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  • 2015-2019
  • 2010-2014  (53)
  • 1985-1989  (9,473)
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  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The DNA-ligand interactions of a series of phenanthridinium compounds with various combinations of amino, azido, and hydrogen functions at R3 and R8 were examined to determine the contribution of these particular substituents to ligand binding. Spectrophometric titrations using calf-thymus DNA emphasized the importance of amino substituents in conferring a strong interaction and also stabilizing the interaction against reversal by high ionic strength. Although azido groups were not as effective as amino groups, they were more effective than hydrogen functions in enhancing the interaction. Furthermore, an amino substitution at R8 was consistently, though only slightly, more effective than an amino substituent at R3. The results from superhelical titrations using plasmid pBR322 DNA demonstrated that analogs with amino and/or azido functions at both R3 and R8 produced the greatest unwinding, and compounds with an amino or an azido function at R8 proved more effective than those with the corresponding amino or azido substituent at R3.
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  • 2
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic shielding constant of the 31P nucleus of the dimethylphosphate anion is calculated by an ab initio method for different values of the torsion angles about the PO ester bond and different orientations of the methyl groups. The results obtained tend to show that both types of conformational parameters contribute to the value of σ31P. The largest shielding is obtained when the methyl groups are staggered with respect to the PO bond; the smallest, for the eclipsed arrangement. Measurements carried out on the 16 deoxyribodinucleoside monophosphates show that in the majority of cases σ31P is shifted toward lower field for the dimers having large values of 3JPH3′ and 3JPH5′(5″). The theoretical results are discussed in relation to experimental data for polynucleotides and nucleic acids.
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  • 3
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    Biopolymers 23 (1984), S. 471-491 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The optical modes of DNA that displace one strand against the other are modeled by the motion of an oscillator in an asymmetric quartic double-well potential whose minima represent the A- and B-conformations. Assuming that the variation of the polarizability during vibration derives mainly from the tilting of the base rings relative to the helix axis, the total polarizability tensor is shown to possess approximately ellipsoidal symmetry and to depend nonlinearly on the instantaneous displacement of the two strands. The Raman spectrum of a collection of randomly oriented molecules is calculated. It consists of one or more peaks with characteristic shape. The depolarization ratio is 3/4, independent of molecular conformation and frequency. The results are discussed in the light of existing experimental and theoretical information.
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  • 4
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    Biopolymers 23 (1984), S. 511-536 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using 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).
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  • 5
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    Biopolymers 23 (1984), S. 593-599 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of aqueous solutions of DNA were measured at frequencies ranging from 0.1 to 12 GHz. The results are analyzed using the Maxwell mixture theory and yield a value for the hydration of the DNA of about 0.4 g/g, which is in the range observed in other investigations. No evidence was found for an additional absorption effect at microwave frequencies, which has been predicted to occur in certain DNA analogs due to the vibrational excitation of the double helix by the applied microwave field.
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Self-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.
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  • 7
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    Biopolymers 23 (1984), S. 819-829 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-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.
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  • 8
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    Biopolymers 23 (1984), S. 847-852 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectra of the peptides Boc-X-(Aib-X)n-OMe (n = 1, 2, 3) and Boc-(Aib-X)5-OMe, where X = L-Ala or L-Val have been examined in several solvents. The X = Ala and Val peptides behave similarly in all solvents, suggesting that the Aib residues dominate the folding preferences of these peptides. The decapeptides adopt helical conformations in methanol and trifluoroethanol, with characteristic negative CD bands at 222 and 205 nm. In the heptapeptides, similar spectra with reduced intensities are observed. Comparison with nmr studies suggest that estimates of helical content in oligopeptides by CD methods may lead to erroneous conclusions. The pentapeptides yield solvent-dependent spectra indicative of conformational perturbations. Peptide association in dioxane results in an unusual spectrum with a single negative band at 210 nm for the decapeptides. Disaggregation is induced by the addition of methanol or water to dioxane solutions. Aggregation of the heptapeptides is less pronounced in dioxane, suggesting that a critical helix length may be necessary to promote association stabilized by helix dipole-dipole interactions.
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  • 10
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    Biopolymers 23 (1984), S. 831-841 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of poly-5-bromouridylic acid [poly(BU)] with adenosine and 9-methyladenine was studied by equilibrium dialysis, optical melting, and microcalorimetry. The stacking free energy, ω, was estimated as -17.6 kJ/mol for adenosine·2poly(BU) and -18.8 kJ/mol for 9-methyladenine·2poly(BU) from the binding isotherms constructed from equilibrium dialysis results. The binding isotherms constructed from a series of melting curves also gave ω values for adenosine·2poly(BU). The thermal stability of the complex depends on monomer concentration, and the partial molar enthalpies of the complex formation at the midpoint of the transition were evaluated from the Tm coefficients as a function of free monomer concentration. The values of -92.0 and -90.4 kJ/mol were obtained for adenosine·2poly(BU) and 9-methyladenine·2poly(BU) in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0), respectively. Microcalorimetric measurements provided lower integral heats of reaction values for these complexes, i.e., -73.2 kJ/mol for adenosine·2poly(BU) and -71.5 kJ/mol for 9-methyladenine·2poly(BU). A comparison with a polyribouridylic acid system provided a quantitative understanding of a stabilization by bromination in terms of thermodynamic parameters.
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  • 11
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 12
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    Biopolymers 23 (1984), S. 191-194 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 13
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    Biopolymers 23 (1984), S. 257-270 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A 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 DNA molecules.
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  • 14
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    Biopolymers 23 (1984), S. 313-323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ethylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in 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 growth in vitro.
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  • 15
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 16
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the crystal-structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl-3′,5′-adenosine (CpA) and uridylyl-3′,5′-guanosine (UpG). The planar drug molecule is intercalated between C⃛G and U⃛A Watson-Crick base pairs, in a double-helical fragmentlike arrangement. Sugar conformations at the 3′-ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence-dependent effects of the drug binding.
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  • 17
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    Biopolymers 23 (1984), S. 1057-1066 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Helical hydrophobic moment ratios, 〈h2〉/〈H2〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by 〈h2〉, and 〈H2〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h2〉/〈H2〉 tend to be substantially larger than values of the analogous ratio formulated for the mean-square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h2〉/〈H2〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ-hemolysins. It is also large for two other surface-active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h2〉/〈H2〉 is found for melittins. If melittins is to form helices with large 〈h2〉/〈H2〉, the configurational statistics must be governed by effects in addition to those short-range interactions that occur when water is the solvent.
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  • 18
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 19
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy computations have been carried out for the N-acetyl-N′-methylamides of the Pro-Pro, Pro-Gly, and Gly-Pro dipeptides and of the Pro-Pro-Gly-Pro tetrapeptide, serving as models for the conformational analysis of single-stranded poly(Gly-Pro-Pro). The probability of β-bend formation for the Pro-Gly sequence is very high, viz., 0.72 for the terminally blocked Pro-Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β-bend conformations of the Pro-Gly sequence are of low energy in single-chain poly(Gly-Pro-Pro) as well. The β-bend structure had been postulated earlier to be a requirement for post-translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β-bend structure is energetically favorable and hence can be accommodated easily in single-stranded poly(Gly-Pro-Pro).
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  • 20
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of Cu(II) with the protamine scylliorhinine Z3 was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5-6.5, the results suggest the formation of a five-membered chelate ring through the coordination of two nitrogen atoms, the N-terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2 group of Arg; at pH 6.5-8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)-Z3 solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge-transfer dichroic band transitions. At Cu(II):Z3 molar ratios ≥ 2 and at pH 〉 8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in metal-ion complexation.
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  • 21
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Studies of the optical birefringence of solutions of acid-soluble collagen from rat-tail tendon at 22°C in the pH range 1.0-6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt-soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the magnetic field.
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  • 22
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    Biopolymers 23 (1984), S. 1295-1306 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyamines are ubiquitous cellular components that interacts strongly with nucleic acids. Although many of the interactions of oligocations with DNA can be rationalized with polyelectrolyte theories that treat counterions as point charges, some structural effects are evident. We have explored the effects of polyamine structure on one important aspect of DNA behavior, its thermal melting transition, by using a series of spermidine analogs NH3(CH2)3NH2(CH2)nNH33+, where n varies from 2 to 8 [Jorstad et al. (1980) J. Bacteriol. 141, 456-463]. For spermidine itself, n = 4. Tm for calf-thymus DNA in the presence of each of these analogs, and the other naturally occurring polyamines putrescine2+ and spermine4+, was measured over a wide range of NaCl concentrations and polyamine:DNA phosphate ratios. There are modest, but significant structural effects. particularly with the shorter n = 2 and 3 derivatives, whose geometry my not allow full electrostatic interaction with DNA. Longer analogs, on the other hand, are not much different than spermidine in their effects on Tm, though a moderate maximum occurs at n = 5. Since polyamines are important in the cellular condensation and packaging of DNA, we have also delineated the critical polyamine and salt concentrations that are required to cause DNA aggregation. Here again, there are significant structural effects, which are not easily rationalized by any simple considerations.
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  • 23
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    Biopolymers 23 (1984), S. 1315-1323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 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.
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  • 24
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    Biopolymers 23 (1984), S. 1367-1377 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The absorption and CD spectra of the complexes of poly(L-arginine) (PLA) and azo dyes have been measured in aqueous solution. On complexation, Blue-shifted additional absorption bands were observed. In the wide pH 4-11 range, induced CD was observed at the visible wavelengths corresponding to the blue-shifted absorption bands. The induced CD arose from the dimeric dye molecules bound to PLA in the α-helical structure. When a modified analysis of induced CE is made by the excition chirality method, the origin of the induced CD can be assigned to the dipole coupling. The PLA-dye complexes showed the counterlockwise (negative, S) chirality of the transition dipole moments of dyes.
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  • 25
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    Biopolymers 23 (1984), S. 1347-1365 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ionization properties of the tyrosyl groups of bovine plasma albumin in various conformational states - the native state (N), the two acid states (F and E), and the state (B) stable at slightly alkaline pH - were studied by means of a stopped-flow-pH-jump technique. The technique allows us to obtain the tyrosyl titration curve in a conformational state that is unstable in the pH region of the titration. The pH jumps from the N and B states to various alkaline pH's, where the tyrosines ionize to bring about a time-dependent increase in absorption at 296 nm, indicating that a number of the tyrosines buried initially become susceptible to ionization as a result of the alkaline transition occurring above pH 10.8. Extrapolation of the observed absorption change to zero time gives a spectrophotometric titration curve in the initial conformational state. Only 30-401% of the 19 tyrosines of the protein can ionize both in the N and the B state at pH 12. The pH jumps from the F and E states, on the other hand, give a decrease in absorption between pH 9 and 11.7, indicating that the tyrosyl groups initially exposed are remarked by refolding after the pH jumps, and the zero-time titration curves show that essentially all the tyrosyl groups ionize normally in these acid states. The results are discussed in relation to the known results of the tyrosyl exposure of the protein measured by other techniques, and the consistency among them demonstrates the effectiveness of the pH-jump titration method. Hydrogen bonding between the abnormal tyrosyl and carboxylate groups as a mechanism to stabilize native albumin is suggested from characteristics of the alkaline transition, which also involves the exposure of the tyrosyl groups, and from the tyrosyl titration curves in the native and acid states.
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  • 26
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    Biopolymers 23 (1984), S. 1137-1139 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 27
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two 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.
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  • 28
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    Biopolymers 23 (1984), S. 1457-1463 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of sonicated calf-thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix-to-coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.
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  • 29
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    Biopolymers 23 (1984), S. 1465-1479 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The oxidation of L-adrenaline (epinephrine) in the presence of [Fe(tetpy)(OH)2]+ ions bound to poly(L-glutamate) or to poly(D-glutamate) has been studied at pH 7 (tetpy = 2,2′:6′,2″:6″,2‴-tetrapyridyl). Electron transfer from the substrate to the central metal ion, which is rate-determining, proceeds stereoselectively only when extensive and possibly specific interactions between adrenaline and the peptidic residues of the ordered polymer in the close environment of the active sites occur. This ensures different steric constraints for the two diastereomeric precursor complexes, which are thought to affect the separation and orientation of the redox centers differently, leading to the observed phenomena. Some data on the catalytic oxidation of L-dopa(3,4-dihydroxyphenylalanine) are also presented, showing stereoselective effects similar to those observed with L-adrenaline, despite the diverse distance of the chiral center from the reacting OH groups. A mechanistic interpretation of the results is discussed in the light of a few general considerations concerning the structural features of the catalytic systems. Possible explanations for the finding that stereoselectivity occurs at the expense of the efficiency of catalysis are also considered.
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  • 30
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    Biopolymers 23 (1984), S. 1917-1930 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solution-phase Raman spectra of diastereomeric alanyl dipeptides, D-Ala-L-Ala and L-Ala-L-Ala, and various mono- and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled-oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.
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  • 31
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    Biopolymers 23 (1984), S. 1951-1960 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational equilibria of five β-cellobiose conformers have been studied theoretically in 10 solvents. The stability of the conformers in dilute solution has been compared by using the method that has already been tested for 2-methoxytetrahydropyran, β-maltose, and D-glucose. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from the properties of the solute calculated by the PCILO quantum-chemical method and physicochemical properties of the solvents. The calculated abundance of conformers depends on the solvent (e.g., in dioxane C1:C2:C3:C4:C5 = 60.0:34.1:2.9:2.0:1.0; in dimethylsulfoxide, 75.5:22.1:1.8:0.5:0.2; and in water, 82.2:16.2:1.3:0.2:0.1). The results obtained indicate that the preponderant conformer in the aqueous solution is similar to the one adopted by β-cellobiose in the crystalline form. The role of individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and nmr parameters have been calculated and compared with observable properties. The marked differences observed between solvent-induced conformational changes for β-cellobiose and β-maltose have been discussed from the viewpoint of the solubility of the cellulose.
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  • 32
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu-, and Asp-) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G-X 〉 C-X 〉 A-X U-X or T-X, and G · C-X 〉 A · T(U)-X, where X is one of these amino acid residues. It has been shown that Glu- and Asp- can recognize guanine in single-stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double-stranded structures.
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  • 33
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 34
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    Biopolymers 23 (1984), S. 2195-2210 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of histone H1 on the conformation and stability of control and acetylated HeLa high-molecular-weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
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  • 35
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Human fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ-γ ligation was determined from the former. The latter provided the size distribution of ligated end-to-end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p-nitrophenyl-p′-guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end-to-end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ-γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ-γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end-to-end sequences agreed with a theory based on random ligation of ligatable junctions.
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    Biopolymers 23 (1984), S. 201-212 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A 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 Σmi2, 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 ΣHi2, 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 ΣHi2 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.
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    Biopolymers 23 (1984), S. 271-285 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We 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.
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    Biopolymers 23 (1984), S. 337-351 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Brillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high-humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799-2815] with the variations of the sonic velocity with water content.
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    Biopolymers 23 (1984), S. 353-361 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optical rotation, viscosity, and density studies are reported on solutions of α-gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 41
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have recorded high-resolution 13C-nmr spectra of collagen fibrils in the solid state by the cross-polarization-magic-angle-spinning(CP-MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31-helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (Ala—Gly—Gly)nII], and the triple-helical polypeptides [(Pro—Gly—Pro)n and (Pro—Ala—Gly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31-helical (Ala—Gly—Gly)n and triple-helical (Pro—Ala—Gly)n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31-helix, reflecting further conformational change from the 31-helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C = O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1-5.1 ppm), with respect to those of the 31-helical polypeptides. These displacements are interpreted by that Gly C = O of the former is not involved in NH … O = C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
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  • 42
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    Biopolymers 23 (1984), S. 2349-2360 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dermorphin (Tyr—D-Ala—Phe—Gly—Tyr—Pro—Ser—NH2), a potent natural peptide opioid, its synthetic L-Ala2 analog, and all the N fragments from the tripeptide (Tyr—D-Ala—Phe—NH2) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N-terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.
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    Biopolymers 23 (1984), S. 2715-2724 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′-diphosphate reveals that, for each species, the uv-absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
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    Biopolymers 23 (1984), S. 2963-2966 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 24 (1985), S. vi 
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  • 46
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    Biopolymers 24 (1985), S. 49-63 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular model for the complex formed between the jack bean lectin concanavalin A (Con A) and glycopeptides of the complex biantennary class is described. The model was derived using coordinates for Con A determined by x-ray crystalographic refinement techniques, with 1.75-Å resolution data, and coordinates for the glycopeptides obtained from 1H-nmr measurements, using the nuclear Overhauser effect. Previous solution and crystallographic studies provided several constraints on the possible mode of interaction of the lectin and the glycopeptide. Examination of the model suggests that the glycopeptide binding site is defined by four loops on the protein surface made up by amino acid residues: 12-18, 98-102, 205-208, and 226-229. Within these loops, it favorable interactions with high-affinity ligands and tose responsible for the unfavourable interactions with poor ligands.
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  • 47
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Peptide hormones and neurotransmitters are functional amphiphilic substances that deploy their chared and nonpolar substituents as required for traversing aqueous phases en rout to their ultimate transfer into the lipid-rich environment of their membrane-embedded receptors. As a means of determining the role(s)that cellular membrane lipids may play in mediating these events, we describe an experimental approach, using high-resolution 1H-and 13C-nmr spectroscopy, for delineation of the structures of complexes between the (neurotransmitter pentapeptide) enkephalins and micellar and vesicular phospholipid particles. Residue-specific enkephalin interactions with lipid are identified; affinity constants for the hydrophobic component(s) of peptide/lipid association are calculated for enkephalin and several of its analogs; and comparisons with morphine are presented. Finally, based on molecular details obtained from nmr experiments, a model is proposed for the encoutner of a peptide hormone with a phospholipid membrane surface.
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    Biopolymers 23 (1984), S. 719-734 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aggregation of poly(γ-benzyl-α,L-glutamate) and its enantiomer in toluene has been investigated by following the viscosity as a function of temperature, concentration, molecular weight, molecular-weight distribution, helix chirality, and shear rate. The temperature and concentration data for a 138,000-molecular-weight sample was fitted to an open, reversible end-to-end aggregation model. The aggregation numbers resulting from this fit were consistent with the sudden onset in non-Newtonian flow resulting from only a 0.2-wt% increase in concentration. The association equilibrium constant was then used to predict viscosity for comparison with other data, in particular, the effect of molecular weight and molecular-weight distribution. A mixture of right-and left-handed helices showed the aggregation was not chiral selective. The stiffness of end-to-end aggregated (hydrogen-bonded) molecules differed little from their covalent counterparts, at least below a molecular weight of ∼106. We conclude that polybenzylglutamate aggregation in toluene can be described by an open end-to-end aggregation model.
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    Biopolymers 23 (1984), S. 797-808 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic 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.
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    Biopolymers 23 (1984) 
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    Biopolymers 24 (1985) 
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  • 52
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    Topics: Chemistry and Pharmacology
    Notes: Both (dC-dG)4 and d(CGCATGCG) crystallize in hexagonal lattices and their three-dimensional structure has been solved by x-ray diffraction analysis. Both molecules are found to form Z-DNA, although the fine details of the structure cannot be visualized due to the statistical disordering of the molecules along the c-axis, which is brought about by the symmetry constraints of the space group. This represents the first time in which the unmodified dinucleotide sequences CpAp and TpGp have been found to form Z-DNA in a crystalline lattice.
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    Biopolymers 24 (1985), S. 359-377 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Differential melting curves (DMCs) of DNAs pA03 and pBR322 in solutions of different ionic strength (0.02 and 0.2M Na+) were obtained. A previously developed procedure of glyxal fixation of partially denatured DNA molecules at temperatures within the melting range was used to construct electron-microscopic melting maps for pBR322 and pAO3 plasmid DNA and for the replicative form of bacteriophage φX174 DNA, allowing the melting of these DNA molecules to be followed in solutions of low (0.1 × SSC) and high (1 × SSC) ionic strength. In spite of the fact that the melting was at nonequilibrium at the low ionic strength, the melting maps for the two kinds of solutions practically coincided. Experimental data are compared with theoretical calculations based on the Fixman-Freire algorithm. The conclusion is that the melting pattern of these DNAs is, on the whole, correctly described by the theory, although there are appreciable differences between the theoretical and experimental differential melting curves. We have also determined the relation between the melting temperature of a region and its GC content, with allowances made for the boundary conditions of melting in 0.1 × SSC and 1 × SSC solutions, and have analyzed the theoretical shape of peaks of the DMCs.
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    Biopolymers 24 (1985), S. 421-423 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 24 (1985) 
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    Biopolymers 24 (1985), S. 427-439 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Electrostatic effects are believed to determine the molecular structure and function of macromolecules in many ways. In metallo-based enzymes and in metal-macromolecule interactions in solution, these effects may predominate. In order to tackle metal ion-nucleic acid interactions theoretically, we propose a modification of Debye's distance-dependent dielectric function first proposed more than 50 years ago. This function more closely approximates physical reality at small interatomic separations. Our theory yields a dielectric function that gives reasonable agreement with experimental data in preliminary calculations.
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    Topics: Chemistry and Pharmacology
    Notes: It is suggested that the three-dimensional structure of globular proteins is partly determined by a framework of strengthened hydrogen bonds that involves both ionic side chains and water molecules in addition to the polypeptide backbone. This conclusion follows from a combination of the results of ab initio molecular-orbital computations on small model molecules and high-accuracy x-ray data on the rubredoxin molecule. The computations yield the idea of hydrogen-bonded bridges that are built from tens of atoms, and the experimental information yields the idea that the bridges are assembled into clusters, each of which is built from hundreds of atoms. Some 10 such clusters then form a globular protein.
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    Biopolymers 24 (1985), S. 581-581 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 59
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    Biopolymers 24 (1985), S. 581-581 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 60
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    Biopolymers 24 (1985), S. 157-166 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monoclonal antibodies to different parts of bacteriorhodopsin were raised to define its topography in the membrane. It is shown that the amino acid residue Glu 194 is a part of an antigenic determinant and should be located on the membrane surface. We found that the removal of the C-terminal 17 amino acid sequence does not affect the efficiency of the proton transport in bacteriorhodopsin. From a combination of proteolysis and secondary structure prediction methods an experimentally testable structural model for bovine rhodopsin is presented. The complete amino acid sequence of the transducin γ-subunit consisting of 69 residues was determined.
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  • 61
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    Biopolymers 24 (1985), S. 403-419 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fluorescence and absorbance methods were used to study the interaction of daunomycin with calf-thymus DNA over a wide range of temperatures and NaCl concentrations. van't Hoff analysis provided estimates for the enthalpy of the binding reaction over the NaCl range of 0.05-1.0 M. Daunomycin binding is exothermic over this entire range, and the favorable binding free energy arises primarily from the large, negative enthalpy. Both the enthalpy change and entropy change are strong functions of ionic strength. Possible molecular contributions to the enthalpy and entropy are discussed, leading to the tentative conclusion that hydrogen-bonding interactions at the interacalation site are the primary contributors to the observed thermodynamic parameters. The dependence of the enthalpy on the ionic strength is well beyond the predictions of current polyelectrolyte theory and cannot be fully accounted for. The enthalpy and entropy changes observed compensate one another to produce relatively small free-energy changes over the range of solution conditions studied.
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  • 62
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    Topics: Chemistry and Pharmacology
    Notes: Mechanical creep and creep recovery in small shearing deformations have been studied in unligated clots formed with both thrombin and ancrod. In thrombin clots, both A binding sites (which interact with “a” sites to link monomer units within a protofibril) and B sites (which interact with “b” sites to form links between protofibrils) are exposed to enable formation of linkages; in ancrod clots, only the A sites are exposed. Fine clots (with minimal lateral aggregation of protofibrils), coarse clots (with substantial aggregation of fibril bundles), and clots of intermediate coarseness were compared. Fine thrombin clots showed less creep at short times but more creep at long times than coarse or intermediate clots and had more irrecoverable deformation relative to the initial elastic deformation. Ancrod clots had greater irrecoverable deformation than the corresponding thrombin clots, both fine and coarse. The permanent deformation in fine ancrod clots was enormous, corresponding almost to fluid character; the rate of permanent deformation was larger than that in fine thrombin clots by more than two orders of magnitude. For all types of clots, differential measurements of compliance (or its reciprocal, elastic modulus), as well as the applicability of the Boltzmann superposition principle to calculation of creep recovery, showed that the overall density of structure remained constant throughout the mechanical history; i.e., if structural elements were breaking, they were reforming at the same rate in different configurations. The possibility that the weakness of ancrod clots is attributable to partial degradation of α-chains rather than absence of Bb linkages was eliminated by comparisons of clots made with thrombin, ancrod, and ancrod plus thrombin; the last two showed identical partial degradation of α-chains (by gel electrophoresis), but the first and third had essentially identical initial elastic moduli and creep behavior. Two alternative mechanisms for irrecoverable deformation in fine clots are discussed, involving rupture of protofibrils and slippage of twisted segments, respectively.
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  • 63
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    Biopolymers 24 (1985), S. 735-745 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, it was suggested that parallel β-sheets have a significant dipole moment, in contrast to antiparallel sheets. Ab initio molecular-orbital (MO) calculations on parallel and antiparallel β-strands of tetra(Gly) show that they have very similar charge distributions. Interaction energies between two and three strands of tetra(Gly), obtained using the direct reaction field Hamiltonian, show that a particular choice of point charges is probably not crucial for calculating interactions within β-sheets, but that it might be for calculating interactions between these sheets and other parts of a protein, in particular, α-helices. The point-charge representation of our MO-SCF results will probably reduce the hazard of introducing artefacts in electrostatic calculations of protein conformational energies, provided the short-range interactions are treated in a more realistic way, i.e., such that intra- and interchain induction effects are included.
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  • 64
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    Topics: Chemistry and Pharmacology
    Notes: The pH and ionic strength dependence of conformation of the COOH-terminal fragment 206-316 (fragment FII) of thermolysin was monitored by far-uv CD and difference absorption measurements. This fragment was shown previously to possess the properties of a protein domain, i.e., able to refold into a stable nativelike structure [Fontana, A., Vita, C. & Chaiken, I. M. (1983) Biopolymers 22, 69-78]. Analysis of the CD spectra in the pH range of 1-12 indicated that near pH 1, the conformation of fragment FII appears to be in an intermediate state (H) between the fully unfolded one (U) [the guanidine hydrochloride (Gdn · HCl)-induced unfolded state] and the nativelike state (N - that attained at neutral pH). Quantitative analysis of secondary structure from CD spectra revealed that state H at 4°C is characterized by some 30% α-helical structure, compared to 47% for state N. The heat- and Gdn · HCl-mediated unfolding transitions of state H were fully reversible and characterized by little cooperativity, which is taken as an indication that state H corresponds to several species possessing different, and low, conformational stabilities. The midpoint transition from state H to N occurs near pH 2.5, implying that the acid transition results from the titration of carboxyl groups of the fragment with anomalously low pK, as would be expected for groups involved in specific salt bridges. Fragment FII at pH 1 (state H) may be induced to exhibit nearly the same degree of helicity of state N simply by increasing the ionic strength of the solution, thus reducing the repulsive interactions between positive charges within the highly charged fragment at pH 1. The results obtained emphasize the role of electrostatic interactions in the folding and stability of fragment FII and suggest a mechanism of folding of the fragment from U to N involving an intermediate state characterized by an assembly of fluctuating α-helices.
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  • 65
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    Biopolymers 24 (1985), S. 867-882 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA supercoiling is both an interesting problem from the theoretical point of view and an important phenomenon affecting DNA functions in vivo. Experimentally, however, hardly more than the overall hydrodynamic shape, superhelical density, and enzymic or chemical reactivity of the parameters that are in some way related to DNA secondary and tertiary structure in the superhelical state can be determined. Consequently, it is highly desirable to build up models of DNA supercoiling that, on the one hand, match the above type of global data and, on the other, take advantage of the knowledge about DNA structure at lower levels of complexity, i.e., with linear DNA molecules and its synthetic models. One possible approach, presented here, deals with an extension of Fuller's and Benham's general ideas concerning an elastomechanical model of DNA supercoiling. We extend their model with an algorithm suitable for numerical calculations and construct a fast computer program, ROPASE, that displays the rod shapes as dependent on its elastic properties and applied stress. Development of this program made inevitable a detailed analysis of the input parameters found to be degenerate in the sense that not all of them should be considered variable to generate the whole set of possible solutions of the model. Many calculations were performed using ROPASE to test its properties and the properties of the elastomechanical model. Representative DNA shapes are presented.
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    Biopolymers 24 (1985), S. 905-910 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 24 (1985), S. 883-895 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermotropic behavior of lipid vesicles prepared from dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase has been studied by highly sensitive differential scanning microcalorimetry. This protein has a remarkable effect on the gel-liquid crystalline transition of dimyristoylphosphatidylcholine. In the presence of cytochrome c oxidase, the thermogram of the lipid vesicles exhibits a second endothermic peak, which is adjacent to the main lipid phase-transition peak and appears at a higher temperature. As the concentration of added protein increases, the two endothermic peaks become further separated, and the transition temperatures and the heats of transition corresponding to both endothermic peaks decrease. A greater decrease in the transition temperature at the lower-temperature peak with added protein suggests that the lower-temperature peak is more perturbed than the higher-temperature peak. The higher-temperature peak is not thermally reversible. Treatment of sample well above the transition temperature results in a reduction of the magnitude of the higher-temperature peak. The lipid-protein interaction contributing to the higher-temperature peak is discussed.
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  • 68
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    Topics: Chemistry and Pharmacology
    Notes: An intercalation model of a complex between DNA and a bleomycin fragment (BLMF), consisting of the bithiazole core and an amide and a protonated amino substituent, is presented. The model, which shows a preference for BLMF with the protonated amine in the minor groove and the acetyl terminal inserted into either the minor and major grooves, respectively, agrees with recently obtained nmr data. The selection of sites I and II, which have the smallest unwinding of the three theoretical intercalation sites, is consistent with the experimental unwinding angle of 12°. The bithiazole moiety stacks between two base pairs of the double helix, while the protonated substituent interacts ionically with the negatively charged regions of the backbone in the minor groove of the DNA. The protonated amine also forms an intramolecular hydrogen bond with the carbonyl oxygen of the amide group on the same substituent. Analysis of drug complexes with different base-pair sequences reveal four energetically defined groups. The relative energy of the dimer duplex complexes of BLMF correlates with bleomycin's observed base-sequence specificity upon cleavage. The most stable intercalation complexes form adjacent to the bases cleaved most readily. This correlation suggests a primary connection between intercalation and cleavage. A model cleavage site based on these preliminary theoretical calculations and the experimental observations is proposed. It consists of an intercalation site in a trimer duplex. Pyrimidine(p)purine sequences are the predominant sites for intercalation, and the base adjacent to the site at the (3′) end is cleaved.
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  • 69
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    Topics: Chemistry and Pharmacology
    Notes: Boc-L-Leu-Aib-Pro-Val-Aib-Aib-Glu(OBzl)-Gln-Phl (Boc = t-butyloxycarbonyl, Aib = α-aminoisobutyric acid, Bzl = benzyl, Phl = phenylalaninol), C59H90N10O14, the protected C-terminal nonapeptide with the sequence 12-20 of alamethicin, crystallizes in the orthorhombic space group P212121 with a = 15.666, b = 16.192, c = 26.876 Å, and Z = 4. The molecular conformation is right-handed helical with three α-(5 → 1 hydrogen bonds) and three β-turns (4 → 1 hydrogen bonds). All but two of the hydrogen bonds are significantly longer than the usual value and show bifurcation to some extent. The α/310r-helical nonapeptide molecules are arranged head-to-tail along the a direction. The resulting linear antiparallel chains are linked by a weak intermolecular hydrogen bridge, thus forming a two-dimensional layer structure in the ab plane. The conformation of this nonapeptide is almost identical with that of the corresponding C-terminal part found by x-ray crystallography of the eicosapeptide alamethicin.
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    Topics: Chemistry and Pharmacology
    Notes: A newly designed host-guest approach is introduced as a experimental tool to explore the relationship between the sequence of peptides and their secondary structure. From the CD spectra of the host-guest peptides studied, a tentative scale for the α-helix potential in 2,2,2-trifluorethanol of guest amino acids is delineated. The conformational preferences are also examined in β-structure supporting media (solid state, CH2Cl2, CH3OH, H2O) using ir-absorption and CD techniques. Scales for the β-forming tendency of guest amino acid residues in the different media are delineated. It is shown that the preferred conformation of the host-guest peptides is a function of the medium, the chain length, and the protecting groups. Given the fact that conformational effects are important in peptide synthesis, the tentative scales may serve as a guideline to predict secondary structures of side-chain-protected or -deprotected peptides in a given solvent, complementing the well-known empirical conformational prediction parameters.
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    Biopolymers 24 (1985), S. 1107-1111 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 24 (1985) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 73
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    Topics: Chemistry and Pharmacology
    Notes: The interaction of CuCl2 with poly(S-carboxymethyl-L-cysteine) (poly[Cys(CH2COOH)]) and poly(S-carboxyethyl-L-cysteine) (poly[Cys(C2H4COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl2 with polypeptide solutions, absorption bands appeared at 320-325 nm in both polypeptides, and at 255-260 nm in the case of poly[Cys(CH2COOH)]. A stable bound species was formed in the case of poly[Cys(CH2COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu2+ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH2COOH)] + CuCl2 gave simpler aspects than those of poly[Cys(C2H4COOH)] + CuCl2.
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  • 74
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    Topics: Chemistry and Pharmacology
    Notes: The atomic motions from a molecular-dynamics simulation of yeast tRNAPhe are analyzed and compared with those observed in protein simulations. In general, the tRNA motions are of larger amplitude, they are more anisotropic, and they arise from potentials of mean force that are more anharmonic than in the protein case. In both cases, the amplitudes are largest for atoms on the surface of the molecules. On the other hand, the most anisotropic and anharmonic atomic motions are generally found in the interior of the tRNA, while they are found on the surface of the protein. These differences are discussed in terms of the differences in structure between nucleic acids and proteins.
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    Biopolymers 24 (1985) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 24 (1985), S. 947-960 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The purpose of this work was to improve our understanding of quasielastic light scattering from long rigid rods (QL 〉〉 1). For these scatterers, only small angular displacements are required to produce dephasing of the scattering light. This plus the fact that only rods lying perpendicular to Q contribute to the scattered light allow one to simplify the intermediate scattering function to an analytic form. This form is shown to be nonexponential, exhibiting (t)-½ behavior at long delay times. This new scattering function can then be fit to experimental functions using standard methods.
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    Biopolymers 24 (1985), S. 1001-1008 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report high-resolution Raman spectra obtained from the circularly closed double stranded DNA (Form I) of the plasmid pBR322 and from its corresponding linear form (Form III). Comparison of the Raman spectra of the two forms demonstrates that, at a superhelical density (σ) of -0.069, which is of the same order as those found for most naturally occurring circularly closed DNAs, no major structural transitions occur under the influence of supercoiling. It is shown that at least 98% of all bases are fully basepaired, and that the conformation of the sugar-phosphate backbone is essentially identical to that of linear DNA. Thus, the structural influence of supercoiling, under these conditions, is confined to minor stretches of the plasmid DNA.
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    Biopolymers 24 (1985), S. 1075-1087 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The force field established for guanine is applied here to guanine-containing biopolymers by considering the model compound 9-methylguanine, in which the methyl group is taken as a dynamic unit whose mass is concentrated on the carbon. In-plane normal-mode frequencies for this model compound and its N-deuterated analog are calculated. Band frequencies observed for guanine residue in Raman biopolymer spectra, such as those for DNA, RNA, or poly(G), are associated with calculated modes having similar wavelengths. They are discussed by taking into account observed and calculated D, 15N, and 18O isotopic shifts. The atomic displacements for the normal modes corresponding to the principal bands are illustrated and a number of assignments proposed.
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    Biopolymers 24 (1985), S. 935-945 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparative study has been made using molecular mechanics of the ring entity of the active enkephalin analogs, Tyr-cyclo(-Nω-D-XXX-Gly-Phe-Leu-), where XXX is variously A2pr, A2bu, and Orn. Several conformations are favored for all three, and the lower-energy models are compatible with a Gly3-Phe4 bend in the active form of enkephalin. Some difficulties in assuming standard geometries in conformational surveys are illustrated.
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    Biopolymers 24 (1985), S. 961-978 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The x-ray structure of Boc-L-Ala-Aib-Ala-Aib-Ala-Glu(OBzl)-Ala-Aib-Ala-Aib-Ala-OMe(I) represents the first α-helix determined by direct methods. This undecapeptide is a model of the N-terminus of alamethicin, and it exhibits voltage-dependent pores in bilayer membranes at a higher voltage and concentration than alamethicin. The molecule crystallizes in the monoclinic space group P21 with a = 10.602(1), b = 23.884(3), c = 13.622(1) Å, β = 95.61(6)°, and Z = 2. It adopts a right-handed α-helical conformation in the solid state with intramolecular 5 → 1 hydrogen bonds. An additional intramolecular hydrogen bond is bifurcated, forming a stronger 4 → 1 interaction (i.e., a β-turn III) and a weaker 5 → 1 interaction, thus prolonging the α-helical part up to 9 residues. The α-helix radius of 2.1 Å, the height per residue (distance Ni … Ni + 4) of 1.53 Å, the resulting length of the α-helical part of 13.8 Å (9 residues) resp. 15.3 Å (10 residues), the van der Waals radius (4.7 Å), and the minimal diameter of pores formed by aggregation of 3-10 α-helices were calculated omitting the Glu(OBzl) side chain. In the crystal, the α-helices are linked head to tail via two hydrogen bridges forming continuous chains. Adjacent helices are oriented in antiparallel with their helix axes and have only van der Waals contacts.
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    Biopolymers 24 (1985), S. 1009-1022 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Time-resolved fluorescence polarization anisotropy measurements were performed on two fractionated samples of duplex poly(dGdC) containing 230 (+40, -30) base pairs (bp) and 590 ± 40 bp. Deconvolution using the intermediate zone formula for the twisting correlation functions (which is not valid for such short DNAs) yields apparent torsion constants for these two samples that are disparate and, in any case, too low. By similarly deconvoluting simulated data constructed from the correct twisting correlation functions, it can be inferred that these two samples actually exhibit the same torsion constant, α = (4.0 ± 0.4) × 10-12 dyn cm. Within the experimental uncertainties, this value is the same as that reported previously from this laboratory for linear φ29 and linearized M13mp7 DNAs. The 590-bp sample exhibited a peculiar evolution of its apparent torsional rigidity from a very high initial value, \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \alpha $\end{document} = (11 ± 1) × 10-12 dyn cm, to a normal value over a period of several months, during which time many very small fragments appeared to be dissociated from, or annealed out, of the predominant high-molecular-weight species. Possible interpretations of these observations are discussed.
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  • 82
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    Topics: Chemistry and Pharmacology
    Notes: The conformation and internal dynamics of supercoiled pUC 8 DNA (2717 bp) are examined by dynamic light scattering, and the magnitude and uniformity of its torsional rigidity are determined using time-resolved fluorescence polarization anisotropy of intercalated ethidium dye. Neither measurement gives any indication of an appreciably reduced bending or twisting rigidity, or anomalously rapid internal motions. For 31P, in supercoiled pUC 8, we measure T2 = (2.0 ± 0.5) × 10-3 s. This lies within the range of present theoretical estimates obtained using normal rigidities. The proton linewidths observed for pUC 8 and pBR322 (4363 bp) DNAs are within a factor of 2-3 of those similarly estimated assuming ordinary rigidities.According to Bendel, Laub and James [(1982) J. Am. Chem. Soc. 104, 6748-6754], supercoiled pIns36 DNA (7200 bp) exhibits an astonishingly long T2 = 1.17 s for 31P, a slowest rotational relaxation time, τ = 5 × 10-9 s, and an enormously reduced bending rigidity. Serious questions raised by these findings are examined here. The 5 × 10-9 s slowest rotational relaxation time is shown to be physically inadmissible.The nmr relaxation theory developed previously by Allison, Shibata, Wilcoxon, and Schurr [(1982) Biopolymers 21, 729-762], is modified to incorporate new results for deformable filaments, which directly introduce the highly nonexponential tumbling correlation function for reorientation of the local helix axis. Essential requirements for a complete calculation of R2, including estimation of the tumbling correlation function and evaluation of the still unknown DIP/CSA cross-term, are described in detail. Slow coil-deformation modes analogous to the Rouse-Zimm modes of linear DNAs are shown to make an important, if not dominant, contribution to the R2 relaxation rate. Geometrical parameters in the theory are chosen to provide good agreement with literature data for 600-bp linear DNA. Using this theory and an informed guess for the tumbling correlation function, we find that the 31P-nmr relaxation data of Bendel et al., if correct, necessarily impose on their DNA one or more extreme properties, such as enormously reduced bending or twisting rigidities. In contrast, the same theory yields reasonable agreement with the T2 reported here for 31P in supercoiled pUC 8 DNA when its rigidities are assumed to be quite ordinary.
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  • 83
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    Biopolymers 24 (1985), S. 1131-1146 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aggregation behavior of the chemotactic peptide analogs, Formyl-Met-Leu-Phe-OMe (1) and Formyl-Met-Aib-Phe-OMe (2), has been studied in chloroform and dimethylsulfoxide over the concentration range of 0.2-110 mM by 1H-nmr spectroscopy. Both peptides associate in CDCl3 at concentrations ≥ 2 mM, while there is no evidence for aggregation in (CD3)2SO. Analog 1 adopts an extended conformation in both solvents favoring association to form β-sheet structures. A folded, γ-turn conformation involving a 3 → 1 hydrogen bond between Met CO and Phe NH is supported by 1H-, 13C-nmr, and ir studies of analog 2. The influence of backbone conformation on the ease of peptide aggregation is demonstrated by ir studies in CHCl3 and CD studies in dioxane.
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  • 84
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    Biopolymers 24 (1985), S. 1169-1188 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A 24-ps molecular-dynamics simulation of motions in yeast tRNAPhe has been completed. The overall structure of the molecule is well preserved, for the motions represent fluctuations about an average structure that is very much like the crystallographic structure. The four helical stems remain intact, the structures of the loop regions do not deteriorate, and even the base stacking in the single-stranded amino acid acceptor terminus is maintained. With two exceptions, none of the sugar puckers is significantly changed. The unconstrained floppy motions of base A76 are responsible for the repuckering of ribose 76. The other sugar that repuckers is ribose, 46, and this is the result of a very small structural change in the center of the molecule that is also responsible for the breakage of one tertiary hydrogen bond. This change in local structure does not seriously distort the base-stacking and intercalation patterns where the variable loop and the D-stem interact.
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  • 85
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    Biopolymers 24 (1985), S. 1233-1246 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The persistence length and effective long-range bending rigidity are derived for a discrete model of an anisotropically bending filament and shown to be independent of the torsional rigidity. The twisting persistence length is found to be independent of the anisotropic bending rigidity. Other statistical properties are briefly discussed, including the dependence of tangent vector projections on contour length. The dependence of a tensor contraction on contour length is derived for an isotropically bending filament with no equilibrium twist.
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  • 86
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    Biopolymers 24 (1985), S. 1257-1263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational CD (VCD) and ir absorption data are reported for a series of films of Boc-(L-Ala)n-OMe homo-oligopeptides (n = 3-7) in the amide I and A regions. The data evidenced a sharp change between n = 3 and n = 4, which parallels the onset of β-structure formation, and another between n = 5 and n = 6, which parallels the full development of β-structure. This represents the first report of the application of VCD to oligopeptide conformation. The data resembled earlier reported film VCD studies of higher-molecular-weight polypeptides of known β-structure.
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  • 87
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    Biopolymers 24 (1985), S. 1271-1291 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy calculations have been carried out in order to determine favorable packing arrangements within a group of α-helices. The influence of side chains and of the number of interacting α-helices on the mode of packing was analyzed. In this work, our earlier methods for computing the packing energy of a pair of α-helices [Chou, K.-C., Némethy, G. & Scheraga, H. A. (1984) J. Am. Chem. Soc. 106, 3161-3170] have been extended to treat the interactions among several helices. Also, new algorithms allow the matching of standard peptide geometry to x-ray coordinates of helical complexes and the analysis of interrelations between several helices. As a specific test case, the packing of three neighboring α-helices, viz., the A, G, and H helices of sperm whale myoglobin, was considered. Minimum-energy arrangements were computed for the separate A-H and the G-H α-helix pairs as well as for the A-G-H three-helix complex. For the packing of the nearly antiparallel G and H α-helices, the same optimal structure was obtained in two- and three-helix complexes, indicating that a single packing arrangement is specifically favored by interhelix interactions. For the pair of nearly perpendicular A and H α-helices, interactions are less specific, so that there is no unique optimal structure in the two-helix complex; in the three-helix complex, however, a specific mode of packing is favored even for the A-H pair. This result indicates that the presence of other nearby α-helices can influence the packing of a given α-helix pair. The computed arrangement of the A-G-H complex is very close to that of the crystallographically determined structure. These results can be used to make deductions about the likely sequence of events in protein folding, where, in this particular case, it appears that the G-H helix pair may form first and then induce proper orientation of the A helix.
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  • 88
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quantum-mechanical equations are derived that are particularly well suited to actual computations of the CD for helical polymers. They make use of cyclic boundary conditions and helical symmetry, so that only two matrices with a size equal to the number of transitions considered need be diagonalized. The final equations are expressed directly in terms of monomer properties and helical parameters to invite the same input as earlier calculations, and are given as a rotational strength times a shape function for ease of comparison with the earlier work. The shape of the helix term is expressed as a derivative with respect to ω and depends on the distance between monomers along the helix axis. Other terms involving two electric transition dipoles depend on the distance from the helix axis to the transition center. These equations are directly comparable to the classical equations derived for cyclic boundary conditions and helical symmetry. We present an outline of the derivation and enough intermediate steps to clarify how the equations arise.
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  • 89
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    Biopolymers 24 (1985), S. 1385-1385 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 90
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    Biopolymers 24 (1985), S. 1479-1491 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Raman and ir spectra of α-helical poly(L-glutamic acid) have been assigned on the basis of a normal mode calculation for this structure. The force field was based on our previously refined main-chain force constants for α-poly(L-alanine) and side-chain force constants for β-calcium-poly(L-glutamate). Despite the identical backbone α-helical structures, significantly different frequencies are calculated, and observed, in the amide III and backbone stretch regions of α-poly(L-glutamic acid), as compared with α-poly(L-alanine). This clearly demonstrates the influence of side-chain structure on mainchain vibrational modes.
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  • 91
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    Biopolymers 24 (1985), S. 1501-1514 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quasielastic light scattering method was used to study the ionic strength dependence of the mutual diffusion coefficient of sodium polystyrene sulfonate (NaPSS) as a function of NaCl and CaCl2 concentrations. The results indicate a splitting in the relaxation times that depends on the ratio Cp/Cs, where Cp and Cs are the polyion and added salt concentrations. A universal relationship taking into account Manning's theory of condensation and the Debye screening due to the added salt is proposed to characterize the fast-slow relaxation time transition.
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  • 92
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 93
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    Biopolymers 24 (1985), S. 1573-1593 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A theory of the electrophoresis of DNA through gels with large interfiber spacing, such as dilute agarose, is presented. We assume that the DNA molecule moves along its axis through a “tube” in a neutral gel under the influence of the electric field. The tube is random except for possible bias due to the effects of the field. When the field is small, we easily recover the inverse-length dependence of the mobility found previously by de Gennes and by Doi and Edwards. At higher fields, a new effect appears; the tube becomes oriented because the field biases the direction of the leading end of the chain as it moves to form an extension of the tube. This leads to an increase of the mobility with increasing field by adding a field-dependent but length-independent term to the mobility expression. In agreement with experiment, we find that the field effect can be important at fields as low as 1 V/cm and that the effect can seriously decrease the sensitivity of the mobility to chain length. We also examine the fluctuation of the migration distance, the degree of orientation induced by the field, and the transient effects occurring when the feld direction is rotated by a right angle.
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  • 94
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    Biopolymers 24 (1985) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 95
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The confortmational behavior of the cholecystokinin-related fragments CCK4, CCK5, and CCK6 as determined by 1H-nmr spectroscopy in DMSO-d6 and water and fluorescence-transfer measurements in aqueous medium are greatly dependent on the ionization states of these peptides. Under netral conditions, the backbones of CCK5 and CCK6 preferentially adopted folded forms with a β-turn including the four residues Gly-Trp-Met-Asp, probably stabilized by a hydrogen bond between the CO of Gly and the NH of Phe. In these structures, possible induced by an ionic interaction between the carboxylic group of Asp32 and the NH3+ group of the N-terminal amino acid, the lateral chains of the various residues are quite distant from each other (15-16 Å). Under acidic conditions, extended structures without interactions between side chains predominate for CCK5 and CCK6, while for CCK4, a conformational change drawing the Trp and Phe side chains in close proximity was shown by fluorescence. The conformations observed in aqueous medium at physiological pH are discussed in relation to the biological activity of these peptides.
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  • 96
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    Biopolymers 24 (1985), S. 1647-1662 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thermally induced helix-coil transitions of myosin rod, light meromyosin, and tropomyosin were studied by optical rotatory dispersion (ORD). Fractional helicity was calculated from both the Moffitt-Yang parameter, b0, and the corrected mean residue rotation [m′] at 231.4 nm. Between 3 and 30°C, [m′] increases linearly with a slope of 59/°C, whereas b0 is virtually constant, indicating apparently different thermal melting behavior. Poly(L-lysine) and poly(L-glutamic acid) in their helical forms and myoglobin also show a nearly linear temperature dependence of [m′]231.4. Muscle proteins in 6M guanidine hydrochloride and the random-coil forms of the homopolymers exhibit temperature-dependent values of [m′]231.4 and b0. We conclude from these observations that ORD properties of both α-helices and random-coil polypeptides have significant intrinsic temperature dependencies. A new method of estimating fractional helicity as a function of temperature is proposed.
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  • 97
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 98
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    Biopolymers 24 (1985), S. 2035-2040 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 99
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of phenylacetyl-D-alanyl-D-alanine in the crystalline state was characterized by Fourier-transform ir and Raman spectroscopy and was unambiguously solved by x-ray single-crystal determination. In the crystalline state, the molecule adopts a partially folded conformation quite similar to that of another cell wall peptide, acetyl-D-alanyl-D-alanine [Benedetti et al. (1981) J. Biol. Chem. 256, 9229-9234], although the crystal structure is stabilized by a quite different intermolecular hydrogen-bond pattern. No significant deviation from the usual trans-planar peptide group geometry was detected. The conformations accessible in the noncrystalline state were investigated by ir measurements in solution and conformational energy calculations. The theoretical study revealed that the peptide is a highly flexible molecule, since 55 minima were detected, within 3 kcal/mol, including the conformation found in the single crystal. The ir data for phenylacetyl-D-alanyl-D-alanine in different solvents were in accordance with virtually extended conformations, with some indication for weak, intramolecularly hydrogen-bonded C5-rings. These conformational data obtained for the cell wall peptide analog are compared with those known for penicillin G in the crystalline state.
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  • 100
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    Biopolymers 24 (1985), S. 1863-1879 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular mechanical calculations were done on complexes of ethidium cation with various base-paired deoxydinucleoside monophosphates [(ApT)2, (TpA)2, (A2 · T2), (GpC)2, (CpG)2, and (G2 · C2)] and deoxyhexanucleoside pentaphosphates [(ATATAT)2, (TATATA)2, (A6 · T6), (GCGCGC)2, (CGCGCG)2, and G6 · C6]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all-atom force field) gave results in good agreement with previous calculations and experimental work. Less-sophisticated models did not perform as well.
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