to the helix–coil transition. It also seems likely that the unfolded chain may have a polarizability which could not be neglected at the high‐temperature side of the transition.
An x‐ray diffraction study of poly‐L‐arginine hydrochloride
Authors: Suwalsky M. , Traub W. 
Published: December 2004

AbstractAn x‐ray study has been made of polyarginine hydrochloride to investigate whether, like polylysine hydrochloride, it can undergo conformational changes merely from variations in the degree of hydration. X‐ray powder and fiber photographs of specimens containing up to about five molecules of water per arginine residue show features characteristic of α‐helical structures including a 5.4‐Å layer line and a meridional 1.5‐Å reflection. Increasing the water content from 1/2 to 61/2 molecules per residue causes the a axis of the hexagonal unit cell to increase from 14.4 Å to 15.8 Å, with no appreciable change in the 27.0 Å c axis. Removal of the last half molecule of water results in a very diffuse α pattern, but on rehydration the sharp pattern reappears.Specimens containing five to twenty water molecules per residue show quite a different pattern, the spacing of which do not vary appreciably with hydration. This pattern includes a meridional 3.4‐Å reflection, a feature commonly shown by β structures, and indeed all the reflections can be satisfactorily indexed in terms of a monoclinic unit cell with a = 9.26 Å, b = 22.05 Å, c = 6.76 Å, and γ = 108.9°. These dimensions are shown by models to be compatible with a β pleated‐sheet structure.
Pressure dependence of the helix–coil transition temperature for polynucleic acid helices
Authors: Gunter T. E. , Gunter K. K. 
Published: December 2004

AbstractThermal denaturation of DNA's and the corresponding helix–coil transformation of artificial polyribonucleic and polydeoxyribonucleic acids have been studied extensively both theoretically1–13 and experimentally. 14–30 Much less work has been carried out on the properties of these polynucleic acids at high pressure, and in particular, on the presure dependence of the helix–coil transition temperature.31–33 Light‐scattering techniques have been used in this study to measure the pressure dependence of the helix–coil transition temperature of the two‐ and three‐stranded helices of polyriboadenylic and polyribouridilic acids and of calf thymus DNA. From the slopes of the transition temperature vs. pressure curves and heats of transition obtained from the literature,20,34 the following volume changes from these helix–coil transitions have been obtained: (a) −0.96 cc/mole of nucleotide base pairs for the poly (A + U) transition, (b) +0.35 cc/mole of nucleotide base trios for the poly (A + 2U) transition, and (c) +2.7 cc/mole of nucleotide base pairs for the DNA transition. The relative magnitudes and signs of these volume changes which show that poly (A + U) is destabilized by increased pressure, whereas poly (A + 2U) and calf thymus DNA are stabilized by increased pressure, indicates that further development of the helix–coil transition theory for polynucleotides is needed.
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

AbstractLow‐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

AbstractA 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

AbstractA 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

AbstractAn 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

AbstractThe 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

AbstractThermal 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

AbstractIndividual 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

AbstractThe 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

AbstractA 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

AbstractCircular 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

AbstractWe 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

AbstractThe 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

AbstractLaser 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

AbstractThe 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.