bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mathematical method for determining the distribution of substituted DNA zone lengths with reference to equilibrium density profiles
Authors: Delcroix C. , Cantraine F. R. L. , Hardt N. 
Published: December 2004

AbstractA method of calculation to determine the profile in density‐gradient sedimentation of bromodeoxyuridine‐substituted DNA lengths prior to sonication is developed. The method may be summarized as follows: (1) A description of a formulation of random cleavage of a substituted zone i in fragments of length m; (2) generalization and application of this formulation to all substituted zone lenghts simultaneously present in a given DNA extract, such generalization being performed by means of a matrix calculation; (3) adjustment of this formulation for the limits of the experimental method, i.e., number of gradient fractions which can be recovered, and for the evolution of the DNA fragment lengths which drop in the course of successive sonications; (4) simulation of the radioactive profiles. By this method it is possible to obtain certain indications concerning the types of initial (i.e., presonication) distributions that are compatible with observed profiles and to test the validity of assumptions relating to the initial distribution. This method has been applied in analyzing DNA synthesis in lymphocytes stimulated by Concanavalin and allowed us to determine the significance of the discontinuties appearing in the elongation with a suboptimal stimulating dose. The proposed method could also be applied to the analysis of all random populations of mixed sequences.
The molecular details of collagen hydration
Authors: Grigera J. Raul , Berendsen Herman J. C. 
Published: December 2004

AbstractNuclear magnetic resonance and dielectric data on hydrated collagen are interpreted in terms of Ramachandran's hydration model. It is found that all data are compatible with this model, indicating two specific binding sites per three amino acids in the threefold collagen helix. Sorption data have been interpreted according to the multilayer theory of Guggenheim and used to derive the fraction of bound water in the primary sites. From magnetic resonance anisotropies structural details of the position of the water molecules can be derived under the assumption that both sites are equally occupied. The residence time of a water molecule in one of these sites in moderately hydrated collagen (45 g H2O/100 g collagen) is 1.2 × 10−6 sec. The remainder of the water is weakly bound and consists of rapidly exchanging species with rotational correlation time shorter than 10−10 sec. The sites are 50% occupied at a water content of 10 g/100 g collagen and may contribute significantly to the stability of the collagen threefold helix.
1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH
Authors: Bundi Arno , Wüthrich Kurt 
Published: December 2004

AbstractThe 1H‐nmr chemical shifts and the spin–spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH in D2O and H2O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pKa values obtained in D2O, with the use of pH‐meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pKa values in H2O. This suggests that the present data are suitable “random‐coil” 1H‐nmr parameters for conformational studies of polypeptide chains in D2O and H2O solutions.
Spectroscopic origin of conformation‐sensitive contributions to polysaccharide optical activity: Vacuum‐ultraviolet circular dichroism of agarose
Authors: Liang J. N. , Stevens E. S. , Morris E. R. , Rees D. A. 
Published: December 2004

AbstractThe vacuum‐uv CD of agarose solid films has been measured to 145 nm and shows a positive band near 180 nm and a larger negative band at around 152 nm. The positive band remains accessible in aqueous solution and has been used to characterize changes in molecular conformation and interaction during the sol–gel transition. The temperature profile of vacuum‐uv CD shows sharp, discontinuous changes around the melting and setting points of the gel, which are interpreted in terms of cooperative intermolecular association through double helices, and pronounced hysteresis, which is discussed in terms of helix–helix aggregation.
Conformational energy calculations with averaged potential functions: Application to the repeat peptides of elastin
Authors: Ralston Evelyn , Somorjai R. L. 
Published: December 2004

AbstractWe present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues (n‐peptide) to the complexity of a computation for (Gly)n. This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone CαHα and CαH2α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space‐averaged effective center‐center and center‐atom potentials, respectively. This averaged‐interaction method is tested on the repeat tetra‐, penta‐, and hexapeptides of elastin, Val‐Pro‐Gly‐Gly (VPGG), Val‐Pro‐Gly‐Val‐Gly (VPGVP), and Ala‐Pro‐Gly‐Val‐Gly‐Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom‐atom calculations and extensive nmr data, coupled with the order‐of‐magnitude reduction in computer time, augurs well for the potential usefulness of the method.
Far‐infrared spectrum of crystalline lysozyme
Authors: Ataka Mitsuo , Tanaka Shoji 
Published: December 2004

AbstractThe far‐ir absorption spectrum of lysozyme was measured at room and liquid‐nitrogen temperatures. Dried layers of single crystals of tetragonal lysozyme chloride with a diameter of 100–300 μm were grown on a silicon plate. Such single‐crystalline samples were considered to have the following advantages in obtaining far‐ir spectra: (1) surface scattering is reduced, (2) the protein molecules are closely packed, and (3) air‐drying of the crystals reduces the number of water molecules without considerably changing the original configuration. The spectrum obtained consisted of a strong background absorption and a number of absorption peaks that were not clearly observed with the sample in the form of lyophilized powder. The peaks were ascribed to various delocalized vibrations of the main and side chains in the molecule. The peaks were also compared with the positions of Raman lines. The uniform background was assigned to the water molecules remaining in the crystals.
Steric effects of cis‐trans isomerism on neighboring residues in proline oligopeptides: A 13C‐nmr study of conformational heterogeneity in linear tripeptides
Authors: Deslauriers R. , Becker J. M. , Steinfeld A. S. , Naider F. 
Published: December 2004

AbstractA series of proline‐containing linear oligopeptides (4 dipeptides and 15 tripeptides) were synthesized and examined in aqueous and nonaqueous solutions using 13C‐nmr spectroscopy. Spectra of linear tripeptides showing cis‐trans isomerism about the X‐Pro bond (X = Pro, Gly, and Ala) also show neighboring effects on the chemical shifts of residues both preceding and following the prolyl moiety. The extent of cis‐trans isomerism observed about the X‐Pro peptide bond correlates not only with the nature of X, but also depends on the size of the residue following proline; the larger substituents favor an increase in cis content about the X‐Pro bond.
An elastic model of the large‐scale structure of duplex DNA
Authors: Benham Craig J. 
Published: December 2004

AbstractA general model for the large‐scale, time‐independent structure of duplex DNA is developed based on elastic considerations. The general conditions of elastic equilibrium are given. These equations are solved for the equilibrium shape of stressed duplex DNA, based on the assumption that the double helix behaves mechanically as a symmetric, linearly elastic rod. It is shown that, in general, two orders of superhelicity will arise at equilibrium. Several possible applications of this approach to the supercoiling of closed circular DNA are described.
Examen par la méthode des orbitales moléculaires des préférences conformationnelles intrinsèques du squelette des acides nucléiques
Authors: Broch Henri , Vasilescu Dane 
Published: December 2004

AbstractThis paper reports a systematic PCILO study of the conformation of the nucleic acid backbone. The authors principally studied the ω′ and ω phosphodiester torsion angles of the disugar triphosphate model as a simultaneous function of (1) the sugar nature, ribose or deoxyribose, (2) the different combinations of the sugar ring puckers C(2′)‐endo‐C(2′)‐endo, C(3′)‐endo‐C(3′)‐endo, C(3′)‐endo‐C(2′)‐endo, and C(2′)‐endo‐C(3′)‐endo, and (3) the different conformations around the ψ(C4′–C5′) exocyclic bond. The dependence of the (ω′,ω) conformational energy maps upon these different factors, is discussed. The results are in very good agreement with the observed structures of ribonucleic (RNA10, RNA11, A′‐RNA12, tRNAPhe) and deoxyribonucleic acids (D‐DNA, C‐DNA 9.3, B‐DNA 10, A‐DNA 11). Thus the validity of this model, the disugar triphosphate unit, is ensured.The main conclusions that can be drawn from this systematic study are the following:

The torsion around P‐05′ (angle ω) is, as a general rule, more flexible than the torsion around P‐03′ (angle ω′).
There is no notable difference between the ribose–triphosphate units and the deoxyribose–triphosphate units for the C(3′)‐endo–C(3′)‐endo and C(3′)‐endo–C(2′)‐endo sugar puckers.
The deoxyribose–triphosphate units with C(2′)‐endo–C(2′)‐endo and C(2′)‐endo–C(3′)‐endo sugar puckers show much more ω′ flexibility than the ribose–triphosphate units with the same sugar puckers and cis position for the 2′hydroxyl group.
The preferred values of ω′ are independent of the sugar nature (ribose or deoxyribose) and of ψ values; they are correlated with the sugar pucker of the first sugar‐phosphate unit:

C(3′)‐endo‐C(3′)‐endo and C(3′)‐endo‐C(2′)‐endo puckers ⟹ ω′ ≃ 240° (g− region)
C(2′)‐endo‐C(2′)‐endo and C(2′)‐endo‐C(3′)‐endo puckers ⟹ ω′ 180° (t region)

The preferred values of ω are independent of the nature and the puckering of the sugars; they are correlated with the rotational state of the torsion angle ψ(C4′–C5′): ψ ≃ 60° (gg) ⟹ ω ≃ 300° (g−), ψ ≃ 180° (gt) or 300° (tg) ⟹ ω ≃ 60° (g+)
The conformation and aggregation of bovine β‐casein A. I. Molecular aspects of thermal aggregation
Authors: Andrews A. L. , Atkinson D. , Evans M. T. A. , Finer E. G. , Green J. P. , Phillips M. C. , Robertson R. N. 
Published: December 2004

AbstractThe conformation of β‐casein A in the monomeric and thermally aggregated states has been investigated by a range of techniques. β‐Casein exists as a monomer in solution at 4°C and at concentrations up to at least 3 g/dl. The molecule is flexible and exhibits a lot of segmental motion, but its secondary structure is not wholly random coil; about one‐third of the polypeptide chain is ordered and the likely locations of these regions are discussed. The radius of gyration, representing the time‐average distribution of the flexible chain, is 46 Å. Increasing temperature leads to aggregation of the β‐casein molecules. The degree of association is very sensitive to experimental conditions, and under our conditions a 14‐mer exists at 20°C. The aggregate is spherical with a radius of about 100 Å. The interior of the aggregate is relatively disordered, and the β‐casein molecules remain in a largely flexible, hydrated conformation. The volume restriction of the protein molecules which occurs on association leads to some immobilization of the hydrophobic C‐terminal region, which is packed toward the center of the aggregate.
Experimental studies of molecular interactions between nitrogen bases of nucleic acids
Authors: Yanson I. K. , Teplitsky A. B. , Sukhodub L. F. 
Published: December 2004

AbstractNew experimental results concerning molecular interactions between the nitrogen bases of nucleic acids in the crystalline phase and in vacuo are reported. The temperature dependence of the evaporation rate is measured for solid species. The sensitivity of conventional methods of sublimation heat measurements was improved essentially using a quartz resonator serving as a precise sensor of evaporation rate. Sublimation heats were found for both canonical bases and a number of their derivatives. The in vacuo formation of base associates interacting through hydrogen bonds was observed with a field mass spectrometer. The dimer formation enthalpies, which are indicative of a stronger attraction in complementary pairs compared with noncomplementary ones, were derived from the temperature dependence of ionic currents. Hydrogen‐bound complexes of more intricate associates (base trimers and aqueous molecules associates) were studied. The energy gain in the formation of trimers of identical molecules was shown to be larger (per base molecule) than that for dimers.
Diffusion–collision model for protein folding
Authors: Karplus Martin , Weaver David L. 
Published: December 2004

AbstractThe basic equations for the elementary step in the diffusion–collision–coalescence model of protein folding are derived for the case of two radially diffusing spherical microdomains. Refinements and biological implications of the mechanism are considered; included are detailed discussions of the parameters of the model, the possibilities of rotational diffusion and surface diffusion in one or two dimensions, the nature of the microdomains, and the application of the model to protein unfolding.
Inelastic light‐scattering study of polyadenilic acid
Authors: Mathiez P. , Weisbuch G. , Mouttet C. 
Published: December 2004

AbstractWe report a systematic study of inelastic light scattering for semidilute solutions of poly(adenilic acid). The results are analyzed in terms of a fast and a slow relaxation time. From their dependence on the wave vector and the polymer concentration, we are able to interpret the results in terms of a collective mode for the fast relaxation time at low wave vector, an individual chain motion for the fast time at large wave vector, and structural relaxation for the slow relaxation time.
Crystal and molecular structure of benzyloxycarbonyl‐α‐aminoisobutyryl‐L‐prolyl methylamide: The observation of an X2‐Pro3 Type III β‐Turn
Authors: Prasad B. V. Venkataram , Shamala N. , Nagaraj R. , Chandrasekaran R. , Balaram P. 
Published: December 2004

AbstractThe crystal and molecular structure of N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐L‐prolyl methylamide, the amino terminal dipeptide fragment of alamethicin, has been determined using direct methods. The compound crystallizes in the orthorhombic system with the space group P212121. Cell dimensions are a = 7.705 Å, b = 11.365 Å, and c = 21.904 Å. The structure has been refined using conventional procedures to a final R factor of 0.054. The molecular structure possesses a 4 → 1 intramolecular N‐H—O hydrogen bond formed between the CO group of the urethane moiety and the NH group of the methylamide function. The peptide backbone adopts the type III β‐turn conformation, with ϕ2 = −51.0°, ψ2 = −39.7°, ϕ3 = −65.0°, ψ3 = −25.4°. An unusual feature is the occurrence of the proline residue at position 3 of the β‐turn. The observed structure supports the view that Aib residues initiate the formation of type III β‐turn conformations. The pyrrolidine ring is puckered in Cγ‐exo fashion.
Thermometric titration studies of the interaction of block polypeptides with surfactants
Authors: Kale K. M. , Vitello L. , Kresheck G. C. , Vanderkooi G. , Albers R. J. 
Published: December 2004

AbstractThe interactions between surfactants and block polypeptides were investigated by titration calorimetry and CD. The polypeptides exhibited signs of an interaction only with surfactants bearing a charge opposite to the charge on the polymer. The stoichiometry of the resulting complex was determined to be approximately equal to the polymer net charge. In general, a decrease in helical content accompanied the interaction between the block polypeptides and the surfactants. Both positive and negative enthalpy changes were noted, depending on the heat of micelle formation. None of the thermal effects noted were preceded by polymer unfolding, as is characteristic of the interaction between surfactants and typical globular proteins.
Effect of some monohydric alcohols on the oxygen affinity of hemoglobin: Relevance of solvent dielectric constant and hydrophobicity
Authors: Cordone Lorenzo , Cupane Antonio , Biagio Pier L. San , Vitrano Eugenio 
Published: December 2004

AbstractWe studied the effect of methanol, ethanol, iso‐propanol, and n‐propanol on the reaction of hemoglobin with oxygen. The oxygen affinity was found to decrease with increasing alcohol concentration and alkyl group size; no detectable effect on Hill's constant was found. Difference spectroscopy indicated KR not to be affected by the presence of alcohols; the lowered affinity was then attributed to an altered equilibrium between T and R conformations of hemoglobin. The results have been analyzed in such a way as to allow separation of electrostatic contributions to free energy difference between the T and R states from nonelectrostatic ones. The nonelectrostatic term has been attributed to protein–solvent hydrophobic interactions. Values of hydrophobic free energy are in good agreement with analogous data estimated by correlating different results previously reported in the literature.
Dynamic mechanical properties of elastin
Authors: Gosline John M. , French Christopher J. 
Published: December 2004

AbstractThe dynamic mechanical properties of water‐swollen elastin under physiological conditions have been investigated. When elastin is tested as a colsed, fixed‐volume system, mechanical data could be temperature shifted to produce master curves. Master curves for elastin hydrated at 36°C (water content, 0.46 g water/g protein) and 55°C (water content, 0.41 g/g) were constructed, and in both cases elastin goes through a glass transition, with the glass transition temperatures of ‐46 and ‐21°C, respectively. Temperature shift data used to construct the master curves follow the WLF equation, and the glass transition appears to be characteristic of an amorphous, random‐polymer network. For elastin tested as an open, variable‐volume system free to change its swollen volume as temperature is changed, dynamic mechanical properties appear to be virtually independent of temperature. No glass transition is observed because elastin swelling increases with decreased temperature, and the increase in water content shifts elastin away from its glass transition. It is suggested that the hydrophobic character of elastin, which gives rise to the unusual swelling properties of elastin, evolved to provide a temperature‐independent elastomer for the cold‐blooded, lower vertebrates.
Viscosometric investigation of the ordinary–extraordinary phase transition in dilute polylysine solutions
Authors: Martin Nicholaus B. , Tripp John B. , Shibata John H. , Schurr J. Michael 
Published: December 2004

AbstractLow shear viscosities have been determined for a 1 mg/ml poly(L‐lysine) solution as a function of added salt concentration in the region of the previously reported ordinary–extraordinary phase transition. The measured viscosities indicate that the polyions are far from completely extended at the transition. Estimates of the longest internal relaxation time for an equivalent free‐draining Rouse‐Zimm chain give τ ≃ 10−5 sec, similar to that of the rapid, angle‐independent component previously observed in the dynamic light‐scattering correlation function at the transition. An unusual peak and valley are observed in the curve of [η]0 versus [NaBr] in the transition region. Possible interpretations of these features, and their bearing on the nature of the extraordinary phase, are discussed.
Differentiation between the α‐helical and coillike conformations of poly(L‐glutamic acid) in aqueous solution through binding of pinacyanol
Authors: Pal M. K. , Mandel M. 
Published: December 2004

AbstractPinacyanol in the presence of an excess of poly(L‐glutamic acid) [polymer/dye ratio (P/D) > 10] exhibits different absorption spectra in the visible region when bound to the slightly charged polypeptide in the α‐helical conformation or to the nearly completely dissociated polypeptide in the coillike conformation. These spectra reveal aggregation of the dye bound to the macromolecular chain in both conformations, although in the coillike one different kinds of aggregates may be present. Dye binding is accompanied by the appearance of CD bands in the visible region which are also different for the α‐helical and the coillike conformations. The aggregates formed in the presence of the latter change slowly in time and seem to induce some conformational changes in the polypeptide chain. Furthermore, they have been found to be, at least partially, stable with respect to a subsequent reversal to the α‐helical conformation. All results could be qualitatively interpreted assuming that in the coillike conformation, ordered regions exist along the chain as proposed by Krimm and Tiffany.
Study of thermal and acid denaturation of DNA by means of voltammetry at graphite electrodes
Authors: Brabec Viktor 
Published: December 2004

AbstractConformational changes in guanine–cytosine (G·C) and adenine–thymine (A·T) pairs in DNA were investigated by means of differential pulse voltammetry at a pyrolytic graphite electrode (PGE). As a monitor of these conformational changes, two separated voltammetric peaks, G and A, which correspond to electrochemical oxidation at the PGE of guanine and adenine residues, respectively, were used. It was found that peak A was first increased in the course of thermal denaturation of DNA. This indicates that, on heating a native DNA sample, regions rich in A·T pairs melt first. In the course of acid denaturation of a native DNA sample, the height of peak A was changed just before the denaturation. It is suggested that protonation of adenine residues in DNA regions rich in A·T pairs was responsible for these changes.
Molecular and crystal structure of an intercalation complex: Proflavine–cytidylyl‐(3′,5′)‐guanosine
Authors: Berman Helen M. , Stallings W. , Carrell H. L. , Glusker J. P. , Neidle S. , Taylor G. , Achari A. 
Published: December 2004

AbstractThe high‐resolution crystal and molecular structure of a 3:2 complex of proflavine and cytidylyl‐(3′,5′)‐guanosine is described. The complex exhibits more than one mode of dye binding to the dinucleoside phosphate. One proflavine cation is symmetrically intercalated between the base pairs. The other proflavine cations and ones related by symmetry stack above and below the base pairs and also hydrogen bond externally to the duplex. The conformation of the CpG is most similar to A‐RNA with all C(3′)‐endo sugar puckering. To allow the base pairs to stretch from the normal 3.4‐Å separation to a 6.8‐Å separation, the torsion angles ϕ and χ of the guanosine are increased by about 60° from the values found in RNA. The crystal structure itself contains disordered sulfate anions and is highly solvated, with all but one water molecule involved in a continuous water–sulfate channel.