bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational induction in copolypeptides of the form AnBm
Authors: Klug Thomas L. , Applequist Jon 
Published: December 2004

AbstractThe 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

AbstractIntrinsic 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractUltraviolet 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

AbstractThe 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

AbstractWe 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

AbstractWater‐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

AbstractTwo 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

AbstractBy 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

AbstractThe 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

AbstractFragmented 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

AbstractBy 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

AbstractInfrared 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

AbstractThree 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.