bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mean‐square hydrophobic moment for partially helical polypeptides
Authors: Hamed Maher M. , Mattice Wayne L. 
Published: December 2004

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, where mi denotes the dipole moment associated with bond i. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣH, where Hi denotes the hydrophobicity of residue i. 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 for 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〉 is illustrated by calculations performed for model sequential copolypeptides.
Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte
Authors: Bret Marc Le , Zimm Bruno H. 
Published: December 2004

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 surface of the polyion.
Distribution of counterions around a cylindrical polyelectrolyte and manning's condensation theory
Authors: Bret Marc Le , Zimm Bruno H. 
Published: December 2004

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 call RM, 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; RM varies 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 polyion radius and charge density.
Interaction of poly‐5‐bromouridylic acid. I. Formation of helical complexes with various adenine and 2‐aminoadenine derivatives
Authors: Higuchi Shigesada 
Published: December 2004

AbstractComplexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9‐substituted adenine and 2‐aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well‐resolved bands in the range of 210–350 nm. Other adenine derivative–poly(BU) complexes also afford similar CD spectra, while 2‐aminoadenine derivative–poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative–poly(BU) complexes are nearly identical in structure except for the ribose–phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9‐methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer–poly(U) system was found to be about 20°C in 0.4M NaCl–0.02M Na–cacodylate–5 × 10−4M EDTA (pH 7.0). Further, it was noted that the monomer–poly(BU) complexes are formed even when the Tm is lower than that of self‐folded poly(BU).
Conformational study of trinucleoside tetraphosphate d(pCpGpCp): Transition of right‐handed form to left‐handed form
Authors: Yoon Chang No , Kang Young Kee , Jhon Mu Shik 
Published: December 2004

AbstractUsing the semiempirical potential functions, conformational energies of the model compounds DMP−, d(pCp), d(pGp), and d(pCpGpCp) are calculated, and the B → Z transition is discussed along the pseudorotational path of the sugar ring. For dimethylmonophosphate anion, DMP−, the energy contour map is presented and the stabilities of the phosphodiester conformations discussed. For the sugar ring without the base attached, the minimum energies for each sugar‐puckering form are calculated along the pseudorotational path. The energy barrier of the interconversion between the C(3′)‐endo form and the C(2′)‐endo form is calculated to be about 2.0 kcal/mol. From the conformational energy calculations of the interconversions of mononucleoside diphosphates, d(pCp) and d(pGp), between the C(2′)‐endo conformer and the C(3′)‐endo conformer, the purine sugar segment is known to be more convertible than the pyrimidine sugar segment. The results also support the finding that the pseudorotational transition occurred with the O(1′)‐endo form more easily than with the O(1′)‐exo form. Based on the results of conformational studies of DMP−, d(pCp), and d(pGp), a topological transition of the handedness of the model compound, d(pCpGpCp), is studied. The left‐handed Z‐form is found to be less stable by about 8.5 kcal/mol than is the right‐handed B‐form. The energy barrier of the Z → B transition is calculated to be about 17.4 kcal/mol. The contributions of the electrostatic and nonbonded energies to the energy barrier are discussed in connection with the conformation changes of the model compound, d(pCpGpCp).
Proton polarizability of poly(L‐tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations
Authors: Zundel Georg , Leberle Klaus 
Published: December 2004

AbstractWe studied films of poly(L‐tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li+, Na+, K+) and of the degree of hydration were clarified. If Li+ ions are present, the OH ⃛−OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li+ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K+ ions are present. In dry films, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K+ ions when compared to the system with Li+ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K+ ions. Furthermore, POH ⃛−OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the ‐PO3− groupings are in a symmetrical environment, indicating that the K+ ions are removed from these groupings. If the degree of hydration increases further, hydrogen‐bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na+ ions are present, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.
Electric birefringence study of the purple membrane of Halobacterium halobium
Authors: Kahn Leo D. , Tu Shu‐I 
Published: December 2004

AbstractAn electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10−14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10−14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X‐100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk‐shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
Self‐association of the neuroregulatory peptide substance P and its C‐terminal sequences
Authors: Rueger Margitta , Bienert Michael , Mehlis Burkhard , Gast Klaus , Zirwer Dietrich , Behlke Joachim 
Published: December 2004

AbstractSelf‐association of substance P and its C‐terminal partial peptide sequences was studied by CD, quasi‐electric light scattering, and sedimentation experiments. CD spectra of these peptides are strongly influenced by self‐association. They exhibit strong characteristic negative ellipticities, suggesting the formation of a presumably B‐type ordered structure. The tendency to form multimers depends on chain length and constitution and has its maximum at the octapeptide (SP 8). The peptide multimers have a broad distribution of sizes in the range of 30‐ and 800‐nm diameter. Subdivision of this distribution into two size classes gives mean diameters of 60–100 nm (predominating)/200–800 nm for substance P and 30–50 nm/200–800 nm for SP 8 multimers.
Cation‐induced conformational changes in tRNA molecules
Authors: Mazzei F. , Onori G. 
Published: December 2004

AbstractThe uv absorption spectra and melting profiles of an initially ion‐free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first‐series transition‐metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4‐TU absorption region. Sharp differences have, however, been detected in the 290–305‐nm range in the presence of the various ions studied. When transition‐metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition‐metal ions are also able to bind directly to the bases.
Quasielastic light‐scattering studies on dinucleosomal‐sized DNA: Ionic‐strength dependence
Authors: Schmitz Kenneth S. , Lu Mei 
Published: December 2004

AbstractQuasielastic light‐scattering (QELS) studies were performed on a monodisperse preparation of dinucleosomal‐sized DNA having an average of 375 base pairs. The QELS data were obtained at several time intervals at each angle examined over the range 30° < θ < 60° for the ionic strength solvents 500, 50, 10, and 1 mM in KCl. What results from this study is that two relaxation domains persist over the entire ionic strength range where the “splitting” between these two domains increases as the ionic strength is lowered. The ordinate intercept of Dapp vs Cp/2Cs, where Cp is the polyion concentration and Cs is the added salt concentration, is shown to give the “true” hydrodynamic value for the diffusion coefficient. The “splitting phenomenon” is interpreted in terms of two models currently in vogue: small ion–polyion coupled modes and translational–rotational coupled modes for rigid rods in congested solutions. Although neither model is in perfect agreement with the experimental results, the small ion–polyion coupled mode theory appears to provide a better quantitative description of the observations.
13C‐NMR chemical shifts and the conformations of rigid polypeptides
Authors: Tonelli Alan E. 
Published: December 2004

Abstract13C‐nmr chemical shifts of backbone carbonyl and side‐chain β‐carbons in polypeptides provide structural information. Recent utilization of substituent effects on 13C‐nmr chemical shifts (principally γ‐effects) has permitted the rationalization of their sequence and conformation dependence when observed in linear, flexible polypeptides. In this report, we apply the γ‐effect method to study the 13C‐nmr chemical shifts observed in solution and in the solid state for the backbone carbonyl and side‐chain β‐carbons in conformationally rigid polypeptides, which are usually cyclic. As found previously for flexible, linear polypetides, the relative 13C‐nmr chemical shifts observed for the backbone carbonyl and side‐chain β‐carbons in conformationally rigid polypeptides are predictable from knowledge of their peptide residue sequence (primary structure) and conformation (secondary structure) via the γ‐effect method.
Solvent isotope effect on the differences in structure and stability between normal and deuterated proteins
Authors: Chen Chang‐Hwei , Tow Fred , Berns Donald S. 
Published: December 2004

AbstractDifferential scanning microcalorimetry was used to investigate the enthalpy (ΔHd) and the temperature (td) of thermal denaturation of normal (nondeuterated) (H‐PC) and deuterated (D‐PC) phycocyanins in D2O solvent. Values of td in D‐PC are about 5–7°C lower than those in H‐PC. The magnitudes of ΔHd in D‐PC are only 21–32% of those in H‐PC. During the protein unfolding, the heat‐capacity changes (ΔCp) in D‐PC are also lower than those in H‐PC. CD was employed to evaluate the secondary structure and the urea denaturation of these proteins in D2O solvent. These proteins have about the same α‐helix content. D‐PC is less resistant to the denaturant urea than is H‐PC. In general, the apparent free‐energy change in the process of protein unfolding at zero denaturant concentration is higher in H‐PC than in D‐PC. Comparisons of the present results for D2O solvent with those previously reported for H2O reveal that solvent isotope effect essentially does not change the α‐helix content in H‐PC and D‐PC. However, D‐PC or H‐PC has a higher random‐coil content in its secondary structure in D2O than in H2O. Substitution of H2O with D2O as the solvent increases td in both D‐PC and H‐PC, lowers ΔHd in H‐PC, and greatly lowers ΔHd in D‐PC. The deuterium solvent isotope effect does not change ΔCp in H‐PC but lowers ΔCp in D‐PC. In the urea denaturation, the magnitudes of (Cu)1/2 in H‐PC and D‐PC are not affected by such a solvent effect, whereas those of ΔG are greatly increased. These results are correlated with the structure and stability of the proteins.
Interaction of poly(I) and poly(I)·poly(C) with chlorodiethylenetriamino platinum(II) chloride
Authors: Hermann Dominique , Fazakerley G. Victor , Guschlbauer Wilhelm 
Published: December 2004

AbstractThe fixation of dien‐Pt on poly(I)·poly(C) leads to only minor changes in the uv and CD spectra at ambient temperature, showing that there is little perturbation of the secondary structure in the rb range studied (up to 0.30). However, the melting profiles show two steps. The Tm for strand separation increases linearly from 61°C (rb = 0) to 80°C (rb = 0.18), after which it declines on further increasing the rb. The second melting step is not complete at 100°C, and the magnitude of the absorbance change in this second step also appears to be at a maximum at rb = 0.18. Although dien‐Pt can only coordinate to one base, the nmr spectra at 80°C also show a second type of interaction with the adjacent bases, which is only destroyed in the presence of a strong denaturing agent, 5M guanidinium hydrochloride. From these results and the spectrophotometric data, we observe that dien‐Pt forms a triple sandwich by hydrogen bonding of the platinum amino groups to the adjacent hypoxanthine bases (N7). The presence of these hydrogen bonds accounts for the increased stability (maximal at one Pt to three hypoxanthine bases) and their rupture is seen in the second melting step. No interaction has been observed with poly(C) strand. Reaction of dien‐Pt with poly(I) shows the formation of the same triple sandwich structure in the nmr spectra.
The effects of alkali‐metal chlorides and of spermidine and spermine on the swelling pressures of DNA gels in the ultracentrifuge
Authors: Richard Alfred J. 
Published: December 2004

AbstractThe effects is solution of the alkali‐metal chlorides on the gel‐like phase of DNA formed in the ultracentrifuge cell have been studied. The polycations, spermidine and spermine, also were shown to affect strongly the swelling pressure of the DNA gel, with evidence for the destabilization of DNA in very dilute spermine, below 10−6 M, and for the collapse of DNA in both spermine and spermidine solutions above 10−6 M.
Circular dichroism of core DNA in mononucleosomes: A theoretical model
Authors: Tobias Irwin 
Published: December 2004

AbstractThe observed difference between the CD spectrum of B‐DNA mononucleosomes and that of free DNA has been attributed to the tertiary structure of the core DNA. This conjecture is tested here. The tertiary structure is modeled as an optical system consisting of two identical, planar, linear retarders rotated with respect to each other. The retarders have the same linear birefringence and linear dichroism as oriented B‐DNA. Such an optical system is circularly dichroic. The predicted wavelength dependence and magnitude of the CD are in reasonably close agreement with the experimental results.
Antifreeze glycoproteins: Influence of polymer length and ice crystal habit on activity
Authors: Burcham Timothy S. , Knauf Michael J. , Osuga David T. , Feeney Robert E. , Yeh Yin 
Published: December 2004

AbstractThe effect of the ice crystalline habit and the length of the polymer on the ability of the antifreeze glycoproteins (AFGP) from polar fish to depress the freezing temperature of water was investigated. The low‐molecular‐weight components of the glycoproteins, AFGP‐ 6–8, are inactive when a solution of such a sample is nucleated at −6°C. A solution of large AFGP (1–4) is fully functional under the same conditions. The low‐molecular‐weight components differ from the height‐molecular‐weight components in that they contain some proline replacing the alanine in the Ala‐Ala‐Thr · disaccharide polymer unit. In the present experiments, antifreeze activity was examined in the presence of two different forms of ice crystal growth habits, and homodimders of AFGP 6 and 8 were prepared to investigate the function of polymer length and the on antifreeze activity at different degrees of supercooling. The results indicate that the ice crystal growth habit and the introduction of proline into the polymer unit may be responsible for the loss of activity at deep supercooling (−6°C) of AFGP 6–8. The loss in the ability of AFGP to depress the freezing temperature of water at deep supercooling is not solely due to polymer length, as carbodiimide‐linked dimers of AFGP 6 do not function under these freezing conditions. A Model of antifreezing action based on Langmuirian adsorption of AFGP on the ice surface and direct competition between water and AFGP molecules for the incorporation sites in the ice crystal lattice is presented.
Synthesis of oligopeptides consisting of L‐leucyl‐L‐leucyl‐L‐ananyl and L‐methionyl‐L‐methionyl‐L‐leucyl repeating units with an improved preparation of Nps‐amino acids
Authors: Katakai Ryoichi , Shida Hitoshi , Takada Toshiaki 
Published: December 2004

AbstractTwo series of peptides with hydrophobic side chains, Nps‐(L‐Leu‐L‐Leu‐L‐Ala)n‐OEt and Nps‐(L‐Met‐L‐Met‐LLeu)n‐OEt (n = 1–6), were synthesized by the fragment condensation method using dicyclohexylcarbodiimide in the presence of N‐hydroxysuccinimide. The tripeptide fragments were prepared stepwise by dicyclohexylcarbodiimide‐mediated reaction of Nps‐amino acids, which were synthesized by an improved rapid procedure.