bluuebunny/crossref_metadata_2025 huggingface dataset:
Caractéristiques géométriques de la séquence HαCαNH de l'isoquinuclidone‐3 examinée dans différents etats physiques influence sur la constante de couplage vicinal J
Authors: Aubry A. , Giessner‐Prettre C. , Cung M. T. , Marraud M. , Neel J.
Published: December 2004

The X‐ray structure analysis of a crystalline sample of 2‐azabicyclo‐[2,2,2]‐octanone‐3 or 3‐isoquinuclidone shows that the molecules of this compound are associated in centrosymmetrical dimers stabilized by two NHOC hydrogen bonds in which the N,H,O atoms are nearly collinear. As a consequence of this interaction, the H atom is shifted from its usual position and the CαNH angle is increased to 125°.

Using infrared spectroscopy (νN–H frequency range), it is possible to demonstrate that 3‐isoquinuclidone is mainly in a dimeric form when dissolved in an inert solvent such as CCl4 and to observe the dimer‐monomer equilibrium on dilution from saturation to a low concentration (0.005 mole/l.). On the contrary, dimers are broken off when operating in a polar medium (acetonitrile, deuterochloroform).

In the same experimental conditions, measurements of the J vicinal coupling constant, by nuclear magnetic resonance spectroscopy, afford a concentration‐dependent result in the case of CCl4 solutions (increasing from 5.4 to 5.7 Hz when diluting from 0.5 to 0.005 mole/l.) and a constant one (5.8 Hz) in the case of CH3CN or CDCl3 solutions. Then the 0.4‐Hz difference can be attributed to geometrical changes in the HαCαNH system when dimers are broken off and the valence angle CαNH consequently decreases from 125° to its standard value (about 115°). This experimental observation is consistent with the result of a theoretical analysis performed by the INDO method.

Then it seems that the use of the formulas proposed by Karplus to account for the valence angle distorsions in ethane‐like systems, in the case of the HαCαNH sequence, could yield overstimated corrections.
Statistical thermodynamics of triple‐helix unzippering for the collagen model (Gly‐Pro‐Pro)n and implications for natural collagen
Authors: Schwarz Martin , Poland Douglas
Published: December 2004

Interpreting the data of Kobayashi et al.1 on the thermal transitions of triple helices of (gly‐pro‐pro)n for n = 10, 15, and 20 using a simple model of unzippering and chain dissociation, the thermodynamic parameters characterizing gly‐pro‐pro triple‐helix formation have been determined. The enthalpy and entropy of triple‐helix formation per repeating unit are found to be −7.4 ± 0.8 kcal/mol and −20 ± 2 eu, respectively. Using these parameters, the nature of the unwinding has been investigated for chains containing up to 300 triplets; it is found that there is only a minor amount of helix unwinding from the ends, the major change in helical content arising from chain dissociation. Experimental data on the melting temperatures of natural collagens as a function of imino‐acid composition are used together with the thermodynamic parameters for (gly‐pro‐pro)n to estimate the thermodynamic parameters for triple‐helix formation of amino versus imino acids (the parameters for the former being found to be similar to those for α‐helix formation). Calculations are given using these parameters for model specific‐sequence collagens; it is found that heterogeneity can have a significant influence on the nature of the unwinding of the triple helix.
Enthalpies of helix–coil transitions in polypeptides
Authors: Karasz F. E. , Gajnos G. E.
Published: December 2004

Certain discrepancies in measured heats of helix–coil transitions in polypeptides are examined in terms of the theory of the effect of solvent composition on transition temperatures and heats in such systems. It is found, generally, that disagreement between enthalpy measurements conducted at fixed solvent compositions and isothermally may be expected because of the possibility of incomplete conversion of the polypeptide from the random‐coil to the helical conformations, or vice versa in one, or both, of these regimes in the course of the transition. The magnitude of the disagreement, if any, can depend quite critically on the particular region in the transition temperature–solvent composition plane in which measurements are undertaken. Application of these results to the system, poly‐γ‐benzyl‐L‐glutamate–dichloroacetic acid‐1,2‐dichloroethane, however, suggests that previously observed discrepancies in enthalpies here cannot be attributed to this phenomenon.
The interaction of β‐cyclodextrin with dinucleoside phosphates
Authors: Formoso Carl
Published: December 2004

Circular dichroism studies of the interaction of β‐cyclodextrin with a series of eight dinucleoside phosphates, and with 3′‐AMP are reported. From results with ApU and ApA, it is shown that β‐cyclodextrin binding is sensitive to dinucleoside stacking in approximately the same way as optical measures of stacking. Some qualitative uses of β‐cyclodextrin binding are suggested, based on the fact that the change in the CD spectrum caused by cyclodextrin binding is unique to each of the dinucleosides studied. Hoffman and Bock have previously suggested the use of β‐cyclodextrin as a probe of nucleic acid structure. Their work indicated that only binding to adenosine and inosine would have to be considered. The present paper shows that binding to other bases cannot be neglected, and will impose serious restrictions on the use of β‐cyclodextrin as a structural probe.
Conformational induction in copolypeptides of the form AnBm
Authors: Klug Thomas L. , Applequist Jon
Published: December 2004

The polymerization kinetics and optical rotatory properties of AnBm polypeptides have been studied, where A = D,L‐Tyr, D,L‐TyrZ, D,L‐LysZ, L‐AspOBzl, or L‐Asp‐ONBzl, and B = D,L‐GluOR (R = Me or Bzl). In most cases where An and Bm prefer the same helix sense, the polymerization of A N‐carboxyanhydride (initiated by Bm in dioxane) shows first order kinetics and produces a monotonic change in optical rotation, while if opposite helix senses are preferred, the kinetics are multiphasic and the change in rotation reverses direction after the addition of several residues. The rotation change in the latter case is interpreted to mean that the helix in the A block is initially induced to take the nonpreferred sense, as originally suggested by Doty and Lundberg from similar observations on (D‐GluOBzl)n‐(L‐GluOBzl)m. It is found here that the CD spectra for the latter polymer show the sign changes required by this hypothesis. The optical rotation curves and CD spectra for (D,L‐Tyr)n‐(L‐GluOBzl)20 suggest, by analogy, that (L‐Tyr)n prefers the same helix sense as (L‐GluOBzl)n. However, it is found that the opposite conclusion is equally consistent with the data if one considers the effects of possible changes in side‐chain conformation on these data in accordance with the calculated CD spectra of Chen and Woody. The optical rotation curves for (D‐GluOBzl)n‐(L‐GluOBzl)20, (D‐Tyr)n‐(L‐GluOBzl)20, and (L‐Tyr)n‐(L‐GluOBzl)20 are all found to be consistent with a two‐state equilibrium model in which the A block initially takes on an induced conformation and has an increasing tendency to revert to its preferred conformation as n increases. It is concluded that in both D‐Tyr and L‐Tyr the side‐chain and/or the backbone conformation is induced by the neighboring L‐GluOBzl block, and the data do not distinguish which type of change is occurring. These results are discussed in connection with other observations bearing on the helix sense of (L‐Tyr)n.
A comparison of five methods for obtaining the intrinsic viscosity of bovine serum albumin
Authors: McMillan Donald E.
Published: December 2004

Intrinsic viscosity [η] is a characteristic of proteins and other molecules related directly to their ability to disturb flow and indirectly to their size and shape. It is usually determined by extrapolating reduced viscosity to zero concentration. Four other methods for deriving [η] have been utilized by previous investigators. Studies of the intrinsic viscosity of bovine serum albumin had been carried out two years apart as a test of viscometry technique; the data obtained were used to compare the five methods. Four of the five produced [η] values ranging from 3.92 to 4.21 ml/g. Agreement was good between the two studies. The five methods were compared to each other using linearity of regression, statistical error of determination, effect of varying solvent time, and result obtained in different concentration ranges. By these four criteria, use of the regression of specific fluidity (1 − 1/ηrel) with concentration was found superior to other methods. Its only deficiency was a requirement that solution density be corrected for at each concentration studied rather than applying a single correction for density after using kinematic viscosity data.

All methods for deriving intrinsic viscosity are based on one of three equations; flow is expressed either in terms of reduced viscosity (Huggins), inherent viscosity (Kraemer), or specific fluidity. Of these three equations, specific fluidity is the most closely related both to theoretical analyses and to experimental studies of rigid spheres. There is abundant evidence in past reports that in contrast to rigid spheres, flexible polymers do not produce a linear rise in specific fluidity as their concentration increases, strongly suggesting that their molecular conformation is changing with concentration. A linear relation between fluidity and concentration has been observed for almost all proteins and protein mixtures studied. When this linear relation is present it indicates both that molecular conformation during flow is independent of concentration in the range studied and that the specific fluidity method for deriving intrinsic viscosity is the most appropriate.
Calculations of the circular dichroism of double‐helical nucleic acids. II. Effects involving n → π* transitions
Authors: Studdert David S. , Davis Robert C.
Published: December 2004

The circular dichroism of double‐helical nucleic acids was calculated as a function of geometry, including terms involving n → π* transitions. The “nonbonding” n or σ orbitals were of the azine type, delocalized, but concentrated at the nitrogen atoms of the purines and pyrimidines. Dynamic coupling of the magnetic moments of the n → π* transitions with the electric moments of π → π* transitions generated important terms. Mixing of electric dipole character into n → π* transitions by the static electric field perturbation of the molecule is of lesser importance. The largest contributions of n → π* transitions to the circular dichroism of double‐helical nucleic acids are comparable in magnitude to the sum of π → π* terms only for geometries where the circular dichroism is weak. Using both n → π* and π → π* contributions one is able to match experimental and calculated circular dichroism spectra for DNA's over a much wider range of conditions than was possible previously.
Assignment of the proton nmr chemical shifts of the TN3H and GN1H proton resonances in isolated AT and GC Watson‐Crick base pairs in double‐stranded deoxy oligonucleotides in aqueous solution
Authors: Patel Dinshaw J. , Tonelli Alan E.
Published: December 2004

The 300‐MHz proton nmr spectra (between 11 and 14 ppm) of a series of double‐stranded deoxy oligonucleotides of known sequence have been recorded in H2O solution. These resonances have been assigned to the GN1H and TN3H protons of specific base pairs from an evaluation of the temperature dependence of the ring NH linewidths and from the selective ring NH chemical shift changes on actinomycin‐D binding. The deoxy oligonucleotides exist predominantly in the DNA‐B conformation as evaluated from antibiotic binding studies. Ring‐current calculations have been utilized to evaluate the up‐field shifts of the GN1H and TN3H protons in Watson‐Crick base pairs due to the ring currents from the pyrimidine and purine rings of nearest neighbor base pairs in regular DNA‐B‐ and RNA‐A‐type helices. The perturbations on these up‐field ring‐current contributions that arise from twisting and tilting a base pair adjacent to the ring NH under study have been evaluated and found to change the calculated chemical shift by ±0.6 ppm for twist and tilt distortions of <30°C in a single adjacent base pair. A knowledge of the experimentally assigned ring NH chemical shifts of specific base pairs in known sequences of double‐stranded deoxy oligonucleotides coupled with the ring‐current tables for the DNA‐B helical structure permit the assignment of 13.6 ± 0.1 ppm and 14.6 ± 0.2 ppm for the GN1H proton of an isolated GC base pair and the TN3H proton of an isolated AT base pair, respectively.
Polymer concentration effects on helix–coil transition widths
Authors: Grover Morgan K. , Zwanzig Robert
Published: December 2004

A theoretical study of effects of excluded volume intermolecular interactions on the sharpness of helix–coil transitions in solutions of polyamino acids or simple proteins indicates that the transition width may vary appreciably as a function of polymer concentration. The analysis is based on a second virial approximation for the excess free energy of mixing of a solution of polymers of varying degrees of helicity. The virial coefficients involved are roughly estimated on the basis of gross polymer geometry. For large N (degree of polymerization) the transition is found, typically to sharpen with increasing concentration, becoming second order and then first order at sufficiently high concentrations. The critical polymer concentration is found to be roughly of the order N−1.2 𝔡0−1 for an “all or none” model and of order σ1/2 N−0.2 𝔡0−1 for a model with continuously variable degree of helicity (𝔡0 is the volume of a single helical molecule and σ1/2 the normalized statistical weight of a helix–coil interface). In the second case for N ∼ 103 and σ ∼ 10−2–10−4, the predicted critical concentration is in the range 10−1–10−3 g/cm.3 Comparison is made with experiments on solutions of poly(γ‐benzyl‐L glutamate).
The far‐infrared properties of polyamino acids
Authors: Shotts W. J. , Sievers A. J.
Published: December 2004

The far‐infrared absorption between 3 and 650 cm−1 of several amino acids and polyamino acids is measured under a variety of conditions. The far‐infrared spectra of amino acids and short‐chain oligomers are extremely temperature dependent with the appearance of numerous narrow absorption lines at 4.2 K. These absorption lines broaden or disappear at 300 K or for absorption measurements on samples in solution. For longer polymers, relatively broad nearly temperature‐independent absorption lines are observed with little difference between the spectra of polymers in solution or in the solid state. These results are explained in terms of the crystalline order of the samples.
The conformation of polyriboadenylic acid at low temperature and neutral pH. A single‐stranded rodlike structure
Authors: Stannard Bethel S. , Felsenfeld Gary
Published: December 2004

The conformation of single‐stranded polyrA in aqueous solution has been measured at temperatures down to −12°C. The radius of gyration of low‐molecular‐weight polyrA varies very little with temperature in this range. By studying the dependence of radius of gyration on temperature for several polyrA fractions, we show that the dependence of the radius upon chain length is consistent with formation of a single‐stranded rodlike structure at low temperature. The structure has an approximate length of 3.2 Å/nucleotide.
Studies of the conformation of apomyoglobin in aqueous solutions and denaturing organic solvents
Authors: Herskovits Theodore T. , Solli Nicholas J.
Published: December 2004

The properties of apomyoglobin were examined in aqueous solutions and various helix‐ and random‐coil‐forming solvents by solvent perturbation, optical rotation, circular dichroism, and viscosity measurements. The solvent perturbation data obtained in neutral aqueous solutions suggest 25–40% exposure of the two tryptophyl residues and 50–60% exposure of the three tyrosyls. The estimates of burial of these groups are in the ranges expected for myoglobin based on its X‐ray structure. In the helicogenic alcohols, methanol, ethanol, 2‐chloroethanol, trifluoroethanol, and 1‐propyl alcohol, as well as in acidic solutions, 8 M urea and 6M guanidine hydrochloride, essentially all the tryptophyl and tyrosyl residues are found to be exposed to solvent based on this method. Analysis of the ORD and CD data indicates that in the alcohols the α‐helix content of apomyoglobin has in most cases changed from 58–59% to about 80–95%. Analysis of the intrinsic viscosity data based on the equations of Simha and Kirkwood and Auer indicates that the polypeptide chain in these solvents has the dimensions of fully extended α‐helical rods, with lengths of 221–251 Å and mean diameters of 12.8–13.6 Å. It is concluded that apomyoglobin in the various alcohols must have an extended but somewhat irregular rodlike structure, having a few bend or irregular sequences between the α‐helical segments due largely to the presence of the four proline residues, 37, 88, 100, and 120 in the amino acid sequence.
Circular dichroism spectra of poly[d(AC):d(GT)], poly[r(AC):r(GU)], and hybrids poly[d(AC):r(GU)] and poly[r(AC):d(GT)] in the presence of ethanol
Authors: Gray Donald M. , Ratliff Robert L.
Published: December 2004

Ultraviolet circular dichroism spectra have been obtained in aqueous solutions in the presence and absence of ethanol for a synthetic DNA, poly[d(AC):d(GT)], a synthetic RNA, poly[r(AC):r(GU)], and two DNA:RNA hybrids, poly[d(AC):r(GU)] and poly[r(AC):d(GT)]. In the absence of ethanol, we find that the RNA and DNA spectra are dissimilar, while the spectra of the hybrids show differing degrees of similarity to that of the RNA. In the presence of 60–80% ethanol by weight, the spectra of the DNA and both hybrids become much closer to the spectrum of the RNA, which remains relatively unchanged. We interpret the results as indicating that DNA can undergo a change to an A‐type conformation in the presence of ethanol and that the DNA:RNA hybrids are not wholly restricted to an RNA‐like conformation in the absence of ethanol.
Calorimetric studies of the interactions of guanidinium hydrochloride and potassium iodide with model amides in aqueous solution
Authors: Stimson Evelyn R. , Schrier Eugene E.
Published: December 2004

The enthalpies of transfer, ΔHtr, of a series of amides from water to aqueous solutions of either guanidinium hydrochloride (GuHCl) or potassium iodide were obtained from calorimetric measurements at 25°C. The amides were studied at molalities around 10−2 m while salt molalities ranged from 0–10 m. The amides investigated were Ac‐Gly‐NHMe, Ac‐Gly‐Gly‐NHMe, Ac‐Ala‐NHMe, and Ac‐Leu‐NHMe. Use of an additivity assumption allowed the calculation of group contributions to ΔHtr in these two salt systems for the methyl group, leucyl side chain, and the peptide backbone unit. Values of the entropy of transfer were also obtained. The great ability of GuHCl to randomize protein structures appears to arise from effects on polar and nonpolar groups, which are characterized by enthalpies and entropies of transfer not substantially different from those with KI, a salt comprised of ions of comparable size and polarizability. The difference in the sign of the free energies of transfer of nonpolar groups from water to MX solutions, negative for GuHCl and positive for KI, is the result of these small differences in enthalpies and entropies of transfer. Variations in water structure produced by differences in ionic properties rather than a mode of action for GuHCl very different from that of other salts characterizes its superior denaturing ability.
Polypeptide models of collagen: Properties of (Pro‐Pro‐βAla)n
Authors: Bhatnagar Rajendra S. , Rapaka Rao S.
Published: December 2004

We have synthesized (Pro‐Pro‐βAla)n as a model for collagen. The synthetic polytripeptide, mol wt 6500, exhibits a large negative optical rotation with a very strong negative Cotton effect centered at 216 nm. The optical rotatory dispersion of (Pro‐Pro‐βAla)n followed a single‐term Drude equation and the λc was 195 nm. The rotation decreased markedly on heating with the midpoint of the broad transition at 55°C. Preliminary studies also showed loss of structure in guadinine HCl. The circular dichroism spectrum of the polymer exhibited a deep trough at 190 nm. The marked similarities of solution properties of (Pro‐Pro‐βAla)n to (Pro‐Pro‐Gly)n suggest that β‐alanine can replace glycine in generating collagen‐like helix in solution.
The β conformation of polypeptides of valine, isoleucine, and threonine in solution and solid‐state: Optical and infrared studies
Authors: Kubota Shigeo , Fasman Gerald D.
Published: December 2004

Water‐soluble polypeptides of L‐valyl and L‐isoleucyl residues flanked with DL‐lysyl blocks [poly(DLLys · HCl)x–poly(LVal)y–poly(DLLys · HCl)x, poly(DLLys · HCl)x–poly‐(LIle)y–poly(DLLys · HCl)x] and homopoly(L‐threonine) were prepared. The β conformation of these polymers in water, as well as in aqueous methanol, was confirmed by infrared spectroscopy and circular dichroism studies. The optical properties of these valyl and isoleucyl polypeptides were quite different from those of previously reported synthetic homopolypeptides in the β structure. Their differences could be explained by the presence of a “single extended β chain” without either intra‐ or interchain association.
Minimization of construction errors in bent‐wire protein models
Authors: Goldberg D. , Saliterman S. , Wetlaufer D. B. , Rose G. , Hopkins Ted E.
Published: December 2004

Two kinds of errors are found in protein models made with the tool of Rubin and Richardson. Global errors result from the accumulation of many errors too small to localize, while local errors are assignable to particular bends in the model. We here locate the sources of local errors, and show how to minimize both kinds of errors.
Specific aggregations of alanine tetrapeptide derivatives as studied by nuclear magnetic resonance
Authors: Goodman M. , Ueyama N. , Naider F. , Gilon C.
Published: December 2004

By use of high resolution nuclear magnetic resonance and infrared spectroscopy, we have found evidence for specific folded forms for the methoxyethoxyethoxyacetyl‐blocked alanine tetramer ethyl ester. It appears that this tetrapeptide derivative exists in a folded form which is in rapid equilibrium with an extended structure (i.e., below 1% w/v). At high concentrations (i.e., above 1% w/v in chloroform) the folded form is stabilized by an association of the alanine tetrapeptide derivative into a side‐by‐side dimer which contains specific hydrogen bonds between the amine terminal regions of the two folded structures.
Hydrophobic interaction and structural changes in the solvent
Authors: Ben‐Naim A.
Published: December 2004

The effect of structural changes in the solvent (usually water) on the thermodynamics of the hydrophobic interaction process is examined within the framework of classical statistical mechanics.

The concept of the “structure of water” is first defined in a precise way, yet reflecting the conventional definition that has been, implicitly and qualitatively, employed by many authors. Using this concept, we proceed to show that structural changes in the solvent, induced by the hydrophobic interaction process, cannot affect the strength of the hydrophobic interaction. On the other hand, the entropy and enthalpy changes, associated with the same process, may well be affected. Some qualitative arguments are presented showing that large structural changes are expected from a complex solvent such as water.
Helix–coil transitions of compositionally heterogeneous DNA
Authors: Pritchard A. E. , Eichinger B. E.
Published: December 2004

Fragmented and mitomycin C cross‐linked E. coli DNA was fractionated according to base composition by means of hydroxylapatite chromatography and density‐gradient centrifugation in order to determine the effect of compositional heterogeneity on the breadth of the helix–coil transition. The transitions of some of the fractions are broader than that of the unfractionated DNA, due, presumably, to nonrandom sequences in molecules of 5 × 105 daltons. Analysis of the transition breadths in terms of the known heterogeneity leads to reconsideration of current DNA helix–coil transition theory. We propose that partially denatured states include those for which the chains do not remain in strict register. Denaturation profiles are comprehensible only if this multitude of entropically favorable, degenerate states is included in the theory.
Synthesis and characterization of stereoregular poly(D‐methionyl‐L‐methionine) and poly(L‐methionyl‐D‐methionyl‐L‐methionine)
Authors: Dellacherie Edith , Néel Jean
Published: December 2004

By use of a polycondensation procedure free of racemization, stereoregular polymethionines have been synthesized from C‐activated D‐methionyl‐L‐methionine and L‐methionyl‐D‐methionyl‐L‐methionine.

The poly(D‐methionyl‐L‐methionine) and poly(L‐methionyl‐D‐methionyl‐L‐methionine) so prepared are soluble in chloroform and can be purified through dissolution in this solvent and precipitation by ligroin.

Poly(D‐Met‐L‐Met)which is obtained in a 25% yield, is about 5000 in average molecular weight. It has no discernible optical activity when examined between 400 and 600 nm in a trifluoroacetic acid solution.

Poly(L‐Met‐D‐Met‐L‐Met) (40% yield, M. W. = 10,000) is an optically active polymer. [α]43624 ≈ + 170° for a chloroformic solution (c = 0.2 CHCl3).
Experimental study of the conformation of two stereoregular polymethionines: Poly(D‐methionyl‐L‐methionine) and poly(L‐methionyl‐D‐methionyl‐L‐methionine)
Authors: Dellacherie Edith , Néel Jean , Colonna‐Cesari François
Published: December 2004

Infrared spectroscopy, X‐ray diffraction, and nuclear magnetic resonance spectroscopy have been used in investigating the conformation of two stereoregular polymethionines, poly(D‐methionyl‐L‐methionine) and poly(L‐methionyl‐D‐methionyl‐L‐methionine). When dissolved in a helicogenic solvent, such as chloroform and hexafluoroisopropanol, the polytripeptide is in an α‐helical conformation. A helix‐to‐coil transition can then be induced by addition of trifluoroacetic acid.

On the other hand, it appears that the most stable conformation of poly(D‐Met‐L‐Met) is a β antiparallel folded structure in which the linear polypeptide segments are near to the planar extension. This structure has been evidenced through X‐ray examination of oriented films, casted from solutions in chloroform. It has also been identified in solution in the same solvent, by use of infrared spectroscopy and by measuring the δHα chemical shift which characterizes the Hα proton in the peptide units. This δHα value is found equal to 5.4 ppm and differs significantly from those which are usually attributed to the α‐helical conformation (δHα = 4.2 ppm) and to the random coil (δHα = 4.6 ppm). The β folded conformation of the poly(D‐Met‐L‐Met) appears to be comparatively less stable than the α‐helical one for the poly(L‐Met) macromolecular stereoisomer since hexafluoroisopropanol is a helicogenic solvent for this last solute and a destabilizing one for the poly(D‐Met‐L‐Met) β folded conformer. X‐ray examinations carried out with stretched films, casted from a solution of poly(D‐Met‐L‐Met) in chloroform, result in several data concering the cross β structure of this stereoregular polypeptide in the solid state.
The interaction of collagen with the hydrophobic fluorescent probe 2‐p‐toluidinylnaphthalene‐6‐sulfonate
Authors: Chiang Hsin‐Chou , Lukton Aaron
Published: December 2004

Three kinds of fluorescence enhancement result from the interaction of 2‐p‐toluidinylnaphthalene‐6‐sulfonate and calf‐skin collagen. They are negatively cooperative, independent, and highly cooperative fluorescence enhancement. In the independent region at pH 3.7, the binding number is about 36 moles of 2‐p‐toluidinylnaphthalene‐6‐sulfonate per mole of tropocollagen with a binding constant of 2.0 × 104 M−1; with ΔG = −5.7 kcal/mole, ΔH = −4.0 kcal/mole, and ΔS = 6 e.u. The pH dependence of fluorescence of native collagen shows that the deprotonated forms of the β and γ carboxyl groups of aspartic and glutamic acid decrease the intensity, possibly by charge repulsion of the negatively charged sulfonate group of 2‐p‐toluidinylnaphthalene‐6‐sulfonate. The positive charge of lysine is found to be unimportant in the interaction of 2‐p‐toluidinylnaphthalene‐6‐sulfonate with collagen. Fluorescence enhancement is caused mainly by the hydrophobic interactions of 2‐p‐toluidinylnaphthalene‐6‐sulfonate and collagen. Salt bridge formation between basic and acidic side chains in very low salt concentration may be detectable by 2‐p‐toluidinylnaphthalene‐6‐sulfonate fluorescence.
Effect of temperature and pH on the β–helix transition of poly(L‐lysine) in sodium dodecyl sulfate solution
Authors: Satake Iwao , Yang Jen Tsi
Published: December 2004

The conformational phase diagram of poly(L‐lysine) (4.6 × 10−4 M, residue) in sodium dodecyl sulfate (1.6 × 10−2 M) solution was constructed from circular dichroism results at various temperatures and pH's. Poly(L‐lysine)–sodium dodecyl sulfate complexes undergo a β–helix transition upon raising the pH of the solution. The transition pH tends to shift downward at elevated temperatures. No helix–β transition can be detected for poly(L‐lysine) in sodium dodecyl sulfate solution (pH > 11) even after 1‐hr heating at 70°C. This is in marked contrast with uncharged poly(L‐lysine) solution without sodium dodecyl sulfate, which is converted into the β‐form upon mild heating of the solution above 50°C.
Levans. V. Kinetics of the acid hydrolysis of Streptococcus salivarius levan
Authors: Lauren M. D. , Stivala S. S. , Bahary W. S. , Long L. W.
Published: December 2004

The kinetics of the acid hydrolysis of Streptococcus salivarius levan were studied by examining the weight‐average molecular weight. The molecular weights were obtained in a continuous manner from light scattering. Two first order reactions were observed: an initial rapid reaction in competition with a slower reaction.

Activation energies, activation entropies, as well as the rate dependence upon substrate and hydrogen ion concentrations were determined. The data seem to indicate that the fast reaction is related to the breaking of branch‐point bonds while the slower reaction is related to the breaking of main‐chain bonds. Thus, levan hydrolysis seems to be fundamentally different from the completely random degradation of other branched polysaccharides, i.e., dextran, glycogen, and amylopectin.
Studies on interaction between poly(L‐lysine) and DNA of varied G + C contents
Authors: Li Hsueh Jei , Herlands Louis , Santella Regina , Epstein Paul
Published: December 2004

Interaction between polylysine and DNA's of varied G + C contents was studied using thermal denaturation and circular dichroism (CD). For each complex there is one melting band at a lower temperature tm, corresponding to the helix–coil transition of free base pairs, and another band at a higher temperature t′m, corresponding to the transition of polylysine‐bound base pairs. For free base pairs, with natural DNA's and poly(dA‐dT) a linear relation is observed between the tm and the G + C content of the particular DNA used. This is not true with poly(dG)·poly(dC), which has a tm about 20°C lower than the extrapolated value for DNA of 100% G + C. For polylysine‐bound base pairs, a linear relation is also observed between the t′m and the G + C content of natural DNA's but neither poly(dA‐dT) nor poly(dG)·poly(dC) complexes follow this relationship. The dependence of melting temperature on composition, expressed as dtm/dXG·C, where XG·C is the fraction of G·C pairs, is 60°C for free base pairs and only 21°C for polylysine‐bound base pairs. This reduction in compositional dependence of Tm is similar to that observed for pure DNA in high ionic strength. Although the t′m of polylysine‐poly(dA‐dT) is 9°C lower than the extrapolated value for 0% G + C in EDTA buffer, it is independent of ionic strength in the medium and is equal to the tm0 extrapolated from the linear plot of tm against log Na+. There is also a noticeable similarity in the CD spectra of polylysine· and polyarginine·DNA complexes, except for complexes with poly(dA‐dT). The calculated CD spectrum of polylysine‐bound poly(dA‐dT) is substantially different from that of polyarginine‐bound poly(dA‐dT).
Optical Kerr effect in biopolymer solutions
Authors: Coles H. J. , Jennings B. R.
Published: December 2004

The electric field in a single mode, YAG laser beam has been used to induce orientational birefringence in solutions of tobacco rattle virus, DNA, heparin, and hyaluronic acid. Using this laser in its “fixed‐Q” mode, laser pulses were generated which persisted for up to 200 μsec in which the effective electric field vector rose to 5 kV cm−1. The birefringence amplitudes so produced had a quadratic dependence on the effective field strength and thus obeyed Kerr's law. From the birefringence decay rates, relaxation times were determined which, by comparison with the birefringence induced by pulsed static electric fields revealed the biopolymer orientational origins of the effects. This indicated how these experiments can lead to the evaluation of particle geometry, the electronic contribution to electrical polarizabilities, and the optical polarizability of biopolymers in solution.
Evidence from circular dichroism for the binding of hydrogen ions and calcium ions by poly(L‐proline)
Authors: Lo Jung‐Teh , Mattice Wayne L.
Published: December 2004

The positive circular dichroism band observed near 228 nm with poly(L‐proline) responds in a similar fashion to HCl and CaCl2. The spectra in the HCl solutions are compatible with a simple binding equation and a pK near −2 for the dissociation of a proton from a protonated peptide bond in poly(L‐proline). The data obtained in CaCl2 is susceptible to the same analysis, suggesting a pK near −1.5 for the dissociation of a calcium ion from its complex with poly(L‐proline).
The interaction of poly (N5‐(3‐hydroxypropyl)‐ L‐glutamine) with solvent components in water/dioxane mixtures
Authors: Inoue Hideo , Izumi Taro
Published: December 2004

The preferential binding of solvent components with a nonionic homopolypeptide, poly(N5‐(3‐hydroxypropyl)‐L‐glutamine), ([Gln((CH2)3OH)]n), has been determined in water/dioxane mixtures using differential refractometry. The degree of preferential binding was calculated from the difference between the refractive index increments of [Gln((CH2)3OH)]n obtained from experiments carried out under two conditions: experiments where the molality of dioxane was kept identical in both compartments of the differential cell, and experiments where the chemical potential was kept identical. The polypeptide was preferentially hydrated between 10 and 70 wt % of dioxane; the amount of preferential hydration per gram of the mixed solvent increases monotonically (with a plateau region between 40 and 60 wt %) with the dioxane concentration. A monotonic increase was also observed in the degree of helicity of the polypeptide.

The absolute amounts of water and dioxane bound by [Gln((CH2)3OH)]n were investigated in the frozen state by the method of nuclear magnetic resonance. Hydration was measured using a mixed solvent, water/dioxane‐d8; dioxane solvation was measured using a mixed solvent, dioxane/D2O. The polypeptide binds about 0.35 g of water per g of the polymer in aqueous solution, and hydration decreases gradually with an increase in dioxane concentration. On the other hand, the amount of dioxane solvation increases to 0.04 g per g of the polymer in the dioxane concentration range between 0 and 20 wt %, and then levels off. The rapid increase in solvation is observed before the conformational transition from random coil to α‐helix occurs in [Gln((CH2)3OH)]n.

The dependence of the preferential and absolute binding of solvent components to [Gln((CH2)3OH)]n on dioxane concentration and the conformational change in the homopolypeptide suggest that addition of dioxane to aqueous solutions induces lowering of water activity and that the helical structure of the polypeptide is enhanced by the formation of intrachain hydrogen bonds. The validity of the frozen method is also discussed.
Threshold effects observed in conformation changes induced by electric fields
Authors: Pörschke Dietmar
Published: December 2004

Single‐stranded polynucleotides are used as model systems for the investigation of conformational changes induced by electric fields. It is demonstrated that the single‐strand helix–coil transition in poly(A), poly(dA), and poly(C) can be induced by application of high electric fields. The transition is measured by UV absorbance using polarized light at an angle of 54.8° with respect to the vector of the electric field and by electrodichroism. A linear increase of the absorbance, reflecting the helix‐to‐coil transition, is observed at increasing field strength. When ions are added to the polymer, electric fields do not induce conformation changes, unless a threshold value of the electric field strength E0 is exceeded. At field strengths above this threshold, the degree of transition is a linear function of the increase in field strength. The threshold values E0 show a linear increase with the logarithm of the ion concentration. Bivalent ions cause thresholds at much lower ion concentrations than mo‐novalent ions. The shielding efficiency of ions is correlated to the binding affinity of these ions to the polymer.

The conformation changes induced by the field and the existence of thresholds can be explained on the basis of dissociation field effects. Similar threshold effects may be expected for other macromolecules as well as for membrane structures and may be important in the regulation of bioelectricity.
Étude expérimentale de l'auto‐association des molécules modèles dipeptidiques. II. Association stéréosélective des molécules énantiomères
Authors: Cung Manh Thong , Marraud Michel , Neel Jean
Published: December 2004

Modes of aggregation fo alanine‐, norvaline‐ and valine‐contaiing dpepetides with the general formula R1C1O1N2H2CHR2C2O2N3H3R3 have been studied in CCl4 solution by using infrared and nuclear magnetic resonance spectroscopies. Solutions of the pure L isomer and of the racemic mixture do not give identical data. At a given concentration, the racemic mixtrue is more aggregated than the pure enantiomer, and the difference, negligible in the case of alanine derivative, increases wiht the bulkiness of the side cahin R2.

The results show that a selective interaction takes place between enantiomeric molecules, resulting ina dimer associating tow inverse configurated C5 conformers. The stabilizaion of this dimer proceeds from two symmetrical and intermolecular H3 … O1 hydrogen bondings.
Ring‐current effects in the nmr of nucleic acids: A graphical approach
Authors: Giessner‐Prettre Claude , Pullman Bernard , Borer Philip N. , Kan Lou‐Sing , Ts'O Paul O. P.
Published: December 2004

The spatial dependence of the ring‐current magnetic anisotropy of nucleic acid bases is presented in a series of graphs in cylindrical coordinates. The curves may be used to calculate the ring‐current shift at a point in a cylinder of radius 10Å extending 8 Å above and below each ring of the base. These distance effects are found to influence considerably the predicted chemical shifts of nucleic acid protons, particularly in RNA duplexes. The contribution of polarization (electric field) effects and the diamagnetic anisotropy of individual atoms (local Δχ) are briefly discussed.
Co‐oligopeptides of aromatic amino acids and glycine with variable distance between the aromatic residues. VII. Enzymatic synthesis of N‐protected peptide amides
Authors: Saltman Robert , Vlach Dagmar , Luisi Pier Luigi
Published: December 2004

Several N‐protected peptide amides, containing two aromatic residues spaced by one glycyl residue, have been enzymatically synthesized starting from P‐Ar‐OH and H‐Gly‐Ar‐NH2 (P is the protecting group and Ar is the aromatic residue) and using α‐chymotrypsin as the catalyst for the coupling step. Reactions have been carried out in water solution, at room temperature, and afford yields ranging between 20 and 75% ca. This coupling reaction occurs in a much more restricted set of conditions than the hydrolysis reaction, e.g., only within a small pH range (ca. 6.5–7.5) and with particular buffering agents. The advantages and limitations of this type of reaction, compared with conventional coupling procedures, are discussed.
Thermodynamics of mucopolysaccharide–dye binding. I. Identification of free and bound dye via membrane filtration: Acridine orange–dermatan sulfate system
Authors: West Seymour S. , Hurst Robert E. , Menter Julian M.
Published: December 2004

Stoichiometric mixtures of acridine orange with dermatan sulfate at total dye concentrations ⩽ 1 × 10−5 M show fluorescence maxima at 540 nm and 660 nm on excitation at 436 nm. By means of membrane filtration, it is directly demonstrated that the species emitting at 540 nm is due only to unbound dye whereas the 660‐nm emitting species is due to bound dye. It is, therefore, possible to differentiate unbound acridine orange from its dermatan sulfate complex solely by spectroscopic methods. Thermodynamic binding parameters can be calculated from rapid spectroscopic measurements without disturbing the system.
Theoretical conformational analysis on Cyclo(prolyl‐phenylalanyl) peptides
Authors: Ajò David , Granozzi Gaetano , Di Bello Carlo
Published: December 2004

Empirical energy calculations on cyclo(L‐Pro‐L‐Phe) and cyclo(L‐Pro‐D‐Phe) indicate that different conformations are possible for each molecule. The theoretical results are compared to ir, nmr, and crystallographic data. The interdependence between diketopiperazine ring and side‐chain conformations is also discussed.
Polynucleotide models. II. Prediction of the radial position and tilt of the bases from the helical parameters
Authors: Zimmerman Steven B.
Published: December 2004

A simple geometrical analysis is applied to base‐stacking interactions in helical polynucleotides. A base‐pair or other H‐bonded arrangement of bases is represented by a corresponding plane. In a helical structure, these planes will intersect each other if the bases are not perpendicular to the helix axis. The tilt of the bases and the position of intersection of these planes are geometrically related, and demonstrate the interrelation of the tilt of the bases with their radial position. This approach may be coupled with a constraint which predicts the radial position of the bases based solely upon the helical parameters. These two constraints taken together allow a simple means to predict the approximate position and tilt of a given H‐bonded arrangement of bases placed according to specified helical parameters. For a number of polydeoxyribonucleotides, there is more than one base position and tilt consistent with these constraints, while there is only one base position and tilt indicated for each of the polyribonucleotides examined.
Raman spectral studies of nucleic acids. XVI. Structures of polyribocytidylic acid in aqueous solution
Authors: Chou C. H. , Thomas G. J.
Published: December 2004

Raman spectra of polyribocytidylic acid show the formation of an ordered single‐stranded structure [poly(rC)] at neutral pH and an ordered double‐stranded structure containing hemiprotonated bases [poly(rC)·poly(rC+)] in the range 5.5 > pH > 3.7. Below 40°C, poly(rC) contains stacked bases and a backbone geometry of the A‐type, both of which are gradually eliminated by increasing the temperature to 90°C. Below 80°C, poly(rC)·poly(rC+) contains bases which are hydrogen bonded and stacked and a backbone geometry also of the A‐type. In this structure the bases of each strand are shown to be structurally identical, i.e., hemiprotonated, and therefore distinct from both neutral and protonated cytosines. Infrared and Raman spectra indicate the existence of a center of symmetry with respect to the paired cytosine residues, which suggests that the additional proton per base pair is shared equally by the two hydrogen‐bonded bases. Denaturation of poly(rC)·poly(rC+) occurs cooperatively (tm ≈ 80°C) with elimination of base stacking, base pairing, and the A‐helix geometry. Each of the separated strands of the denatured complex is shown to contain comparable amounts of both neutral and protonated cytosines, most likely in alternating sequence [poly(rC, rC+)]. In both poly(rC, rC+) and poly(rC), at 90°C, the backbones do not exhibit the phosphodiester Raman frequencies characteristic of other disordered polyribonucleotide chains. This is interpreted to mean that the single strands, though devoid of base stacking and A‐type structure, contain uniformly ordered backbones of a specific type. Fully protonated poly(rC+), on the other hand, forms no ordered structure and may be characterized as a disordered (random chain) polynucleotide at all temperatures. Several Raman lines of poly(rC) are absent from the spectrum of poly(rC)·poly(rC+) and vice versa. These frequencies, assigned mainly to vibrations of the ribose groups, suggest that the furanose ring conformations are different in the single‐stranded and double‐stranded structures of polyribocytidylic acid. Several other Raman group frequencies have been identified and correlated with the polymer secondary structures.
Reduction of ferriprotoporphyrin IX to the ferroderivative by copoly(4‐vinylpyridine‐N‐(p‐vinylbenzyl)‐3‐carbamoyl‐1,4‐dihydropyridine) in dimethyl sulfoxide
Authors: Tsuchida Eishun , Hasegawa Etsuo
Published: December 2004

The copolymer which has both ligand sites (4‐vinylpyridine) and redox sites (N‐(p‐vinylbenzyl)‐3‐carbamoyl‐1,4‐dihydropyridine) was synthesized by the dithionite reduction of the copoly(4‐vinylpyridine‐N‐(p‐vinylbenzyl)‐3‐carbamoylpyridinium chloride) and the reduction of a central ferric‐iron of ferriprotoporphyrin IX by the above‐described copolymer was studied spectrophotometrically in dimethyl sulfoxide. The rate of the reduction by the copolymer was much faster than by N‐benzyl‐3‐carbamoyl‐1,4‐dihydropyridine. This acceleration by the copolymer could be explained by the intramolecular reduction of ferriprotoporphyrin IX which was coordinated by the pyridine residue of the copolymer.
Determination of the rates and barriers to conformational isomerization in the dipeptide L‐pro‐L‐4hyp by direct 13C nmr thermal equilibration
Authors: Roques B. P. , Garbay‐Jaureguiberry C. , Combrisson S. , Oberlin R.
Published: December 2004

The 13C nmr equilibration method lends itself as a tool for study of conformational rate processes involving aqueous media in conjunction with high activation barriers. This method is applied for measurement of kinetic and thermodynamic parameters of isomerism in the dipeptide L‐Pro‐L‐4Hyp. The activation barrier for cis ⇋ trans interconversion (ω 0° → 180°) is determined, ΔG≠ = 22.3 kcal/mol. From low‐temperature study, an upper limit ΔG≠ < 9.7 kcal/mol is evaluated for cis′ ⇋ trans′ rotation (ψ −40° → 160°). These data are compared with computed values found in literature. The results are discussed in connection with the helix–coil transition of collagen involving Gly‐L‐Pro‐L‐4Hyp as nucleation sites.