ISSN:0006-3525    

DOI:10.1002/bip.360230202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.360230203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractA mean‐square helical hydrophobic moment, 〈h2〉, is defined for polypeptides in analogy to the mean‐square dipole moment, 〈μ2〉, for polymer chains. For a freely jointed polymer chain, 〈μ2〉 is given by Σm i2, wheremidenotes the dipole moment associated with bondi. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣH i2, whereHidenotes the hydrophobicity of residuei. The tendency for correlations in orientations of residue hydrophobic moments in helices therefore dictates the size of 〈h2〉/〈H2〉, where 〈H2〉 denotes the average value of ΣH i2for all helices. The value of 〈h2〉/〈H2〉 will be greater than one in amphiphilic helices. A necessary prerequisite for this diagnostic usage of 〈h2〉/〈H2〉 is that the residue hydrophobic moment be oriented prependicular to the principal axis of the helix. Matrix‐generation schemes are formulated that permit rapid evaluation of 〈h2〉 and 〈H2〉. The behavior of 〈h2〉/〈H2〉

ISSN:0006-3525    

DOI:10.1002/bip.360230204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo‐oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest‐neighbor exclusion. For the ribo‐oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo‐oligonucleotide showed all sites equivalent and no cooperativity. For the ribo‐oligonucleotides the enthalpy for ethidium binding is −14 kcal/mol. The equilibrium constants at 25°C depend on the model; eitherK= 6 × 105M−1for the two strong sites (4 × 103M−1for the weak site) orK= 2.5 × 105M−1for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo‐oligonucleotide the enthalpy of binding is ‐9 kcal/mol and the equilibrium constant at 25°C is a factor of 10

ISSN:0006-3525    

DOI:10.1002/bip.360230205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractOriented fibers drawn from aqueous gels of calf‐thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A‐DNA and B‐DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm−1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D2O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A‐ and B‐DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation‐sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700‐cm−1interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000‐cm−1region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A‐ and B‐DNA structures. The results are extended to Z‐DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleopr

ISSN:0006-3525    

DOI:10.1002/bip.360230206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractA molecular‐dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A‐ or B‐DNA helix with one Na+counterion per nucleotide. Four Na+ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ions were assumed to be Lennard‐Jones spheres that also carried charges. Stillinger four‐point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B‐DNA and 20, 32, and 46 in A‐DNA fragments. The arrangements of the Na+ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of

ISSN:0006-3525    

DOI:10.1002/bip.360230207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractWe report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson‐Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson‐Boltzmann equation when only the species with 1‐Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson‐Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter‐ and co‐ions, but particularly co‐ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surfa

ISSN:0006-3525    

DOI:10.1002/bip.360230208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye‐Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear‐charge‐density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye‐Hückel theory. Therefore, we turn to the analytical solution of the Poisson‐Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we callRM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration;RMvaries as κ−1/2, where κ is the Debye‐Hückel screening parameter. The Manning fraction, 1 – 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ−1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson‐Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson‐Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given

ISSN:0006-3525    

DOI:10.1002/bip.360230209

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractEthylurea was used to weaken hydrophobic interactions during collagen fibrillogenesisin vitro.Intact and enzyme‐digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme‐digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin‐digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C‐terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C‐terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and g

ISSN:0006-3525    

DOI:10.1002/bip.360230210

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractDNA molecules can be organized into ordered aggregates of opposite handedness by complexation with polylysine and other polypeptides; we have investigated the conditions under which ψ(+) and ψ(−) structures are produced with double‐helical synthetic polynucleotides. Both poly(dGdC)·poly(dGdC) and poly(dAdT)·poly(dAdT) readily form ψ(−) structures with polylysine, although the method of preparation can alter the CD spectra. The GC copolymer, which is more susceptible to conversion into A or Z conformers, forms ψ(+) structures with lysine–alanine copolypeptides more readily than the AT copolymer. Nucleotide base modifications that favor the Z structure, such as bromination and methylation, also favor ψ(+) formation, and the Co(NH3)6Cl3reagent that readily induces the Z structure also leads to ψ(+). Thus, the production of the ψ(+) structure seems to be frequently correlated with susceptibility to A or Z formation, although there are some cases in which the B conformer also leads to ψ(+). Polyethylene glycol generally produces a ψ(−) structure; the differentiation between ψ(+) and ψ(−) structures seems to require elect

ISSN:0006-3525    

DOI:10.1002/bip.360230211

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY