bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical mechanics of noncovalent bonds in polyamino acids. VI. A simple model for side‐chain hydrogen bonds between helices
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractThe partition function of paper II for short polypetide chains is incorporated here into one for a simple model for side‐chain hydrogen bonds between helices. It is thus possible to calculate the fraction of amide hydrogen bonds, the fraction of side‐chain hydrogen bonds, and the number of bound protons as a function of temperature and pH. Illustrative data are presented for the probabilities of occurrence of intermediate structures and for the influence of the overall conformation on the observed pK's of ionizable groups.
Heat of the reaction forming the three‐stranded poly (A + 2U) complex
Authors: Ross Philip D. , Scruggs Robert L. 
Published: December 2004

AbstractCalorimetric measurements of the heat of the addition of the second strand of poly U to poly (A + 2U) to form the three‐stranded poly (A + 2U) complex in 0.1M and 0.5M NaCl at 24 and 37°C. are reported. A value of ΔH = −3800 cal./mole of poly (A + 2U) formed was found to be fairly insensitive to the experimental conditions employed. The heat of the addition of the third strand to the preformed poly (A + U) helix is considerably less exothermic than the heat of reaction between poly A and poly U to form poly (A + U). The insensitivity of the heat of addition of the third strand (poly U) to changes in salt concentration and temperature lends qualitative support to the earlier hypothesis that the major portion of the variation of the ΔH of the poly A and poly U reaction with experimental conditions arises from differences in the conformation of poly A. Combining the information obtained in this study for the ΔH of the reaction forming poly (A + 2U) with data for the ΔH of the formation of poly (A + U) indicates that the conversion of poly (A + U) to poly (A + 2U) is opposed by an enthalpy change which increases with temperature. Extrapolation of these values to 52°C. where poly (A + U) is transformed to poly (A + 2U) in 0.5M NaCl leads to a value of ΔH = +3800 cal./mole (A + 2U) formed and ΔS = 11.5 cal./mole of (A + 2U) formed. It is concluded from the calorimetric data that the driving force for the poly (A + U) to poly (A + 2U) conversion reaction is the favorable entropy change.
Sedimentation coefficients of replicating and crosslinked DNA
Authors: Bloomfield Victor A. 
Published: December 2004

AbstractThe sedimentation coefficients of branched and cyclic replicating DNA structures have been calculated taking into account both chain stiffness and excluded volume effects. For branched DNA, the calculated ratio S0(α)/S0(0) of the sedimentation coefficient at degree of replication α to that at α = 0 increases from 1.000 to 1.331 as α goes from 0 to 1. For cyclic replicating DNA, S0(1)/S0(0) = 1.517. The considerable difference between these two ratios for α = 1 suggests that the two types of replicating structures may feasibly be distinguished by sedimentation velocity studies, A similar calculation has been made of the sedimentation coefficient of singly cross‐linked DNA under denaturing conditions, as a function of placement of the crosslink. In 0.195M Na+, the ratio S0(α)/S0(0) varies from 1.000 at α = 0 to 1.124 at α = 0.5, where α is the fractional distance of the crosslink from the end of the chain.
Polypeptides with known repeating sequences of amino acids. Comparison of several methods used for the synthesis of poly‐γ‐D‐ and L‐glutamylglycine and investigation of its serological reaction with antianthrax immune serum
Authors: Kovacs J. , Schmit G. N. , Ghatak U. R. 
Published: December 2004

AbstractTo make a comparison of some of the various polymerization methods, poly‐γ‐D‐and L‐glutamylglycine were synthesized through the mixed anhydride, carbodiimide, and pentachlorophenyl active ester methods. This last method proved to be best, on the basis of weight‐average molecular weights (M̄w). A detailed study was also carried out to determine the optimum conditions for this method. The M̄w, values of the polymers were determined by the sedimentation equilibrium method; it was found that the pentachlorophenyl active ester gave M̄w values of up to 11, 500 but the mixed anhydride and carbodiimide methods gave M̄w, values of only about 1000. Tests with rabbit antianthrax immune serum showed that neither D‐ nor L‐isomer precipitated with the antiserum, but that, both were able to inhibit the precipitation of the antiserum by anthrax polypeptide. In addition, the D‐polymer gave more inhibition than the L, which would indicate a specificity of the antibody for D‐glutamic acid residues.
Proton magnetic resonance and optical spectroscopic studies of water‐soluble polypeptides: Poly‐L‐lysine HBr, poly(L‐glutamic acid), and copoly(L‐glutamic acid42, L‐lysine HBr28, L‐alanine30)
Authors: Bradbury E. M. , Crane‐Robinson C. , Goldman H. , Rattle H. W. E. 
Published: December 2004

AbstractThe helix‐coil transition has been studied by high‐resolution NMR for three water‐soluble polypeptides. Such systems are better models for protein behavior than those in TFA‐CDCl3 solvent. An upfield shift of ∼7 cps is observed for the α‐CH peak of poly(L‐glutamic acid) and poly‐L‐lysine as the helix content increases over the transition. No such shift is found for copoly(L‐glutamic acid42, L‐lysine28, L‐alanine30). The width of the α‐CH peak for poly L‐lysine increases rapidly as helix content rises but for poly L‐glutamic acid and the copolymer, the width of this peak remains unchanged up to 60% helicity. This demonstrates a rapid rate of interconversion between helical and random conformations in partly helical polymer for the latter two polypeptides. All three polymers however, show no apparent α‐CH peak at 100% helicity. Side‐chain resonance lines also broaden as helix content increases and, to a greater extent, the closer the proton is to the main chain.
Reinvestigation of the primary structure of yeast alanine tRNA
Authors: Merril Carl R. 
Published: December 2004

AbstractThe primary structure of alanine transfer RNA reported by Holley and his colleagues contained a number of inconsistencies between the data and the proposed sequence. In order to resolve these inconsistencies, alanine tRNA was isolated from yeast by using countercurrent techniques similar to those employed by Holley. The alanine accepting RNA obtained by this procedure was found by further purification employing reverse phase partition chromatography, to contain two different species of alanine tRNA. One of these, tRNAala I, could be shown to be similar to Holley's proposed structure with the addition of a guanine between positions 47 and 48 and only 2 dihydrouridines instead of the 2.5 reported by Holley.
Proflavine binding to yeast rRNA and ribosomes as related to structure
Authors: Schoentjes M. , Fredericq E. 
Published: December 2004

AbstractProflavine binding experiments were carried out with yeast rRNA, native and “unfolded” ribosomes; the binding constants and the number of binding sites were calculated by a spectroscopic method. The study of the intercalation complexes by fluorescence and electric dichroism shows the intercalation binding sites to involve two subtypes of sites, which could be related to different nucleotide composition and secondary structure of the rRNA regions, i.e., binding sites located in the (A + U)‐rich single strands and binding sites located in the (G + C)‐rich double‐helical strands (fluorescence quenching sites). Electric dichroism of complexed proflavine is interpreted in terms of rRNA conformation within the ribosomes. The conclusions are in agreement with the ribosomal model of Cox and Bonanou and show that, according to this model, the base planes of the nucleotides are not all parallel in the native ribsome, but rather radiate around the folding axis of the ribonucleoprotein sheet.
Thermal and charge‐induced coil to α‐helix transition of poly‐L‐glutamic acid and random L‐glutamic acid–L‐alanine copolymers
Authors: Warashina Akira , Ikegami Akira 
Published: December 2004

AbstractThermal and charge induced random coil to α‐helix transitions of poly‐L‐glutamic acid (PGA) were measured by optical rotatory dispersion in various solvents. The data of PGA in 0.1M Nacl were analyzed by the Zimm‐Rice theory. Enthalpy and entropy changes for the coil‐to‐helix transition in the unionized state were obtained: ΔH° = −1020 ± 100 cal/residue mole; ΔH° = −3.0 ± 0.4 e.u./residue mole. The initiation parameter, σ, of the Zimm‐Rice theory was given by a value of 5 ± 1 × 10‐3. Random copolymers of L‐glutamic acid and L‐alanine containing 10, 30, and 40 molar percents of alanyl residue were synthesized. Stabilities of α‐helix of the copolymers were compared to that of PGA. In water and water‐ethanol solutions, stabilities of the polymers were almost equal after the simple correction about the ionized charge density of the polymers. In 0.1 M NaCl solution these copolymers showed some deviations from the transition curve of PGA, which would suggest the hydrophobic contribution of the alanyl residues.
Conformational studies on polypeptides. The effect of sodium perchlorate on the conformation of poly‐L‐lysine and of random copolymers of L‐lysine and L‐phenylalanine in aqueous solution
Authors: Peggion E. , Cosani A. , Terbojevich M. , Borin G. 
Published: December 2004

AbstractCircular Dichroism measurements have been carried out on poly‐L‐lysine (PLL) and on random copolymers of lysine and phenylalanine at various pH values and in the presence of different amounts of NaClO4. The results indicate that either the homopolymer or the copolymers at pH conditions at which the side‐chain amino groups are fully protonated, assume the right‐handed α‐helical conformation in the presence of NaClO4. The results are interpreted in terms of specific binding of ClO4− ions on charged side‐chain amino groups.
Evidence for stereospecific collision complexes of cyclo(tri‐L‐prolyl) with benzene
Authors: Torchia D. A. , Deber C. M. 
Published: December 2004

AbstractNMR spectra of cyclo(tri‐L‐prolyl), c‐(P)3, show large shifts of the Hα resonance on adding C6D6 to a solution of c‐(P)3 in CD2Cl2. CPK models and observed coupling constants indicate a rigid c‐(P)3 conformation, independent of solvent composition, suggesting that these shifts result from formation of stereospecific C6D6–c‐(P)3 collision complexes in which the c‐(P)3 Hα lie near the face of the aromatic ring. The temperature dependence of the Hα shifts and the solvent dependent shifts observed on adding toluene‐d8 or nitrobenzene‐d5 to the c‐(P)3 solution suggest that preferred C6D6–c‐(P)3 orientations result from attractive interactions between the electron‐rich aromatic ring and the electropositive Hα's and/or δ+ nitrogen atoms in the peptide backbone. Reports of such interactions in increasingly diverse peptide model systems suggest that they may play a role in stabilizing protein structures.
Use of the ising model for doubly ordered macromolecules
Authors: Tenenbaum A. , Triolo L. 
Published: December 2004

AbstractWe developed a statistical model, based on a one‐dimensional Ising model, for a recently studied polypeptide which displays an endothermic helix‐to‐coil transition with an “anomalous” behavior in the heat of solution. The model supports the assumption of an ordering of the chains due to a specific hydrogen bond interaction among them, beside the helical ordering of the backbone; this double ordering of the macromolecule produces the “anomalous” experimental behavior. With the hypothesis of a highly coopertive interaction among amide groups and side chains, we find that the backbone cooperation increases the chains cooperation, but not vice versa; this influence when the cooperation in the backbone increases.
Thermodynamics of oligo(A)N·2poly(U)∞ from the dependence of the temperature of the helix–coil transition on oligomer concentration
Authors: Blake R. D. 
Published: December 2004

AbstractOn the basis of elementary two‐state, ideal solution thermocynamics, a modified expression for the melting of oligo. polynucleotide helices is derived which is applicable to variations in TmN and/or oligomer concentration, Cm with oligomer length, N:

ΔHr is the enthalpy per helix residue, i.e., per base‐pair or base‐triplet, Vrf is the thermodynamic “available” or “reaction” volume, in liters/mole of helical residues; and n is the number of polynucleotide strands, e.g., n = 2 for oligo (A)N·2 poly(U)∞. Some earlier treatments have engendered confusion in the interpretation of the “reaction volume,” but with the derivation herein, the entropic origin and physical significance of Vrf is unequivocal.The following approximation was arrived at for the reduction expected in the configurational entropy, ΔSrconf, ∞, for (A)∞·2(U)∞, when the poly(A), strand is substituted for by an equivalent strand of contiguous oligo(A)N,′s:

This adjustment of ΔSrconf, ∞ represents the source of the coefficient to 1/Tm∞ in expression (I). The expectation that ΔSrconf, N < ΔSrconf, ∞ is due to the effect of releasing normal internucleotide configurational restrictions every Nth residue in one‐third of the strands of the (A)N·2(U)∞ helix.Although the reduction in ΔSrconf, ∞ (II) may seem small (i.e., only 5.5% for the tetramer), its effect on the magnitude of Vrf in expression (I) is exponential. Thus, without these considerations the quantitative applicability of earlier expressions is questionable.By examining the variation in TmN with cm for a single N, all assumptions, required for evaluating Vrf or the entropic effects of discontinuities in the (A)N strand are avoided in the determination of a reliable enthalpy. We have therefore examined the system

and obtained a ΔHr = 12.58 ± 0.08 kcal per mole (A)·2(U) base‐triplets between 5 and 2.5°C. That this value for ΔHr is in such excellent agreement with all calorimetric values reported for (A)∞·2(U)∞ suggests that the enthalpy for reaction(III) is not significantly affected by disconnections in the backbone of (A)4·2(U)∞. From (I), Vrf = 6.0 × 10−4 1/mole or 1 Å 3per helical residue. ΔHr°, corrected for residual single‐strand stacking in (A)4, is in excellent agreement with that found earlier for (A)1·2(U)∞. A residual heat capacity of 90 kcal(±20) per mole (A)·2(U) base‐triplets per °C is deduced from the decrease of ΔHr° with temperature.
The determination of the thermodynamic parameter of the helix‐coil transition of polypeptides by means of dipole moment measurements
Authors: Dufour C. , Marchal E. 
Published: December 2004

AbstractThe theoretical change of the mean‐square dipole moment of a polypeptide during the helix‐coil transition is compared with the change in helix content. It is shown that, according to the theory, the determination of the helix initiation parameter σ and the enthalpy of helix formation ΔH can be determined. Experimental data on poly‐benzyl‐L‐gluatamate in two different solvent mixtures are given.
Complementary DNA base interactions: Application of recently refined electrostatic interaction theory
Authors: Stamatiadou Mary N. , Swissler T. J. , Rabinowitz James R. , Rein Robert 
Published: December 2004

AbstractElectrostatic interactions between the DNA bases in the Watson‐Crick hydrogen bonding configuration are examined in both the molecular and the atomic multipole representation using three different methods of calculation: (a) CNDO wave functions and definitions of moments, (b) IEHT wave functions and division of two‐center densities and (c) IHET wave functions with equally divided overlap densities. It is shown that the inclusion in the interaction series of terms at least as high as the quadrupole‐quadrupole is required to quantitatively characterize the interactions. Convergence is more rapid with the atomic multipole representation and is unaffected by the type of assignment of formal charges. A quantitative approach to the problem of the role of electrostatic interactions in hydrogen bonding in DNA is thus provided, with obvious impact on the investigation of molecular recognition processes.
The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation
Authors: Gray Donald M. , Tinoco Ignacio , Chamberlin Michael J. 
Published: December 2004

AbstractWe present CD spectra of four trinucleoside diphosphates, UpUpG, GpUpG, ApUpA, and ApUpG, of four single‐stranded polymers, poly AC, poly GU, poly AU, and poly AdU, and of five double‐stranded polymers, poly A:U, poly G:C, poly AU:AU, poly AdU:AdU, and poly GC:GC. The measured spectra are compared with empirical firstneighbor calculations. Our results, taken together with data from the literature, suggest that UpA and UpG sequences are relatively unstacked in a single‐stranded RNA compared with these isolated dimers in solution. These sequences may influence the structure and function of natural RNAs. Our results on double‐stranded RNAs indicate that the spectral changes which occur upon formation of a double helix are unique to the type of base pair involved and are relatively independent of sequence.
Characterization of two sequential polytripeptides containing glycine and ethyl‐glutamate residues
Authors: Rippon W. Barton , Chen H. H. , Anderson J. M. , Walton A. G. 
Published: December 2004

AbstractThe polytripeptides poly(glu(OEt)‐gly‐gly) and poly(glu(OEt)‐glu(OEt)‐gly) have been synthesized and characterized using infrared linear dichroism, ultraviolet circular dichroism spectroscopy, and electron microscopy. Both polymers have been obtained in a cross β conformation with antiparallel chains, however, there appear to be significant differences in the stability of this conformation for the two polymers. Poly(glu(OEt)‐gly‐gly) has also been shown to exist in a 31 polyglycine II type helix in aqueous solution whereas films cast from this solution appear to be random. Finally this same polymer can be obtained in either a random or an extended form trifluoroacetic acid depending on the nature of the substrate used for film casting.
“Increased‐valence” formulas for the iron–ligand bonding of some ferrohaemoglobin compounds
Authors: Harcourt R. D. 
Published: December 2004

AbstractValence formulas are constructed for the iron–ligand groups of the oxy‐, carboxy‐, nitric oxide‐, and nitrosobenzene derivatives of haemoglobin. To do this, the newly developed “increased‐valence” theory3 is used. The most stable of these valence formulae are able to account simply for certain iron‐ligand properties, with the iron remaining essentially as ferrous, as it is in haemoglobin.
Three‐stranded helix–coil equilibrium in polyuridylic acid–adenosine complex
Authors: Damle Vinayak N. 
Published: December 2004

AbstractInteraction of poly U (polyuridylic acid) and adenosine is studied by following the changes in ultraviolet absorbance in the wavelength region near the isochromic wave‐length for the complex formation. The interaction is studied as a function of temperature, concentration of adenosine, and ionic strength, while the concentration of poly U was held constant. It is confirmed that only the three‐stranded complex with the stoichiometry 1A to 2U is formed and that it dissociates directly into free poly U and adenosine. No discontinuity of any kind was apparent in the melting curves, and poly U was found to possess no ordered structure above 10°C under the conditions used. The results were, therefore, analyzed in terms of an exact helix–coil equilibrium theory using the mismatching model, i.e., assuming that either completely formed base triplet or completely free unbonded bases only exist, and that the two sections of the polymer chains forming closed loops need not contain the same number of unbonded bases. Self‐association of free adenosine was taken into consideration. (Base triplet is analog of base pair for a three‐stranded helical complex. It refers to a unit of three coplanar bases, in this case two uracils and one adenine, hydrogen bonded to one another to form a triplet. Such triplets may stack over one another along the helical axis, and when they are so stacked the bases of two triplets next to each other may have stacking interactions between them.)The values for enthalpy and entropy changes, both per mole of base triplets, were obtained for the following processes at neutral pH and moderate to high salt concentrations. (1) Growfh: Binding of one adenosine molecule to two uracil residues (one from each poly	U strand) to form a base triplet next to an already formed base triplet with which it has stacking interactions, a process that involves both hydrogen bonding and base stacking interactions, ΔHs, = −19 ± 2 kcal, ΔSs = −55 ± 6 clausius; (2) Initiation: Binding of one adenosine molecule to two uracil residues (one from each poly U strand) to form an isolated base triplet, a process that involves only hydrogen bonding interactions, ΔHb* = 4.5 ± 2 kcal, ΔSb* = 6.6 ± 3 clausius; and (3)Interruption: Unstacking of two stacked base triplets initially next to each other by formation of an interruption (viz. a closed loop) between them, a process that involves only base stacking interactions, ΔHb = 23.5	± 3 kcal, ΔSb = 61.6 ± 7 clausius, where the entropy changes include contributions other than the configurational entropy of closed loops. The discrepancy between our results and the calorimetric ΔHs of −13 kcal is attributed to (i) the possible effects of salt arid polymer on the self‐association of free adenosine, (ii) the uncertainty in the value of the parameter for the probability of ring closure, and (iii) the contributions due to the partial molal enthalpy of the solvent and the unstacking of any poly U structure to the calorimetric enthalpy.
Electrical conductivity in the solid state of sodium salts of calf thymus DNA
Authors: Lecompte M. F. , Muller D. , Jozefowicz M. 
Published: December 2004

AbstractA dc conductivity study of native and denatured samples of sodium salts of calf thymus DNA in the solid state was performed at different temperatures and water content. From the results obtained it appears that the major carrier of conductivity is either electronic or ionic, depending upon the temperature of the sample, the water content, and the fact that the conductivity of native samples is higher than that of the denatured ones. These results have been confirmed by dc conductivity studies of poly U and poly A.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. III. Co‐oligopeptides of L‐phenylalanine, L‐tryptophan, and glycine: Synthesis and ultraviolet absorption properties
Authors: Guarnaccia Rocco , Rizzo Vincenzo , Gianola Pietro , Luisi Pier Luisi 
Published: December 2004

AbstractThe preparation of the co‐oligopeptides of the series H‐Gly‐Phe‐(Gly)n‐Trp‐Gly‐OH (n = 0, 1, 2) and of other free peptides of glycine, L‐tryptophan, and L‐phenylalanine is reported. The syntheses have been carried out by conventional methods, using N‐hydroxysuccinimide esters for the coupling steps. The ultraviolet absorption properties of the free peptides have been investigated in water. No hypo‐ or hyperchromicity was found for the aromatic chromophores, with the exception of H‐Gly‐Phe‐Trp‐OH, which shows a small but significant hypochromicity. The contribution of the peptide bond to the molar absorptivity in the far ultraviolet has been separated from that of the side chain plus the COO− group by plotting the measured molar absorptivity ϵ of the farthest accessible uv maximum as a function of the number of peptide bonds (nA). The peptide bond contribution proved to be independent of nA in the range nA = 1–5, thus ruling out the onset of helical conformations in the longer chain peptides.