bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational behavior of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine in water–methanol mixtures studied by 13C nmr and CD spectroscopy
Authors: Di Blasi R. , Verdini A. S. 
Published: December 2004

AbstractThe helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine (PHPLG) has been studied in methanol–water by CD and cmr spectroscopy. For polydisperse PHPLG, two separate peaks arising from residues in helical and random‐coil conformations are observed during the transition for both main‐chain carbons. These results are discussed and compared to those observed in the case of a polymer sample obtained by racemization of PHPLG in 0.1 M NaOH and of PHPLG samples of controlled molecular weight and dispersity. The dominant influence of the molecular‐weight heterogeneity on the double‐peak phenomenon has been verified. The linewidths and chemical shift of the 13C resonances are discussed in terms of side‐chain–main‐chain interactions and side‐chain solvation.
The nature of the helix–random coil transition of biological macromolecules attached to a surface
Authors: Dimarzio Edmund A. , Bishop Marvin 
Published: December 2004

AbstractThe effect of the presence of a surface on the helix–random coil transition is investigated. It is found that a grand canonical ensemble formation used previously to solve exactly the problem of a polymer between two plates can be used to solve approximately the problem of DNA near a plane surface. The formalism is applied to the homogeneous perfect‐matching model of infinite molecular weight. A crucial part of the calculation for double‐stranded molecules involves the evaluation of the entropy of the loops connecting the helical portions of the double‐stranded chains. One obtains as a measure of the configurational freedom of a loop Asi/jc where c has the following values: for a loop connecting two helical regions both off the surface c = 3/2; for a loop connecting a helical region on the surface to a helical region off the surface c = 5/2; for a loop connecting helixes both on the surface c = 4. Corresponding values for an n‐stranded molecule are c = (3n − 3)/2, c = (4n − 3)/2, c = (5n − 2)/2. In all cases, the effect of the surface is to sharpen the transition. In the case of double‐stranded molecules, the transition becomes first order. We take the view that self‐assembly of biological macromolecules can be considered as a sharp thermodynamic phase transition. Thus, the above systems become models of self‐assembling systems. They are also relevant to the problem of surface‐induced enzymatic activity.
Conformational change of the triple‐helical structure. IV. Kinetics of the helix‐folding of (Pro‐Pro‐Gly)n (n = 10, 12, and 15)
Authors: Sutoh Kazuo , Noda Haruhiko 
Published: December 2004

AbstractThe kinetic curves of the helix‐refolding of (PPG)n (n = 10, 12, and 15) were analyzed with an all‐or‐none model. The Arrhenius plot of the overall rate constant of the helixfolding kF showed a negative activation energy at high temperature. With the aid of a sequential model, it was concluded that the reason for the anomaly was the instability of short helices (shorter than seven helical units in a trimeric molecule), and/or the more rapid rates of helix‐folding and helix‐opening for shorter helices.The rate constant of the formation of one helical unit composed of three tripeptides at an end of a long helix was calculated to be 102–4 sec−1. It was much smaller than that for other kinds of helices, such as an α helix (1010 sec−1) or a double helix of nucleic acids (107–9sec−1).
Raman scattering of collagen, gelatin, and elastin
Authors: Frushour Bruce G. , Koenig Jack L. 
Published: December 2004

AbstractThe Raman spectra of collagen, gelatin, and elastin are presented. The Raman lines in the latter two spectra are assigned by deuterating the amide N‐H groups in gelatin and by studying the superposition spectra of the constituent amino acids. Two lines appear at 1271 and 1248 cm−1 in the spectra of collagen and gelatin that can be assigned to the amide III mode. Possibly, the appearance of two amide III lines is related to the biphasic nature of the tropocollagen molecule, i.e., proline‐rich (nonpolar) and proline‐poor (polar) regions distributed along the chain. The melting, or collagen‐to‐gelatin transition, in water‐soluble calf skin collagen is studied and the 1248‐cm−1 amide III line is assigned to the 31 helical regions of the tropocollagen molecule.Elastin is thought to be mostly random and the Raman spectrum confirms this assertion. Strong amide I and III lines appear at 1668 and 1254 cm−1, respectively, and only weak scattering is observed at 938 cm−1. These features have been shown to be characteristic of the disordered conformation in proteins.
Nmr studies of mixtures of poly‐L‐lysine hydrobromide with water
Authors: Darke A. , Finer E. G. 
Published: December 2004

Abstract1H, 2H, 13C, and 81Br nmr measurements of mixtures of poly‐L‐lysine hydrobromide with water have been carried out over a range of temperatures and water contents. When n (number of molecules of water per residue) ∼13 at room temperature, a transition occurs from a gel to a liquid phase. The liquid phase contains polymer molecules that are flexible, but contain more intramolecular structure than the same molecules in trifluoracetic acid solution. The gel phase contains junction zones of hexagonally packed α‐helices, linked by flexible regions of polypeptide chain. The α‐helical residues impart to their associated water molecules a slight anisotropy of motion, which is dectable by 2H nmr. These residues bind up to about seven molecules of water each; the other six required to complete the gel–liquid transition space out the polymer molecules, allowing increased segmental motion of the residues in the flexible regions. This increased motion reduces the energy of the flexible regions and thus increases the proportion of residues in them (increasing the temperature has the same effect); the transition occurs when insufficient residues remain in the α‐helical junction zones.
Quasi‐elastic light scattering by calf thymus DNA and λDNA
Authors: Schmitz K. S. , Pecora R. 
Published: December 2004

AbstractThe quasi‐elastic light‐scattering (homodyne) time‐correlation functions of calf thymus and λDNA are shown to contain contributions from at least two relaxation processes. A method of asymptotic analysis is described and used to obtain an estimate of the longest relaxation time as well as the “average” relaxation time and the mean‐squared dispersion in this average. Most theories of scattering from macromolecules in the limit of inifinite dilution predict that the longest relaxation time is due to translational self‐diffusion. The data obtained, however, indicate that the longest time is not simply related to the translational self‐diffusion coefficient of unaggregated macromolecules. It is also shown that the longest relaxation time of λDNA decreases in the later stages of the denaturation transition region. Some possible mechanisms for the origin of this long time are discussed, including a model of restricted motion of a molecule by its neighbors.
Circular dichroism of some mononucleosides
Authors: Brunner Wendel C. , Maestre Marcos F. 
Published: December 2004

AbstractThe circular dichroism (CD) and absorption spectra of uridine, thymidine, purine ribonucleoside, and the four adenine derivatives 2′‐deoxyadenosine, adenosine, adenosine‐3′,5′‐cyclic phosphate, and arabinosyl adenine were measured in water at pH 7 and pH 2. The absorption and CD spectra of the pyrimidines were simultaneously fitted to four Gaussian bands, and the dipole and rotational strengths of the electronic transitions determined. Adenine‐derivative CD spectra were determined by computer averaging six runs. The spectra showed CD bands at 268, 226, 209, and 195 nm. The band at 226 nm probably is an n–π* transition; the band at 209 nm cannot be detected without a computer. The CD and absorption spectra of purine ribonucleoside indicate three transitions in the 230–310‐nm region.
Spécificité de l'interaction DNA‐platine dosage du platine, pH métrie
Authors: Macquet J. P. , Theophanides T. 
Published: December 2004

AbstractInteraction between the sodium salt of a DNA extracted from salmon sperm (41% GC) with [Pt(NH3)4]Cl2, [Pt(NH2(CH2)2NH(CH2)2NH2Cl]Cl,cis‐Pt(NH2(CH2)2NH2)Cl2,cis‐Pt(NH3)2Cl2,trans‐Pt(NH3)2Cl2, K[Pt(C2H4)Cl3], and K2[PtCl4) indicates at least three types of complexation. A correlation is found between the change of pH and the number of platinum atoms fixed per (AT + GC) unit. The first binding site is located on the G‐C pairs (guanine–cytosine), most likely the N‐7(G) site, as it was shown in a previous study of the guanosine‐platinum salts. The fixation of the second platinum atom by the pair (AT + GC) takes place with liberation of protons. In the case of the complexescis‐Pt(NH2(CH2)2NH2)Cl2,cis‐Pt(NH3)2Cl2, andtrans‐Pt(NH3)2Cl2the second interaction seems to involve simultaneously the N‐7(A) and the N‐1(G) and N‐3(C) sites. This latter intercrosslink between guanine and cytosine obviously liberates protons and the decrease of pH is related in this case to thetranseffect of the platinum compounds. The first two platinum atoms in the reaction of K2PtCl4] or the Zeise salt, K[Pt(C2H4)Cl3] with DNA are fixed on the G‐C pairs. A maximum of six platinum atoms per (AT + GC) unit were fixed in this case. Preliminary experiments with a DNA extracted from bacteriaMicrococcus lysodeikticus(72% GC) give similar results.
Conformational studies of alanine oligopeptides by nuclear magnetic resonance
Authors: Goodman M. , Ueyama N. , Naider F. 
Published: December 2004

AbstractWe have studied the nmr spectra of the series of alanine oligopeptides containing a methoxyethoxyethoxyacetyl blocking group on the N‐terminal residue and a morpholino blocking group on the C‐terminal residue. Spectra were measured in chloroform–trifluoroacetic acid solvent systems. For oligomers with chain lengths of five or more, “double peaks” are observed for the α‐CH protons. Addition of trifluoroacetic acid causes the peaks to coalesce. The amount of trifluoroacetic acid necessary for coalescence increases from the pentamer to the nonamer. These findings are general since alanine oligomers with different blocking groups exhibit similar “double peak” phenomena. We explain the “double peak” phenomenon in terms of specific folded forms of the oligopeptides which arise from intramolecular hydrogen bonding. Additional evidence for such hydrogen bonding is presented based upon infrared studies. Slight aggregation probably occurs for the pentamer and hexamer which may stabilize the folded forms.
Infrared spectroscopy of collagen and collagen‐like polypeptides
Authors: Doyle Barbara Brodsky , Bendit E. G. , Blout Elkan R. 
Published: December 2004

AbstractThe set of synthetic polytripeptides and polyhexapeptides which can adopt a triple‐helical form constitute a good model system for investigating collagen structure. Here we consider previous and new infrared spectroscopic studies on collagen and present the infrared spectra of a number of polymers with collagen‐like features.The amide A band position for all triple‐helical polypeptides is higher than that observed for most proteins and polypeptides, and this high frequency appears to be related to the degree of supercoiling of the triple helix. It is possible that with increased supercoiling of the three chains the angles between the groups involved in the intramolecular hydrogen bonds become less favorable, or these bonds may become unusually long.The frequency of the amide I band varies considerably for triple‐helical polypeptides with different amino acid sequences, and often minor bands are observed. This finding contrasts with the observations for polypeptides in a pleated sheet or α‐helical form, where the same amide I frequency is observed regardless of the amino acid composition. An explanation for this variation is proposed in terms of the hydrogen bonding properties of imino acids.Significant spectral changes in the amide I region are observed on hydration in the spectra of some triple‐helical polypeptides, but corresponding changes have not been found in the collagens examined.
Differences in the red fluorescence of acridine orange bound to single‐stranded RNA and DNA
Authors: Ichimura Sachiko 
Published: December 2004

AbstractFluorescence of acridine orange bound to RNA or DNA in the single‐stranded form including single‐stranded synthetic polyribo‐ or polydeoxyribonucleotides was measured in the expectation that some distinct structural characteristic between single‐stranded RNA and DNA might be reflected by a specific fluorescent behaviour of bound dyes. It was found that the complex of the dye with single‐stranded RNA emits a weaker red fluorescence around 650 nm than the complex with single‐stranded DNA at low phosphate‐to‐dye ratios. The fact could be explained neither by a direct interaction of bound dyes with the 2′‐hydroxyl group of ribose in RNA nor by the difference in the G‐C content of the nucleic acids. On the basis of the character of dye molecules emitting the red fluorescence, it was suggested that the bases in single‐stranded RNA might be buried in some hydrophobic environment that would make the dyes less likely to interact with them, compared with the bases in single‐stranded DNA. It was further inferred that some conformational rigidity of single‐stranded RNA may partially be responsible for the weaker red fluorescence.
The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X‐ray diffraction data
Authors: Kolaskar A. S. , Lakshminarayanan A. V. , Sarathy K. P. , Sasisekharan V. 
Published: December 2004

AbstractThe possible nonplanar distortions of the amide group in formamide, acetamide, N‐methylacetamide, and N‐ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X‐ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles θN and Δω defining the nonplanarity of the amide unit are correlated approximately by the relation θN = −2Δω, while θC is small and uncorrelated with Δω. The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (ϕ,ψ), in working out polypeptide and protein structures.
Synthesis and conformational study of sequential polypeptides, (L‐Ala‐L‐Val‐Gly)n and (L‐Val‐L‐Ala‐Gly)n
Authors: Katakai Ryoichi , Oya Masanao , Iwakura Yoshio 
Published: December 2004

AbstractAs an approach for elucidating the role of sequences of amino acids in protein structures, model polypeptides having the same composition but different sequences of amino acids, (L‐Ala‐L‐Val‐Gly)n and (L‐Val‐L‐Ala‐Gly)n, have been prepared by the method involving facile monomer synthesis using N‐carboxy α‐amino acid anhydrides and N‐hydroxysuccinimide esters. The yields and the molecular weights of the polypeptides formed by polycondensation do not depend on the monomer concentrations, but on the sequences of the amino acids in the monomers. Infrared spectra in the solid state showed that (L‐Ala‐L‐Val‐Gly)n can take the α‐helical conformation but (L‐Val‐L‐Ala‐Gly)n cannot. The results suggest that the conformations of polypeptides are influenced by the sequences of the amino acids in the polypeptides.
Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations
Authors: Claverie Jean‐Michel , Dreux Henri , Cohen René 
Published: December 2004

AbstractA very general approach to the chemical equilibria between many interacting molecules during sedimentation (boundary, band, or active enzyme) taking into account boundary conditions, cell geometry, equilibrium constants, diffusion, enzyme kinetics, etc., is presented. Through a Fortran program, the method has been applied to two very simple but typical cases. With only minor adjustments, the method presented here for sedimentation studies can be extended to all sorts of problems in which “pools” of various species are interacting with each other.
Competitive cooperative bindings of a small ligand to a linear homopolymer. I. Extension of the Ising model to the case of two competitive interactions
Authors: Dourlent M. 
Published: December 2004

AbstractThe theoretical study of the cooperative binding of a small ligand to a linear homopolymer is extended to systems in which two different complexes can form. The binding isotherms are derived under the assumption that the cooperative interactions exist only between molecules belonging to the same type of binding mode and are limited to nearest neighbors (Ising model). The binding to a single‐stranded chain is first considered and two extreme cases are studied: (1) the two complexes can form independently from each other (model of independent classes of binding sites); (2) only one class of binding site exists, each possessing two different states of complexation (three‐state model).Binding to a double‐helical chain is also considered. Three simple types of competition between the different modes of binding are distinguished. The corresponding models are defined as: (1) the model of independent classes of binding sites; (2) the model of monoexclusive interactions between the different kinds of complexes (the symmetric and asymmetric cases are both considered); (3) the model of biexclusive interactions. The comparative study of the different cases shows that the binding isotherms are very similar at large polymer‐to‐ligand concentration ratios, while they can be very different at low polymer‐to‐ligand ratios. This can be used to obtain information on the mechanism of dye binding to nucleic acids by equilibrium studies as shown in a subsequent paper.
Helix–coil transition kinetics in aqueous poly(α,L‐glutamic acid)
Authors: Cummings Arthur L. , Eyring Edward M. 
Published: December 2004

AbstractA polarimetric electric‐field‐jump relaxation apparatus is described and used to determine the relaxation spectrum for the helix–coil transition of poly(α,L‐glutamic acid) in water at 24°C. A maximum relaxation time of 1.7 μc occurs at the transition midpoint (pH = 5.9) yielding a rate constant for helical growth of 6 × 107 sec−1.
Effects of Na+ and Mg++ ions on the helix–coil transition of DNA
Authors: Record M. Thomas 
Published: December 2004

AbstractThe effects of monovalent (Na+) and divalent (Mg++) cations on the temperature and breadth of the helix–coil transition of phage DNA have been investigated. The experimental results confirm the findings of Dove and Davidson [J. Mol. Biol. 5, 467–478 (1962)] for the limiting cases of zero divalent ion concentration and saturating levels of divalent ion, and extend their findings to the intermediate region of Mg++ concentrations. A theory for the dependence of transition temperature on the ion concentrations is developed, utilizing the approach of Wyman [Adv. Protein Chem. 19, 223–286 (1964)], modified to account for electrostatic nonideality of the polyelectrolytes. The theory is in agreement with Manning's treatment of the experiments of Dove and Davidson [Biopolymers 11, 937–949, 951–955 (1972)] and is in fair agreement with experimental data over the entire range of ion concentrations. Further investigation of the structure and ion‐binding properties of the denatured form will be required before a quantitative comparison between theory and experiment can be performed.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. I. Synthesis of co‐oligopeptides of tryptophan and glycine
Authors: Guarnaccia Rocco , Lorenzi Gian Paolo , Rizzo Vincenzo , Luisi Pier Luigi 
Published: December 2004

AbstractThe preparation of the co‐oligopeptides of the series H‐Gly‐Trp‐(Gly)n‐Trp‐Gly‐OH (n = 0, 1, and 2) and of a number of other unprotected co‐oligopeptides of glycine and tryptophan is reported. The syntheses have been carried out by conventional methods, using, in general, N‐hydroxysuccinimide esters for the coupling steps. All the oligopeptides were obtained after purfication as colorless and crystalline products, and gave only one spot on thin‐layer chromatography. Specfic problems connected with the synthesis and purficiation of optically pure tryptophan‐containing peptides are discussed.
Premelting effects in DNA under saltfree conditions
Authors: Grassi Henri , Rix‐Montel Marie‐Agnès , Kranck Hubert , Vasilescu Dane 
Published: December 2004

AbstractWe have studied the electrical conductivity of NaDNA solutions under “saltfree” conditions at temperatures well below the melting point of DNA, using radio‐frequency dielectric and noise measurements. A conductivity discontinuity is observed at a temperature well below that at which the usual denaturation processes and trans conformation may commence. The radio‐frequency permittivity also exhibits a discontinuity at the same temperature. For the premelting phase, the conductivity versus temperature curves consist of two linear regions with a change in slope occurring at 23°C. This effect is related to the behavior of the ionic sheath covering the DNA macromolecule. The activation energy of the alternative current conductivity as well as that the equivalent noise conductivity results as 3.11 kcal/mole below and 4.08 kcal/mole.
The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC
Authors: Broyde Suse B. , Stellman Steven D. , Wartell Roger M. 
Published: December 2004

AbstractIn order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)‐endo and C(2′)‐endo [or C(3′)‐exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A‐form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)‐endo. For dGpdC, a B‐form helical conformer, with sugar pucker C(2′)‐endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low‐energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson–Crick model of the double helix. In contrast, for GpC, the C(2′)‐endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low‐energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)‐endo. This conformation—ω′,ω near 20°,80°—was not observed for C(2′)‐endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)‐endo dGpdC has one low‐energy valley. It is in the B‐form helical region (ω′ ∼ 260°, ω ∼ 300). When the sugar pucker is C(3′)‐endo, dGpdC has two low‐energy regions: the A‐form helical region and the region with the minimum at ω′ = 16°, ω = 85°.
Polynucleotide circular dichroism calculations: Use of an all‐order classical coupled oscillator polarizability theory
Authors: Cech Carol L. , Hug Werner , Tinoco Ignacio 
Published: December 2004

AbstractAn all‐order classical coupled oscillator theory in which monomer band shapes are explicity taken into account is applied to the calculations of polynucleotide circular dichroism. Calculations are shown for ApA and oligoadenylic acid of varying chain lengths, in both RNA and B‐DNA geometry, and the advantages of this theory are assessed. By introducing an effective dielectric constant, good agreement with measured spectra is obtained. Variations in monomer parameters are tested in an attempt to eliminate remaining discrepancies between calculated and measured spectra.