bluuebunny/crossref_metadata_2025 huggingface dataset:
The electrostatic potential of a discretely charged cylinder in solution
Authors: Bailey James M.
Published: December 2004

The electrostatic potential of an infinitely long cylinder with a periodic, discrete charge density was calculated, assuming the cylinder was immersed in a simple 1 : 1 electrolyte solution. The charge density of the simple electrolyte was taken to be the linearized Debye‐Hückel charge density. It was also assumed that the discrete charge density, was within the cylinder (rather than on its surface), and that the interior of the cylinder had a unique dielectric constant Dh, which was treated as a parameter. Although this model (except for the Debye‐Hückel assumption) more realistically represents DNA than previous models, the calculated potential was found to be ambiguous, depending on the value chosen for the depth of the discrete charge below the cylinder surface. However it was also found that the dependence of the potential on the simple electrolyte concentration was well‐defined and was identical to that of a continuously charged cylinder. It was concluded that the continuously charged cylinder model adequately describes differential salt effects.
Observation of small conformational changes in the sperm‐whale myoglobin by the far‐infrared spectra
Authors: Chirgadze Yu. N. , Ovsepyan A. M.
Published: December 2004

Small conformational changes in a molecule of sperm‐whale myoglobin in its native solid state for different pH values at room temperature as well as during heat denaturation in alkali medium at different stages of unfolding of the globule were observed by using far‐infrared spectroscopy in the region from 30 to 600 cm−1. The changes appeared in the absorption bands near 420 and 470 cm−1 ascribed to the side‐chain vibrations of helical segments of the myoglobin molecule. For the first time the high structural sensitivity of the far‐infrared region of the skeletal vibrations has been confirmed experimentally and the applicability of this technique to globular proteins demonstrated.
Far‐infrared spectra of sequential polypeptides with α‐helical and polyglycine II structures
Authors: Itoh Koichi , Katabuchi Hiroaki
Published: December 2004

The sequential copolymers of glycine and L‐alanine, L‐valine and L‐alanine, L‐leucine and L‐alanine, and L‐phenylalanine and L‐alanine and those containing the L‐proline residues were synthesized. The infrared spectra in the region from 700 to 200 cm‐1 were measured for these polypeptides with the α‐helical conformation or the polyglycine II structure and compared with the spectra of the β‐form structures. The results showed that several infrared bands observed in the region from 600 to 200 cm‐1 clearly reflect not only the backbone conformations but also the local conformations of component amino acid residues of polypeptides with the α‐helical, β‐form and polyglycine II structures.
Kinetics of the acid hydrolysis of heparin from its Cu (II) complex and its relation to biological activity
Authors: Stivala Salvatore S. , Yadlowsky Slawko , Yuan Leon
Published: December 2004

The acid‐catalyzed hydrolysis of heparin from Cu(II) complex was studied as a function of time and temperature. Four independent calculations showed that the hydrolysis, during the 5‐hr period examined, obeys the first‐order kinetic law. Specific rate constants, calculated at 50°C, 57°C, 65°C, 71°C, and 80°C, were 3.3 × 10−5 sec−1, 6.5 × 10−5 sec−1, 10.4 × 10−5 sec−1, 15.1 × 10−5 sec−1, and 26.6 × 10−5 sec−1, respectively. Arrhenius plots of the data yielded 14.7 kcal as the energy of activation. An independent run of the self‐hydrolysis of heparin at 57°C also obeyed first‐order kinetics and its specific rate constant of 6.4 × 10−5 sec−1 is in excellent agreement with that of the hydrolysis of Cu(II)‐heparin at 57°C. The anticoagulant activity of heparin and of the Cu(II)‐heparin are not appreciably different. Further, the inactivation of heparin closely parallels Cu(II) release from the Cu(II) complex which in turn parallels desulfation.
Copper ion binding and heparin interactions of human fibrinogen
Authors: Lages Bruce , Stivala S. S.
Published: December 2004

The binding of copper ions to fibrinogen was studied by the equilibrium dialysis technique in neutral Tris buffer. The presence of copper causes precipitation of fibrinogen‐copper complexes, the amount of which varies with the copper ion concentration. Solutions of 96% clottable fibrinogen (whole fibrinogen) displayed a maximum binding capacity about four times greater than that of fibrinogen solutions from which the cold‐insoluble precipitate had been removed (cold‐soluble fibrinogen). Binding in both systems apparently involves two classes of sites in fibrinogen, and the class of lower affinity is associated with cooperative interactions with copper. The copper concentration at which this cooperative uptake occurs is identical to the concentration at which the amount of precipitated material increases sharply and also to the concentration at which a sharp decrease is observed in the sedimentation coefficient of soluble fibrinogen, suggesting some relationship between copper binding, solubility, and solution properties.

The presence of heparin markedly affects the sedimentation coefficient of fibrinogen in the presence of copper ions, although showing a lesser effect in the absence of the metal. The sedimentation coefficient of fibrinogen is increased in the presence of heparin and copper ion, compared to the value of fibrinogen‐copper systems without heparin, and this effect is enhanced by changing the fibrinogen:heparin molar ratio to larger values. The precipitation of fibrinogen from solution, apparently without a coincident removal of heparin, also increases with increasing copper ion concentration and fibrinogen:heparin molar ratio. The possible significance of these effects in terms of heparin anti‐coagulant activity is discussed.
Rotational relaxation of macromolecules determined by dynamic light scattering. I. Tobacco mosaic virus
Authors: Schurr J. Michael , Schmitz Kenneth S.
Published: December 2004

The intensity autocorrelation function for the depolarized component of forward‐scattered light from a solution of large polymeric molecules is derived in terms of the correlation function for the amplitudes of the Y2,±1(θ,ϕ) fluctuations in the anglar distribution of segments in the solution without any assumptions regarding the statistical properties of the scatterad light field. Effects arising from the use of polychromatic incident light and from the mixing of the scattered and polychromatic incident light beams are examined in detail.

Apparatus for observing the depolarized forward‐scattered light, digitizing and storing the fluctuating phototube current at rates from 10 to 540,000 times per second, and computing the correlation functions directly in the time‐domain is described herein. Correlation functions were obtained for 0.05 mg/ml solution of tobacco mosaic virus at pH 9.1 and also at pH 6. The degree of association of the virus appears to be independent of pH, and the monomer relaxation times (corrected to 25°C) extracted from the data by a least‐squares procedure lie in the range 0.44–0.49 msec, also independent of pH. The absence of faster component in the correlation function between 6 μsec and 0.5 msec is used in conjunction with thermal fluctuation theory to infer a lower limit for the effective Young's modulaus of the rod, E ≤ 2.5 × 107 dynes/cm2.
Dielectric study of the urea denaturation of delipidated and relipidated bovine serum albumin
Authors: Rosseneu‐Motreff M. Y. , Soetewey F. , Lamote R. , Peeters H.
Published: December 2004

Dielectric relaxation and viscosity measurements were performed on delipidated and relipidated samples of bovine serum albumin (BSA) at urea concentrations between O and 6M. By the combined interpretation of these two hydrodynamic methods the characterization of conformational changes of the molecule during urea denaturation is possible.

The denaturation of delipidated BSA results from two mechanisms. The first one is a slow, time‐dependent elongation of the molecule; the second one is a rapid swelling which becomes most pronounced at urea concentrations higher than 4M. For relipidated albumin, the slow elongation mechanism occurs but the presence of fatty acids protects the protein aganist molecular swelling. In both cases these conformational changes are accompanied by an increased disymmetry of charge repartition and a concomitant increase of the dipole moment.

From these results it follows that lipidated albumin (as occurs under physiological conditions) is less sensitive to denaturation than delipidated albumin.
Non‐bonded interatomic potential functions and crystal structure. Correction of the functions for use with macromolecules and application to polypeptide helixes
Authors: Nelson Donald J. , Hermans Jan
Published: December 2004

On the basis of a set of nonbonded interatomic potential functions derived earlier from heats of sublimation and experimental crystal structures, we derive a second, less repulsive, set which is to be used in the absence of the expansion caused by thermal motion and in particular in macromolecular systems where thermal motion is much reduced compared with crystals of small molecules. Working with a pair of octane molecules, we calculate the intermolecular potential (U) in the presence of thermal motion from potentials U° (in the absence of thermal motion), by letting a system of pairs of molecules assume a Boltzmann distribution over the intermolecular distance, in the presence of a force of varied magnitude applied to obtain different equilibrium distances. The potential U° is adjusted until the calculated and the empirical potentials U agree. Finally, best interatomic Lennard‐Jones potentials which reproduce the function U° are calculated. The resulting functions are tested by calculating the crystal structure of benzene and comparing it with experimental data at low temperature, by energy minimization of the crystal structure of polyethylene and of the β‐structure of poly‐L‐alanine, and by comparing the energy of the α‐helix and the β‐structure of poly‐L‐alanine. In all cases, the corrected functions give more satisfactory results than the uncorrected set.
The electrical properties and stability of DNA to UV radiation and aromatic hydrocarbons
Authors: Snart R. S.
Published: December 2004

Studies of the d. c. conductive behavior of solid gels of DNA under high vacuum have shown that a reproducible energy gap of 2.4 eV and a photoelectric effect may be obtained following extensive evacuation procedures. Admission of air for short periods has a reversible effect on this photoelectirc effect and semiconductive behavior. After prolonged illumination in air the sample becomes permanently affected and will not reproduce the photoelectric effect or give rise to a semiconduction energy gap of 2.4 eV but give rise to a permanently lower energy gap of 1.6 eV. The effect of ultraviolet irradiation on the thermal denaturation of DNA in the presence of six aromatic hydrocarbons has been examined in order to determine the extent to which the presence of the hydrocarbon protects the DNA against ultraviolet damage.
Translational and rotational diffusion of tobacco mosaic virus from polarized and depolarized light scattering
Authors: King T. A. , Knox A. , McAdam J. D. G.
Published: December 2004

The translational and rotational dynamics of tobacco mosaic virus in sodium phosphate buffer (pH =7.5) solutions has been investigated by polarized and depolarized light scattering Rayleigh linewidth studies. For concentrations ranging from 1.75 × 10−4 g ml−1 to 0.25 × 10−4 g ml−1 the translational diffusion coefficient (DT) has been found to be slightly concentration dependent and extrapolation to zero concentration gives D020°C = 0.34 ± 0.01 × 10−7 cm2S−1. A full analysis of the polarized spectra obtained at high and low scattering angles and the depolarized spectra at near zero scattering angles has enabled these techniques to be compared and the rotational diffusion constant DR to be determined. At a solution concentration of 1.75 × 10−4 g ml−1 a mean value is found to be DR20°C = 350 ± 30s−1. These values of DT and DR are in approximate agreement with calculations based on models of the tobacco mosaic virus molecule as a cylindrical rod.
Oscillator strengthes of the 1La and 1Lb absorption bands of tryptophan and several other indoles
Authors: Strickland E. Hardin , Billups Carolyn
Published: December 2004

The intensities of the indolyl 1La and 1Lb absorption bands were investigated by using 5‐methoxyindole as a model compound. With 5‐methoxyindole dissolved in weakly interacting solvents, almost the entire 1Lb electronic transition occurs at longer wavelengths than the 1La transition. The resolved spectrum of 5‐methoxyindole permitted estimation of its oscillator strengths and also those of other indoles dissolved in cyclohexane: indole, 0.129 (1La), 0.019 (1Lb); 5‐methylindole, 0.129 (1La), 0.027 (1Lb); 5‐methoxyindole, 0.138 (1La), 0.045 (1Lb); 3‐methylindole and N‐stearyl‐L‐tryptophan n‐hexyl ester, 0.127 (1La), 0.027 (1Lb). Hydrogen bonding to 1‐methyl‐2‐pyrrolidinone does not measurably affect the total near‐ultraviolet oscillator strength of indoles (less than 5% change). In water and ethanol, the oscillator strength of 3‐methylindole and tryptophan is 15–20% less than that of 3‐methylindole dissolved in cyclohexane. The spectra of the N‐stearyl n‐hexyl esters of tryptophan and 1‐methyltryptophan dissolved in methylcyclohexane can be generated by using 1La and 1Lb bands having shapes similar to those observed for 5‐methoxyindole, if the 1La and 1Lb bands are shifted so that their O‐O bands overlap (289.5 nm for tryptophan and 299.5 nm for 1‐methyltryptophan).
Cooperative binding of oxygen to hemoglobin: Analysis of accurate equilibrium binding data
Authors: Deal Walter J.
Published: December 2004

Accurate equilibrium binding data for the oxygenation of hemoglobin are used (a) to show that various models for cooperativity are inconsistent with the best available experimental data, (b) to determine the equilibrium constants for binding of 2,3‐diphosphoglycerate to hemoglobin molecules in intermediate stages of oxygenation, and (c) to deduce a mechanism for allosteric effects in hemoglobin which is consistent with the best available experimental data. The total free energy of cooperativity is defined and discussed.
Laser Raman studies of conformational variations of poly‐L‐lysine
Authors: Yu Tain‐Jen , Lippert Joseph L. , Peticolas Warner L.
Published: December 2004

The frequencies and intensities of the laser Raman spectra of poly‐L‐lysine (PLL) have been observed in the following studies: (1) the thermally induced α‐to‐β transition which occurs with increasing temperature at high pH; (2) the ionized form to α transition at 10°C by increasing pH; and (3) the ionized form to α transition by ionic strength at low pH.

The frequency‐dependent bands which have been observed are the amide I (in H2O), amide I′ (in D2O), amide III, and C–C stretch. It has been found possible to assign an unique set of frequencies and intensities to each conformation of PLL of α, β, and ionized form. In this way the nature of the conformations intermediate in the transitions can be determined. The frequencies of the amide III and amide III′ are very weak in the α‐helix and somewhat higher than usual in the β form. Hence it appears the amide III and amide III′ bands may differ from one type of polypeptide to another with the same backbone conformation.
Low‐frequency vibrational spectra of some homopolypeptides in the solid state
Authors: Fanconi Bruno
Published: December 2004

Low‐frequency Raman and far‐infrared spectra of polyglycine, poly‐L‐alanine, and poly‐L‐valine have been measured. The Raman spectra exhibit an intense band near 100 cm−1 for these homopolypeptides. Lattice calculations of the polyglycines are used to assign the intense Raman band to a rotary lattice mode. For homopolypeptides in the β conformation, an infrared band is observed whose frequency varies inversely with the square root of the mass of the peptide repeating unit. This infrared band is assigned to the hydrogen bond stretching lattice vibration.
Study by circular dichroism and optical rotatory dispersion of polypeptides with aromatic side‐chain chromophores
Authors: Barny Pierre Le , Loucheux‐Lefebvre Marie H.
Published: December 2004

Poly(ortho‐, meta‐, and para‐γ‐nitrobenzyl‐L‐glutamates) were studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in two helicogenic solvents, hexafluoroisopropanol (HFIP) and dichloroethane (EDC), and two non‐helicogenic solvents, dichloracetic acid (DCA) and trifluoroacetic acid (TFA). The corresponding glutamates were also studied in DCA and TFA. The symmetric nitrobenzylic chromophore is optically active when the polymers are in solution in DCA and TFA. The corresponding glutamates are also optically active under the same conditions. Thus, it was not possible to explain the origin of the optical activity of the side‐chain chromophore when the polymer is in solution in a helicogenic solvent. Nevertheless, from a side‐chain dichroic band, a helix–coil transition curve was determined and the stability of each poly(γ‐nitrobenzyl‐L‐glutamate) given; this stability depends on the position of the nitro substituent on the aromatic ring.
Calculated minimum energy. Conformations of nonactin
Authors: Lee Yan N. , Hamori Eugene
Published: December 2004

Nonactin is a cyclic actinomycete metabolite which has been implicated as an ion carrier in the passive transport of potassium across certain biological membranes. In order to discover the conformations of the molecule which are involved in its biochemical function, computer calculations were initiated to derive the energetically favored conformations of the nonactin ring. By assuming that all the relevant three‐dimensional conformations of nonactin have the same symmetry property as that suggested by the chemical structure of the molecule (S4) it was possible to generate a representative sample of all sterically allowed conformations of nonactin. The energies of these conformations were calculated by taking into account the nonbonded interactions among the 116 atoms of the molecule and the torsional potential energy of the 20 rotatable backbone bonds of the ring. The initial results reported in this paper indicate that even in the absence of potassium ion the nonactin ring folds into the same compact tennis‐ball seam‐like conformation that was found by an X‐ray crystallographic investigation of the nonactin/KNCS complex.
Interactions between mucopolysaccharides and cationic polypeptides in aqueous solution: Hyaluronic acid, heparitin sulfate, and keratan sulfate
Authors: Gelman R. A. , Blackwell J.
Published: December 2004

Circular dichroism spectroscopy has been used to study the interactions of hyaluronic acid, heparitin sulfate, and keratan sulfate with cationic polypeptides. The results indicate that the presence of these mucopolysaccharides has an effect in the conformation of poly(L‐lysine) and poly(L‐arginine), such that the former adopts the “random” form and the latter takes up the α‐helical conformation, rather than the “charged coil” form expected at neutral pH. The relative strengths of the interactions can be judged from the melting temperatures above which they are disrupted. Both the stoichiometry and the strength of the interactions depend on the position, number, and type of anionic groups attached to the polysaccharide backbone. Such considerations place the six common mucopolysaccharides in order of increasing strength of interaction: hyaluronic acid < chondroitin 4‐sulfate < heparitin sulfate < chondroitin 6‐sulfate < keratan sulfate ⩽ dermatan sulfate. These differences should be paralleled by differences in the interaction of the mucopolysaccharides with collagen and fibrous proteins.
Circular dichroism of films of polynucleotides
Authors: Brunner Wendel C. , Maestre Marcos F.
Published: December 2004

The CD spectra of films of the lithium salt of E. coli and calf thymus DNA, and alternating d‐AT : AT were measured as a function of relative humidity. Films of the ammonium acetate salt of DNA were also measured. The ammonium films yield the previously reported A‐form CD spectra. A possible explanation for the small magnitude of the 260‐nm band of the A‐form film spectra compared to double‐stranded RNA spectra is that the film DNA is in a different conformation than RNA within the A family of conformations.

At relative humidities of 92% or lower, a negative nonconservative CD spectrum with negative minima near 270 and 210 nm is observed with the lithium films. The magnitude of the minima varies from film to film. In films of DNA the magnitude ranges from a delta epsilon of −5 to −35; d‐AT : AT films show magnitudes to −300. CD spectra of this type are designated Ψ spectra. Similar spectra have been reported from reconstituted complexes of DNA and polylysine or f‐1 histone. If the origins of the film and protein–DNA complex spectra are similar, the complex spectra are not the result of specific secondary structural changes induced in the DNA by the protein fraction. Theoretical analysis suggests that Ψ spectra are not the result of changes in the secondary or tertiary structure of DNA. Instead, the previously proposed explanation based on liquid crystals is favored. The DNA could form asymmetric structures with long‐range periodicity. It is likely that the observed CD spectra of f‐1 complexes are artifacts of DNA aggregation. The possibility that some other previously published spectra of protein–DNA complexes also reflect artifacts is suggested.
Proton magnetic resonance study of complex formation between N6‐methyladenosine and polyuridylic acid
Authors: Bangerter Benedict W. , Modestas Zivile
Published: December 2004

The interaction between N6‐methyladenosine and polyuridylic acid in D2O solution at neutral pD has been studied as a function of temperature and N6‐methyladenosine concentration by proton magnetic resonance spectroscopy. A rigid double‐stranded 1:1 complex is formed below ∼10°C, involving hydrogen‐bonded N6‐methyladenine:uracil base‐pairing and stacking of the adenine bases. This complex is less stable than the 1:2 complex formed between adenosine and polyU, and involves a more rapid exchange of the monomer between free and polymer‐bound environments.
Differences of nucleotide stacking patterns in a crystal and in binary complexes— the case of adenine
Authors: Caillet Jacqueline , Claverie Pierre
Published: December 2004

Calculations of the intermolecular interaction energy between stacked planar molecules show that, for this type of configuration, there is no well‐defined minimum. (The energy surface exhibits a rather large flat basin and not a deep, sharply defined, minimum.) As a consequence, the relative position of the molecules is very likely to change under environmental modifications, e.g., when the molecules become part of a crystal. Detailed calculations are carried out for the case of adenine and show that the experimental structure actually displays the lowest energy among all structures tried, although no binary configuration in the crystal is identical with that giving a minimum for a binary complex. On the contrary, for a column of stacked molecules, the minimum of the total interaction energy is still practically obtained when the successive stacked pairs of the column are in the binary minimum configuration. It is concluded that, for such configurations with a loosely defined minimum like stacking, crystal structure data may be used only with great caution for assigning a precise configuration to the binary complex.
The V amylose–H2O system: Structural changes resulting from hydration
Authors: Zaslow Bert , Murphy Vincent Gerard , French Alfred Dexter
Published: December 2004

X‐ray diffraction and stereochemical analyses were used to study the hydrated structure of the helical amylose polymorph having a fiber repeat spacing of 8 Å. Intensity calculations using computer models confirmed six as the number of residues per turn and supported the space group P212121. Both diffraction intensity and stereochemical methods indicate the suitability of residue G3 from the potassium acetate complex of cyclohexaamylose as opposed to residues with longer O(4)–O(1) vectors. Comparison of the present results with those obtained for V amylose dehydrate indicated no major conformational differences between the two helix skeletons. A net helical rotation of approximately 30° accompanied the hydrate–dehydrate transition and the rotational position in the hydrate allowed packing that was less close. Hydration water molecules were not located; noncarbohydrate peaks on the electron density maps were primarily due to Fourier series termination errors.
Dynamic light scattering studies of poly‐L‐lysine HBr in the presence of added salt
Authors: Lee Wylie I. , Schurr J. Michael
Published: December 2004

Clipped autocorrelation functions for the fluctuating intensity of light scattered from dilute solutions of poly‐L‐lysine in 0.2 M NaBr have been observed over a wide range of time scales down to 1.83 μsec, and over a wide range of pH. Two poly‐L‐lysine samples of molecular weight 35,000 and 200,000, respectively, were compared to determine the extent of draining of the so‐called random‐coil configuration. The observed correlation functions were in general very satisfactorily represented by simple translation diffusion of single molecules. At high pH ∼10–10.4, there was evidence of considerable aggregation, but no indication whatsoever of any unusually fast component, as reported recently by Jamieson et al. for poly‐L‐lysine HBr in the absence of salt.

A 30% rise in the diffusion coefficient to a peak at pH 10 parallels the previously reported dip in the intrinsic viscosity, and is interpreted in terms of a more compact structure in that pH region between the coil and helix extremes.
Double‐helical DNA and RNA circular dichroism. Calculations on base–sugar‐phosphate helix interactions
Authors: Moore Dexter S. , Wagner Thomas E.
Published: December 2004

Theoretical calculations of the near ultraviolet (uv) circular dichroism of double‐helical DNA and RNA models were performed in order to evaluate the effects, on the calculated circular dichroism, of including the interactions of near uv quantum transitions of the nucleic acid bases with classical polarizable bonds of the sugar‐phosphate backbone. Double‐helical models (A‐form, B‐form, and C‐form DNA and RNA‐11) from X‐ray diffraction data were used in the calculations. The results indicate that the contributions to the circular dichroism in the near uv region, of these types of interactions, provide calculated spectra that are slightly altered from calculated spectra when only base–base transition interactions were considered.
Synthesis and optical studies of L‐methionine oligopeptides in solution
Authors: Naider Fred , Becker Jeffrey M.
Published: December 2004

A series of L‐methionine oligomers [BOC‐(Met)n‐OMe] (n = 2–7) and the corresponding diastereomeric di‐ and tripeptides were synthesized using the mixed anhydride method. Oligomers prepared in this manner were optically pure and were obtained in reasonable yield. Preliminary optical examination of the peptides suggests that secondary structures may begin forming in the pentamer or hexamer in trifluoroethanol. BOC‐(Met)4‐OMe and BOC‐(Met)5‐OMe were also synthesized using an insoluble resin containing BOC‐L‐methionine as the nitrophenol active ester.
Dispersion equation and polarizability of bovine serum albumin from measurements of refractive indices
Authors: Andersen M. , Painter L. R. , Nir S.
Published: December 2004

Refractive indices of bovine serum albumin solutions in saline and in 2‐chloro ethanol are measured for the spectral region 1770–10000 Å by a reflectance method. A procedure for the determination of a dispersion formula for binary mixtures is developed and applied. The electronic polarizability of bovine serum albumin is determined and is found to be almost independent of the solvent and concentration. Hence it follows that the electronic polarizability of bovine serum albumin is almost independent of the molecular environment.
Optical rotatory properties of L‐cystine conformational isomers. Theoretical analysis
Authors: Strickland R. W. , Webb J. , Richardson F. S.
Published: December 2004

The near ultraviolet chiroptical properties of L‐cystine conformational isomers are examined on a static, “one‐electron” model in which the disulfide moiety is the chromophoric group and the atoms of the L‐alanyl fragments are treated as perturbers. The zeroth order chromophoric wave functions are calculated on a semiempirical molecular orbital model in which excited states are constructed in the virtual orbital‐configuration interaction approximation. The perturbing environment is represented by point charges located at the atomic centers of the L‐alanyl fragments. Chromophore–perturber interactions are expressed as charge–multipole moments with only the charge–dipole and charged–quadrupole terms being retained in the calculations. Vicinal contributions to the rotatory strengths of the five lowest energy disulfide transitions are computed for 30 conformational isomers of the L‐cystine dizwitterion. The results provide support for the view that vicinal or peripheral effects can account entirely for the observed near ultraviolet (λ > 230 nm) chiroptical properties of L‐cystine and its derivatives and that these properties are diagnostic of conformational features external to the disulfide moiety.
A demonstration of two‐component behaviour of the circular dichroic spectra of poly(L‐tyrosine, 3‐bromo‐L‐tyrosine) in trimethylphosphate
Authors: Applequist Jon , Lunde Barbara K.
Published: December 2004

The circular dichroic spectrum of poly(Tyr,TyrBr) in trimethylphosphate from 180 to 320 nm is found to be a linear function of composition from 25 to 68% TyrBr, and the spectra of the Tyr and TyrBr components are resolved. For Tyr the resolved spectrum is in agreement with available CD spectra of poly(Tyr). These results are interpreted to mean that the side‐chain conformations of Tyr and TyrBr are not affected by the other component, and that for Tyr the conformation is the same as in poly(Tyr). It is also concluded that poly(Tyr,TyrBr) is helical with the same helix sense as poly(Tyr). The restrictions on the side‐chain conformations are discussed, and it is suggested that the Tyr and TyrBr side chains are all in the same χ1 region.
Raman spectral changes induced by side‐chain interactions in racemic poly‐γ‐benzyl glutamate
Authors: Wilser Walter T. , Fitchen D. B.
Published: December 2004

Laser Raman spectra are reported for solid films cast from a series of solutions containing mixtures of right‐ and left‐handed α‐helices of poly‐γ‐benzyl‐L‐ and D‐glutamate. Procedures were established for producing spectra that were reproducible in position to ±0.3 cm−1 and in relative intensity to a few percent for features of interest. Spectra for the pure L and pure D polymers were identical, as expected. Several small but definite spectral changes appear in the mixtures, reaching a maximum for the racemic 50:50 mixture. The changes are a shift of −1.4 cm−1 in the amide I peak at 1650.5 cm−1; a shift of about −5 cm−1 in the partially resolved amide III peak at 1291 cm−1; a shift of +2.5 cm−1 in the benzyl peak at 3062.5 cm−1; changes in relative intensity of as much as 50% in several regions; and the marked enhancement of several peaks, particularly that at 254 cm−1. These changes are discussed in terms of side‐chain interactions in the packing of right‐ and left‐handed helices.
Stacking specificity and polarization. Comparative synopsis of affinity data
Authors: Lawaczeck Rüdiger , Wagner Karl G.
Published: December 2004

An explanation is given of the specificity of stacking associations based on suggestions of the contribution of dipole‐induced dipole interactions, which emphasize bond moments as the origin of the polarizing power and polarizability of the π‐electron ring system concerned. This explanation is consistent with our own experimental data and with those of other authors on nucleoside self‐association, the mixed interaction of different nucleic acid constituents, and the interaction of aromatic amino acids with nucleosides, nucleotides, and nucleic acids.
Spatial configuration of single‐stranded polynucleotides. Calculations of average dimensions and nmr coupling constants
Authors: Tewari Ravindra , Nanda Rabindra K. , Govil Girjesh
Published: December 2004

The probability distributions of the torsional angles (Φ′, ω′, ω, Φ, and ψ), which fix the structure of nucleotide backbone, have been calculated using the results of energy calculations based on extended Huckel theory (EHT), complete neglect of differential overlap (CNDO), perturbative configuration interaction using localized orbitals (PCILO), and classical potential functions (CPF) methods. Statistical average values of the vicinal 1H1H, 1H31P, and 13C31P nmr coupling constants 〈J〉 have been calculated from the generalized Karplus relations using the probability distribution in the Φ′, Φ, and ψ space. Experimental 〈J〉 values for polyribouridylic acid (polyU) support the theoretical predictions for these torsional angles. Using Monte Carlo technique, random coils of single‐stranded polynucleotides have been simulated and the mean‐square end‐to‐end distance 〈r2〉 has been calculated. Molecular orbital methods (EHT, CNDO, and PCILO) suggest considerable flexibility around OP bonds, leading to fairly small values for the characteristic ratio (C∞ ∼ 4). Observed values of the unperturbed characteristic ratio for polynucleotides are quite large (C∞ ∼ 18) suggesting a relatively rigid nucleotide backbone. The results based on molecular orbital calculations can be reconciled with the experimental values by introducing an additional stabilization of ∼2 kcal mol−1 for the predicted minimum energy ragion (Φ′ ∼ 240°, ω′ ∼ 290°, ω 290°, Φ 180°, and ψ 60°). Such a stabilization may arise from the association of water molecules and metal ions with the phosphate group and (or) Coulomb interaction between neighboring phosphate groups. The calculations provide a semiquantitative estimate of torsional rigidity in the nucleotide backbone.
The influence of alcohol–water solvents on the conformation of deoxyribonucleic acid
Authors: Frisman E. V. , Veselkov A. N. , Slonitsky S. V. , Karavaev L. S. , Vorob'ev V. I.
Published: December 2004

The influence of alcohol–water solvents on the conformation of native DNA was studied by the methods of flow birefrigence and viscometry. Conformational transitions of DNA were observed at low alcohol concentrations corresponding to the destruction of the water spatial structure. A change in the secondary structure of the DNA molecule was observed at high ethanol concentrations and is discussed in the paper.
The stability of RNA hairpin loops containing A–U–G: An–U–G–Um
Authors: Wickstrom Eric , Tinoco Ignacio
Published: December 2004

RNA oligomers with the sequence An‐U‐G‐Um, n = 7–9, m = 5–10, have been synthesized and found to form hairpin loops in 21 mM or 101 mM Na+. The hairpin loops displayed melting temperatures 13°–29°C greater than that of the hairpin loop A6‐C8‐U6 in the same solvent. The increased stability of these hairpin loops is attributed to the presence of the trinucleotide A‐U‐G in the loop.

Circular dichroism (CD) spectra were taken of the hairpin loops A7‐U‐G‐U6,7,8, A8‐U‐G‐U6,7,8, and A9‐U‐G‐U6 in 21 mM Na+, and compared with circular dichroism spectra of A6‐U6 in 1 M Na+. Difference spectra were calculated between each An‐U‐G‐Um and 11.5 mM (nucleotide) A6‐U6 at similar temperatures and identical singlestrand fractions to give the “experimental” CD spectrum of the unbase‐paired nucleotides in the loop, assuming, five, six, or seven base pairs. CD spectra were calculated for each of the assumed unbase‐paired sequences using the measured CD spectra of ApA, A‐U‐G‐, A, and U, and compared with the experimental spectra. The best agreement was found for hairpin‐loop models containing five base pairs and five to eight unbase‐paired nucleotides in the loop.
Effect of hydration upon the thermal stability of tropocollagen and its dependence on the presence of neutral salts
Authors: Luescher Madeleine , Rüegg M. , Schindler P.
Published: December 2004

The endotherm enthalpy changes ΔHD and temperatures TD of thermal denaturation of tropocollagen fibers were measured by DSC calorimetry as functions of water content. The denaturation temperatures decrease with increasing water content. The enthalpy change values increase sharply in the range 0–28% of water content, where a maximum of 14.3 cal g−1 is reached. The effect of water uptake on the enthalpy term is explained by water bridge formation within the collagen triple helix. Evidence is given for the existence of approximately three intercatenary water bridges per triplet at the enthalpy maximum, their H‐bond energy amounting to approximately 4000 kcal/mol of protein. In the 30–60% range of water content, ΔHD decreases by 2 cal−1 probably due to interactions between secondary water structures and the stabilizing intrahelical water bonds.

The influence of two neutral potassium salts, with a structure‐stabilizing and a structure‐breaking anion (F− and I−), on the hydration dependence of ΔHD and TD was also studied. It was shown that the primary hydration is not influenced by these ions, but that TD and ΔHD are altered in an ion specific way in the presence of interface and bulk water. Hydrophobic interactions do not explain the experimental results. A reaction mechanism of the effects of ions upon the structural stability of collagen is proposed and discussed in terms of interactions of the medium water molecules with the intrahelical water bonds, and in terms of proton‐donor/proton‐acceptor equilibria between peptide groups, hydrated ions, and intrahelical water molecules.
Lattice vibrational modes of poly(rU) and poly(rA)
Authors: Eyster James M. , Prohofsky Earl W.
Published: December 2004

A normal coordinate analysis has been performed for the polyribonucleotides poly(rU) and poly(rA). The polymers are assumed to be 11‐fold infinite helical structures in the A conformation. The hydrogen atoms have been rigidly attached to the appropriate atoms in order to reduce the dimension of the problem. The potential energy is defined in terms of a valence force field initially and a model for the inclusion of nonbonded interactions has been presented. A method for factoring the secular equation for infinite helical polymers in Cartesian coordinates is presented. All of the general features of polyribonucleotide spectra have been reproduced and, in many cases, good quantitative agreement between observed and calculated frequencies is obtained. More specific assignments are offered for some of the observed lines.
Lattice vibrational modes of poly (rU)·poly(rA). A coupled single‐helical approach
Authors: Eyster James M. , Prohofsky Earl W.
Published: December 2004

The eigenvalues and eigenvectors of 11‐fold double‐helical poly(rU)·poly(rA) have been calculated. The vibrational potential energy of the double‐helical structure is initially considered to be a sum of the vibrational potential energy of the single‐helical structures poly(rU) and poly(rA). Coupling between the single helices is introduced by including a stretch force constant for each hydrogen bond between the uracil and adenine base residues. In addition, a model is presented for nonbonded interactions between nearest neighbor base pairs, which is consistent with a previous model for such interactions in the single helices. Because of the simple structural relationship between the uncoupled single helices and the double helix we are able to cast the secular equation for poly(rU)·poly(rA) in a form suitable for the use of perturbation theory using the previously calculated normal modes for the single helices as the unperturbed modes. Perturbation theory was found to be inapplicable for the region of the spectrum ≲450 cm−1. In this region an exact Green function technique is used to calculate the strongly coupled modes. We explicitly display one aspect of these double‐helical normal modes. The stretching motions of the hydrogen bonds in the region of the spectrum <450 cm−1 have been plotted as bar graphs for each mode.
Melting and premelting phenomenon in DNA by laser Raman scattering
Authors: Erfurth Stephen C. , Peticolas Warner L.
Published: December 2004

Raman spectra of DNA from calf thymus DNA have been taken over a wide range of temperatures (25°–95°) in both D2O and H2O. A study of the temperature dependence of the Raman spectra shows that the temperature profiles of the intensities and frequencies of the various bands fall into four different categories: (1) base bands that show a reversible increase in intensity prior to the melting region, i.e., a definite premelting phenomenon; (2) base bands that show little or no temperature dependence; (3) deoxyribose‐phosphate backbone vibrations that show no temperature dependence up to the melting region, at which point large decreases in intensity occur; and (4) slow frequency changes in certain in‐plane vibrations of guanine and adenine due to deuteration of the C‐8 hydrogen of these purines in D2O.

Certain Raman bands arising from each of the four bases, adenine, thymine, guanine, and cytosine have been found to undergo a gradual increase in intensity prior to the melting region at which point large, abrupt increases in intensity occur. The carbonyl stretching band of thymine, involved in the interbase hydrogen bonding actually undergoes both a gradual shift to a lower frequency as well as an increase in intensity. These changes provide evidence that some change in the geometry of the bases relative to each other begins to occur around 50°C, well below the melting region of 70°–85°C.

From the spectra taken at various temperatures, the DNA appears to remain in the B conformation until the melting point is reached, at which time the DNA progresses into a disordered random‐coil form. No A‐form conformation is found either in the premelting or the melting region.
Conformational studies of poly‐β‐1‐naphthylmethyl‐L‐aspartate
Authors: Ueno Akihiko , Ishiguro Toshio , Toda Fujio , Uno Keikichi , Iwakura Yoshio
Published: December 2004

Poly‐β‐1‐naphthylmethyl‐L‐aspartate and copolymers of β‐1‐naphthylmethyl‐L‐aspartate and γ‐benzyl‐L‐glutamate were prepared. From the results obtained by a study of infrared and circular dichroism spectra, poly‐β‐1‐naphthylmethyl‐L‐aspartate was found to be a left‐handed α‐helix both in the solid state and in solution. The fluorescence spectra of these polymers showed excimer emission of the naphthyl chromophores and gave some information about the arrangement of the side‐chain chromophores. By optical titration experiments, it was found that an increasing amount of β‐1‐naphthylmethyl‐L‐aspartate residues in the copolymers induces a progressive instability of the helical structure.
Electric birefringence studies on polyglutamic acid
Authors: Kobayasi Syoyu , Ikegami Akira
Published: December 2004

The electric birefringence for the aqueous solution of poly‐L‐glutamic acid (PGA) in the helical form was studied. PGA samples were fractionated by gel column chromatography. PGA showed a positive electric birefringence. The permanent dipole moment of the PGA molecule was suggested to be largely suppressed. The measurements of the intrinsic Kerr constants for various molecular lengths showed that the electric anisotropy (polarizability) of PGA is proportional to the 1.5 power of the length. The electric birefrigence measurement was also carried out in the helix–coil transition region. The Kerr constant of PGA was largely reduced on going from the helical form to the coiled form.
The precipitation of poly‐L‐glutamic acid. II. β‐Precipitation
Authors: Zimmerman S. S. , Clark J. C. , Mandelkern L.
Published: December 2004

Infrared and X‐ray diffraction studies have established that in the β‐precipitation region of poly‐L‐glutamic acid the chains are in the β‐conformation. Therefore, a major molecular conformational change has taken place upon precipitation. It is shown that the size of the α‐helical aggregates remains constant with time in the β‐region. Strong evidence can be offered to indicate that the transformation involves a transitory random‐coil intermediate. Reasons are advanced, in view of the stability of the β‐form, as to why two distinct precipitation regions exist.
Studies on cyclic peptides. III. The specific interaction of cyclic peptides with benzene and an application of the solvent‐induced nmr shift to the conformational analysis of cyclo‐(Pro‐Sar‐Gly)2
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

The interaction between cyclic peptides [cyclo‐(Sar4), cyclo‐(Pro‐Sar‐Gly)2, cyclo‐(Sar‐Sar), and cyclo‐(Sar‐Gly)] with benzene has been investigated by nmr spectroscopy. The experiment with cyclo‐(Sar4) showed that benzene interacted preferentially with the trans peptide bond in a similar manner to the dimethylformamide–benzene interaction. The solvent‐induced nmr shift was then applied to the conformational analysis of cyclo‐(Pro‐Sar‐Gly)2 with the aid of the molecular model. The major conformation was proved to possess the C2 symmetry with internally hydrogen‐bonded glycine residues, in which all peptide bonds were trans. The interaction of cyclo‐(Sar‐Sar) and cyclo‐(Sar‐Gly) with benzene was also studied. The association constant was 0.115‐kg solution per mole of cyclo‐(Sar‐Sar) and 0.089‐kg solution per mole of cyclo‐(Sar‐Gly) in chloroform.
The binding of adenosine to polyuridylic acid in which uracil residues are chemically altered
Authors: Burr J. G. , Mcdowell T. L. , Christian S. D.
Published: December 2004

The binding of adenosine‐14C to polyuridylic acid (poly(U)) and several modified poly(U)s has been studied by equilibrium dialysis. The poly(U) was modified by addition of appropriate reagents across the 5,6‐double bond of the uracil ring to form the photohydrate, photodimer, dihydrouracil, the HOBr addition product and the HSO3− addition product. Modification of the uracil rings decreases the amount of adenosine which can be bound to the poly(U); the decrease in binding is a function of the fraction of uracil rings which have been changed. Using the expression S = S0(1 − αr)2 to relate the fraction of uracil rings modified (r) to the number of binding “sites” remaining (S), it is found that α is about 1 for all the modifications except photodimer where it is about 2. These observations are taken to mean that the loss of binding capacity of the poly(U) resulting from modifications of the uracil ring is caused by loss of planarity of the uracil rings caused by the modifications, and consequent loss of double helix structure, but that for all modifications except photodimer there is no disruption of the poly(U) double helix on either side of the leison. There does appear to be local melting on either side of the photodimer lesion. The sigmoidal binding isotherms (Ab versus Ca) of modified and unmodified poly(U) can be approximated closely by the following equation:

(1) where Ab = bound A, Ca = free A, n = minimum number of adjacent A′s in complex, S = concentration of sites on poly(U), and K1 = (Km)1/m for all m ≥ n.

The stacking energy of adenosine (w) can be calculated accurately using the following equation, where dθ/d ln Ca is obtained from Eq. (1).

(2) For unmodified poly(U), w is −2.0 kcal/mole and ΔG° (−;RT ln K1) is −3.2 kcal/mole. The difference (−1.2 kcal/mole) is attributed to hydrogen bonding. Heavily photohydrated poly(U) does not bind guanosine or guanosine‐5′‐phosphate.