bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segmental flexibility in pig immunoglobulin G studied by neutron spin‐echo technique
Authors: Alpert Yolande , Cser László , Faragó Béla , Franěk František , Mezei Ferenc , Ostanevich Yuriy M. 
Published: May 2005

AbstractThe dynamic behavior of pig immunoglobulin G in deuterium oxide solutions was investigated by the neutron spin‐echo technique. This novel technique makes it possible to study intramolecular motion without introducing probes into the macromolecule. Using neutron spin‐echo, the effective diffusion coefficient, Deff, was obtained as a function of the transferred momentum, κ. For interpretation of the experimental data, two models were designed, and computed Deff values were compared with experimental data. The rigid T‐shape model was compatible with the experimental data only by assuming an unrealistically high rotational diffusion coefficient, and it was therefore unacceptable. Reasonable agreement with all available experimental data was obtained with a flexible model of immunoglobulin G molecule, which the Fab arms are assumed to wobble around the hinge region within an angle of 50°.
Thermodynamics of the helix–coil transition in polypeptides in mixed organic solvents: The influence of inert solvent and side chain
Authors: Jeremic K. , Karasz F. E. 
Published: May 2005

AbstractThe thermally induced coil–helix transition of poly(γ‐benzyl‐L‐glutamate) (PBLG) and poly(γ‐methyl‐L‐glutamate) (PMLG) in binary solvent mixtures was investigated by calorimetric and optical rotatory dispersion (ORD) measurements. Dichloroacetic acid was the common active solvent, and the inert solvent was one of the chlorinated hydrocarbons, such as chloroform, 1,3‐dichloropropane, 1‐chlorobutane, or 1‐chlorooctane.The thermodynamic parameters characterizing the intramolecular polypeptide and polypeptide–solvent interactions were calculated using the Karasz and Gajnos theoretical model [(1973) J. Phys. Chem. 77, 1139–1145]. It was found that the enthalpy (ΔH1) and entropy (ΔS1) of helix stabilization in the absence of the active solvent depend on the inert solvent, but only in the case of PBLG. This is explained by the additional helix stabilization achieved by the stacking of the benzyl groups. The stacking is more pronounced in less polar chlorinated hydrocarbons with longer aliphatic chains. The results obtained indicate that the maximum helix stability is reached in chlorinated hydrocarbons with 12 C atoms. In the case PMLG, with an aliphatic ester side group, ΔH1 and ΔS1 are independent of the inert solvent.The ORD measurements were used to determine the maximum fraction of helicity attained at constant solvent composition and the transition temperature, Tc, at the point where fH = 0.5. It was found that, for the same solvent composition, Tc was higher than the temperature of the midpoint of the calorimetric peak. This is explained by the fact that the maximum fraction of helicity is less than unity. The finite transition width was taken into account by calculating the phase boundaries for different fractions of helicity using the value of σ estimated from the calorimetric and van't Hoff enthalpies in the usual manner.
Analysis of the ring‐closure probabilities of isotropic wormlike chains: Application to duplex DNA
Authors: Hagerman Paul J. 
Published: May 2005

AbstractThe configurational properties of an isotropically bendable wormlike chain have been investigated using a Monte Carlo approach. In particular, radial distributions for end‐to‐end separation, ring closure probabilities, and the angular correlation of the two ends of the chain have all been determined as a function of the contour length of the chain. The results of this analysis, when applied to the data of Shore et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 4833–4837] for the length dependence of ring closure for doublehelical DNA, yields a value for the persistence length of DNA in remarkable agreement with earlier hydrodynamic studies.
DNA Motions in the nucleosome core particle: A reanalysis
Authors: Schurr J. Michael , Schurr Rebecca L. 
Published: May 2005

AbstractTransient photodichroism (TPD) data of Wang, Hogan and Austin [(1982) Proc. Natl. Acad. Sci. USA 79, 5896–5900] for methylene blue intercalated in nucleosomal DNA are reanalyzed using correct expressions for the twisting correlation functions of short DNAs. The data are found to rule out several models, including one in which the helix axis is constrained to girdle the equator of the sphere (representing a core particle) but the DNA is everywhere able to undergo twisting deformations and/or spinning around its local helix axis. However, when the ends of the DNA are rigidly clamped (against twisting/spinning) to the sphere, the same model gives an excellent fit to the data with suitable choices of parameters. From these and other observations, it is concluded that nucleosomal DNA must be rigidly clamped to the core particle at one or more points, although it is free to twist at most sites of binding of the dye. Moreover, if the dye is actually bound between two clamped points, then the torsional rigidity of DNA in the nucleosome is at least 2.5 times smaller than that of an ordinary linear DNA.
Adsorption of polypeptides on a solid surface. IV. Adsorption and β‐structure–coil transition
Authors: Birshtein T. M. , Borisov O. V. , Karaev A. K. , Zhulina E. B. 
Published: May 2005

AbstractA theory of adsorption of a polypetide chain capable of undergoing the coil–β‐structure transition on a solid planar surface has been developed. The mutual influence of two order–disorder phase transitions, a conformational and an adsorption transition, was investigated. Various types of adsorption transitions are possible, depending on the initial conformational state (partly or completely β‐structured) and the selectivity of adsorption: (a) the second‐order phase transition, in which the chain is partly structured, both in adsorbed and desorbed states; and (b) the first‐order phase transition, in which the chain exhibits a regular β‐structure, at least on one side of the adsorption transition boundary. The chain bonding to the surface alters the degree of β‐structure, both in the case of selective and nonselective adsorption (similar to the adsorption of the chains with other types of secondary structure). We show that the slope of the adsorption curves for partly β‐structural chains increases as a result of an increase in the degree of β‐structuring, and this effect is even stronger than the analogous effect of β‐structuring.
Secondary structure of peptides. 18. 15N‐nmr and 13C‐nmr CP/MAS investigation of the primary and secondary structure of (Ala/Val) copolypeptides
Authors: Kricheldorf Hans R. , Müller Detlef , Hull William E. 
Published: May 2005

AbstractVarious copolypeptides were prepared by benzylamine or tertiary amine‐initiated copolymerizations of alanine–N‐carboxyanhydride (Ala‐NCA) and valine–N‐carboxyanhydride (Val‐NCA). The number‐average molecular weights of these copolypeptides were detemined by 1H‐nmr spectroscopic end‐group analyses and viscosity measurements. The sequences were characterized by 15N‐nmr spectra in solution, and the average lengths of the homogeneous blocks were determined from the signal intensities. The 50.3‐and 75.4‐MHz 13C‐nmr CP/MAS spectra of the solid copolypeptides are not sensitive to sequence effects, but allow qualitative and quantitative analyses of the secondary structures. In contrast to other methods, the 13C‐nmr spectra allow determination of the extent to which individual amino acids are incorporated into β‐sheet or α‐helix phases. Depending on primary structure and molecular weight, the secondary structure of (Ala/Val) copolypeptides may vary significantly. Both monomer units may be predominantly helical or predominantly β‐sheet structure, or the Val units may prefer the β‐sheet structure with most Ala‐units forming β‐helices. However, these secondary structures are more or less thermodynamically unstable and revert to the stable conformations on reprecipitation from trifluoroacetic acid/water.
Vibrational circular dichroism of polypeptides. VI. polytyrosine α‐helical and random‐coil results
Authors: Yasui S. C. , Keiderling T. A. 
Published: May 2005

AbstractWe have measured the VCD of polytyrosine in the amide I and II regions in dimethyl sulfoxide (DMSO) and in 80:20 mixtures of DMSO with trifluoroethanol, trifluoroacetic acid (TFA), and dichloroacetic acid and in 50:50 mixtures of DMSO and trimethyl phosphate (TMP). Additionally, VCD was obtained for deuterated polytyrosine in DMSO and DMSO:D2O, DMSO:TFA(d1), and DMSO:TMP mixtures as before. Amide A VCD was obtained in DMSO and DMSO:TMP mixtures. In the pure solvent, VCD of an opposite sign was seen as compared with that seen in the mixtures. The latter were characteristic in sign pattern and shape of right‐handed α‐helices for poly(L‐tyrosine). The pure polytyrosine:DMSO results are similar to those of polylysine:D2O at neutral pH and poly(β‐benzyl‐aspartate) in DMSO and may be characteristic of random‐coil VCD.
Vibrational circular dichroism of polypeptides, V. A study of 310‐helical‐octapeptides
Authors: Yasui Sritana C. , Keiderling Timothy A. , Bonora Gian Maria , Toniolo Claudio 
Published: May 2005

AbstractWe have measured vibrational CD spectra in the 3600–1250 cm−1 region of two monodisperse, protected octapeptides, which form right‐handed 310‐helices in CDC13 solution. The spectra are similar in sign pattern to those obtained for right‐handed α‐helices in solution but are smaller in magnitude and, additionally, provide evidence of some line‐shape differences. The delineation of this type of ordered conformation was accomplished by means of 1H‐nmr. Such a solution structure is consistent with the x‐ray crystal structure of one of these molecules.
Conformational study of bacterial lipopeptides: Refinement of the structure of iturin A in solution by two‐dimensional 1H‐nmr and energy calculations
Authors: Marion Dominique , Genest Monique , Caille Anita , Peypoux Françoise , Michel Georges , Ptak Marius 
Published: May 2005

AbstractIturin A is a lipopeptide extracted from strains of Bacillus subtilis. Seven peptide residues form a cycle closed by a β‐amino acid carrying a hydrophobic tail. This compound is an antifungal and induces the formation of conducting pores in black lipid membranes. Two‐dimensional 1H‐nmr was used for investigating its conformation in pyridine. A complete set of nuclear Overhauser effects (NOEs) was obtained from which interproton distances were deduced in a rather broad range of 2.2–4.2 Å. A special procedure was then used to optimize simultaneously experimental parameters and intramolecular energy calculated by semiempirical methods. A model of the conformation is proposed for the backbone for which there is an excellent coherence between NOEs, coupling constants, and intramolecular energy. The conformations of Asn, Gln, and Ser side chains appear to be much more flexible because of their interactions with the solvent. From this picture, iturin A seems to have a rather stiff ring surrounded by mobile side chains. Further studies of this lipopeptide and of other members of the family should enable us to approach some structure–activity relationships for this class of antibiotics.
Number of binding sites of DNA and polynucleotides with tris(2,2′‐bipyridyl)ruthenium(II) cations
Authors: Stradowski Czeslaw , Görner Helmut , Currell Leslie J. , Schulte‐Frohlinde Dietrich 
Published: May 2005

AbstractThe binding of tris(2,2′‐bipyridyl)ruthenium(II) cations [Ru(bpy)] with single‐ and double‐stranded (ss and ds) DNA, and the polynucleotides poly(A), poly(C), poly(G), poly(I), poly(I) · poly(C), and poly(U), was studied in aqueous solution. Steady‐state electrical conductivity measurements with the polynucleotides, ssDNA, and dsDNA reveal that approximately three nucleotides offer one binding site. This may be compared with the ratio [nucleotide]/[Mg2+] of 2.4 : 1 for dsDNA. After laser excitation (353 nm), the luminescence of Ru(bpy) bound to nucleic acids shows two decay components. The contribution of the fast component, which is interpreted as resulting from quenching processes of the absorbed ruthenium complex, exhibits a maximum with increasing [nucleotide]/[Ru(bpy)] at a ratio of about three to one. Bound Ru(bpy) can be released from the strand by addition of NaClO4 [half‐concentration: 2.5 and ≤ 10 mM for poly(U) and dsDNA, respectively].
Calculation of the CD of oligo (dG‐dC): Influence of basic optical parameters
Authors: Richterich Peter , Pohl Fritz M. 
Published: May 2005

AbstractThe CD spectra between 180 and 300 nm of (dG‐dC)4 · (dG‐dC)4 in the A, B, and Z form of DNA were calculated with the classical polarizability theory of DeVoe. The use of the simple point dipole approximation for the calculation of interaction coefficients led to results comparable to those obtained with the point monopole approximation in previous calculations. The background oscillator strengths, effective dielectric constant, helix winding angle, and some transition moment directions were varied systematically. Very satisfying agreements between calculated and measured CD spectra were obtained with transition‐moment directions that are in agreement with experimental results, except for the second transition of guanine. A value of 40° for this transition gave the best results. Possible reasons for this deviation from the experimental results and some problems inherent in the calculations of CD spectra are discussed.
Poly[d(A‐T)‐Cs+] conformations studied by IR spectroscopy
Authors: Adam S. , Bourtayre P. , Liquier J. , Taboury J. A. , Taillandier E. 
Published: May 2005

AbstractInfrared absorption and ir linear dichroism measurements have been performed on poly[d(A‐T)‐Cs+] films at various relative humidities. At high relative humidity, samples are in a B form; at low relative humidity, in a C form. The B → C conformational transition is shown to be a noncooperative one corresponding to a gradual evolution of the backbone geometry of the polynucleotide within the B family. the C‐form‐type spectrum is characteristic of an alternated phosphodiester chain with a dinucleotidic repeat unit.
Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA
Authors: Van Dijk Leendert , Gruwel Marco L. H. , Jesse Wim , De Bleijser Jan , Leyte Jaap C. 
Published: May 2005

AbstractThe field‐dependent23Na nuclear relaxation in aqueous DNA solutions has been obtained for a range of temperatures, including the DNA melting region. At least two correlation times are needed to characterize the spectral density function for the23Na relaxation. For the slow process (with the largest correlation time), the temperature dependence of the coupling constant and the correlation time were determined, and important premelting effects were observed. Possible origins of the slow process are discussed. The last process is shown to be correlated with the properties of the hydration water of DNA as reflected by the17O relaxation rates in these solutions. The influence of the polyelectrolyte and NaCl concentrations on the23Na relaxation rate is compared with previous results from solutions of linear flexible polyelectrolytes.
The distribution of void sizes in a reticulate gel
Authors: West Roger 
Published: May 2005

AbstractThe conformational properties of reticulate gels are examined in detail. The distribution of void sizes in a reticulate gel is shown to be usually indistinguishable from that in a hypothetical gel comprising a scaffolding of long, straight, randomly oriented, nonintersecting gel fibers. Agarose gel is used as the principle model throughout, but the conclusions are shown to be extendable to other species of gel.
Helix–coil transition theory including long‐range electrostatic interactions: Application to globular proteins
Authors: Vasquez Max , Pincus Matthew R. , Scheraga Harold A. 
Published: May 2005

AbstractAn extension of the Zimm–Bragg two‐state theory for the helix–coil transition in polypeptides, which takes into account the effect of peptide charge–dipole interactions on helix stability, is presented. This new theory incorporates these interactions in an expression that is parameterized on recently obtained experimental data on polypeptides for which electrostatic effects are known to influence helix content. Unlike previous two‐state or multistate models, which are parameterized on protein x‐ray data, the present theoretical treatment in independent of such protein data. The theoretical model is applied to a series of peptides derived from the C‐peptide of ribonuclease A, which have been the object of recent spectroscopic studies. The new theoretical approach can account for most of the structural information derived from studies of these C‐peptides, and for overall average helix probabilities that are close in magnitude to those observed for these polypeptides in solution. An application of this new formulation for the prediction of the locations of α‐helices in globular proteins from their amino acid sequence is also presented.
Structural models for the N‐ and C‐terminal telopeptide regions of interstitial collagens
Authors: Jones E. Yvonne , Miller Andrew 
Published: May 2005

AbstractSecondary‐structure prediction has been used to investigate the conformation of the N‐ and C‐terminal telopeptides for type I and type III collagen. The three predictive methods (Chou and Fasman, Robson and co‐workers, Lim) indicate mainly aperiodic conformations. A common structural motif is provided by the positioning of β‐turns, particularly in the vicinity of the residue sites involved in intermolecular cross‐links. An alternative model to that of Helseth et al [(1979) Biopolymers 18, 3005–3014] for the secondary structure of the N‐terminal telopeptide of type I collagen is proposed. The general features of these two contrasting structures have been surveyed by model‐building techniques employing molecular graphics and energy minimization. The role of the telopeptide component in the structural design of the biomaterial collagen is assessed. Notably, the alternative model clearly serves to demonstrate the compatibility of current cross‐linking evidence with the quasi‐hexagonal model for the packing of molecules within a collagen fibril.
A Monte Carlo study of the excluded‐volume effect on the amylosic chain conformation
Authors: Kitamura Shinichi , Okamoto Takahiro , Nakata Yasushi , Hayashi Takeshi , Kuge Takashi 
Published: May 2005

AbstractA Monte Carlo procedure was used to determine the effect of excluded volume on the conformational dimensions of amylosic chains. The excluded volume was introduced into the model by assuming that hard spheres, which cannot overlap each other, exist at the center of mass of each glucose unit in the chain sequence. Monte Carlo chains, which were generated to be distributed consistent with the potential energy of nonbonded nearest‐neighbor interactions, underwent self‐intersections, and the attrition rate in the generation of self‐avoiding chains was found to obey an exponential decay law with increasing chain length x. Thus, in order to generate effectively a large number of self‐avoiding chains with long sequences, we used the Wall–Erpenbeck s‐p method of chain enrichment [F. T. Wall and J. J. Erpenbeck (1959) J. Chem. Phys. 30, 634–637]. By examination of the radial distribution of the end‐to‐end distance and the chain‐length dependence of the quantity 〈r2〉/xl2 (〈r2〉 is the mean square end‐to‐end distance and l is the virtual bond length), it was found that unperturbed amylosic chains change in overall conformation from a non‐Gaussian chain having a helical character to Gaussian as x is increased, whereas perturbed chains do not show Gaussian behavior even at x = 500. For the perturbed chains, 〈r2〉 can be expressed by the equation 〈r2〉 = axb in the range of 100 ≤ x ≤ 500, where a and b > 1 are constants. From comparisons of the persistence vectors and perspective drawings of representative unperturbed and perturbed chains, we felt the local conformation of the amylosic chains, i.e., the local helical character, is also affected by the long‐range excluded‐volume interaction.
Selective binding and solvent denaturation
Authors: Schellman John A. 
Published: May 2005

AbstractA primitive model for solvent denaturation is that the denaturant binds independently to sites exposed by the unfolding of the protein. For reagents like urea and guanidinium salts, this binding must be very weak since denaturation occurs only at very high concentrations. Standard formulas for very weak binding lead to thermodynamic inconsistencies. In this paper, binding by denaturants is treated as selective solvation. This introduces a factor of K 1 into the binding isotherm and binding free energy, where K is the equilibrium constant for selective interaction with the sites. This leads to a thermodynamically consistent description of the binding and the denaturation since, when K = 1, there is no selective interaction and no effect on denaturation, even in concentrated solutions where site occupancy is inevitable.
Correlation between the sequence‐length distribution and structure of statistical copolymers of L‐valine and γ‐benzyl‐L‐glutamate
Authors: Saudek V. , Stejskal J. , Schmidt P. , Zimmermann K. , Škarda V. , Kratochvíl P. , Drobník J. 
Published: May 2005

AbstractStatistical copolymers were prepared from N‐carboxyanhydrides of L‐valine and γ‐benzyl‐L‐glutamate in dioxan with triethylamine as an initiator. The copolymerization conversion was determined by ir spectroscopy, the copolymer composition by amino acid analysis, and the molecular weights by light scattering. The monomer reactivity ratios were found to be rVal = 0.14 and rGlu(OBzl) = 6.4. High‐molecular‐weight copolymers are formed even at low conversions. The content of β‐structure in the copolymers was estimated from the ir spectra in copolymerization mixtures. The sequence‐length distribution of L‐valine and γ‐benzyl‐L‐glutamate copolymers was calculated and its dependence on copolymerization conversion is discussed. Relations between the sequence‐length distribution and the content of β‐structure were studied. It was found that the content of β‐structure in samples with the same composition is different for low‐ and high‐conversion copolymers. The formation of β‐structure in copolymers in the copolymerization mixture requires a certain minimal sequence length, which has been found to be about 6 valine units.
Electrophoretic mobility of λ phage HIND III and HAE III DNA fragments in agarose gels: A detailed study
Authors: Hervet H. , Bean C. P. 
Published: May 2005

AbstractThe electrophoretic mobility (μ) of DNA fragments from λ phage and ΦX 174, split by restriction enzyme to molecular lengths from 3 × 102 to 2.36 × 104 base pairs, has been investigated in 0.6–4% agarose gels at various field strengths, ionic strengths, and temperatures. As already observed, μ is seen to be very sensitive to the field, increasing with field strength. The sensitivity increases with the molecular length of the DNA and decreases at high gel concentration. Our data are in qualitative agreement with recent theoretical predictions that concern the influence of the electric field on electrophoretic mobility. Mobility data have been extrapolated to zero field. This enables a comparison of our experimental results with theoretical predictions on the dependence of μ on the molecular weight of the DNA fragments. Our data fit, quite closely, a reptation model, where the tube path is described as a semiflexible entity with a persistence length equal to the pore diameter. The influence of the agarose concentration and the ionic strength of the buffer on the two parameters of the model—intrinsic electrophoretic mobility (μ0) and the number of base pairs per element of the tube (g)—are well described by the model. The temperature dependence of the electrophoretic mobility, together with the influence of the agarose concentration on μ0, indicate that the hydrodynamic drag is the leading frictional force on the DNA molecules in the gel.