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  • Polymer and Materials Science  (94,637)
  • 1
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 307-321 
    ISSN: 0006-3525
    Keywords: morphology ; crystal structure ; recombinant silk-like molecule ; silk I ; wide angle x-ray scattering ; electron diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Morphology and crystal structure of a recombinant silk-like molecule, SLP4, were studied. Wide angle x-ray scattering (WAXS) and electron diffraction revealed that SLP4 lyophilized powder and thin films were isomorphic with the silk I crystal structure. Transmission electron microscopy of SLP4 thin films demonstrated a morphology of flat, variable width, crystallites that may aggregate in an epitaxial manner. Theoretical diffraction patterns from silk I crystal structure models were critically compared with SLP4 WAXS data. The analysis concluded that while the crankshaft model is capable of describing details of the SLP4 structural data well, the out-of-register model does not explain the experimental results. In particular, the predicted intensities of the crystallographic reflections for the out-of-register model are inconsistent with the SLP4 WAXS data. © 1998 John Wiley & Sons, Inc. Biopoly 45: 307-321, 1998
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  • 2
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
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  • 3
    ISSN: 0006-3525
    Keywords: pea starch ; Pisum sativum ; granular structure ; gelatinization ; C-type starch ; birefringence ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have used a combination of techniques to study the structure and properties of C-type starch from pea seeds. It was found that all C-type starch granules contain both types of polymorph; the B polymorphs are in the center of the granule and are surrounded by the A polymorphs. During heating in excess salt solution the A and B polymorphs within C-type granules melt independently, giving a double transition in heat capacity and a two-step swelling, compared with single transitions for A- and B-type starches. It was shown that B polymorphs gave a transition with a lower peak temperature than A. The disruption of crystallinity during gelatinization began from the hilum area and was propagated along the granule, accompanied by swelling of disrupted areas. It is proposed that the swelling of disrupted parts of the granule decreases the melting temperature of the neighboring crystallites resulting in the progressive disruption of crystalline areas. The gelatinization process is dependent on the arrangement of A and B polymorphs within the granule. © 1998 John Wiley & Sons, Inc. Biopoly 45: 323-332, 1998
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  • 4
    ISSN: 0006-3525
    Keywords: structure of GlyGly peptide ; crystalline state ; x-ray diffraction ; solid state 13C-nmr ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new type of crystal of glycylglycine (GlyGly) hydrate was crystallized from an aqueous solution, and the structure of the crystal has been determined by x-ray diffraction. The crystal is monoclinic, and the space group is C2/c, with the cell constants of a = 15.941(2) Å, b = 4.774(2) Å, c = 19.428(2) Å and β = 109.884(7)° at 296 K. There are eight GlyGly molecules and six water solvent in the cell. The GlyGly molecules are packed in a parallel β-sheet arrangement. The single crystal was obtained with a maximum size of 10 × 7 × 4 mm and is not stable under atmospheric conditions. The transparent crystal turned to turbid with the elapse of time. The isotropic 13C chemical shifts obtained from the 13C cross polarization magic angle spinning nmr experiments reveal that GlyGly hydrate was changed into GlyGly (form α) by dehydration. © 1998 John Wiley & Sons, Inc. Biopoly 45: 333-339, 1998
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  • 5
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 341-346 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 6
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 347-350 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 7
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 351-353 
    ISSN: 0006-3525
    Keywords: free energy of hydrolysis ; glycyl peptides ; hydrolysis ; peptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For every n amino acids linked in a protein there are n - 1 peptide bonds. The free energy of peptide bond hydrolysis and formation in aqueous solution defines the equilibrium position between peptide and amino acid hydrolysis products. Yet few experimental values exist. With a minimum of assumptions, this paper deduces the free energies of hydrolysis of a variety of peptide bonds. Formation of a dipeptide from two amino acids is about eight times more difficult than subsequent condensations of an amino acid to a dipeptide or longer chain. Condensation of an amino acid to a peptide of any size is five times more difficult than joining two smaller peptides of at least dipeptide size. Thus in an abiogenesis scenario there is a kind of nucleation in peptide bond formation with the initial condensation of two amino acids to yield a dipeptide more difficult than subsequent condensations to a growing chain. © 1998 John Wiley & Sons, Inc. Biopoly 45: 351-353, 1998
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  • 8
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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  • 9
    ISSN: 0006-3525
    Keywords: fractal measures ; high-performance capillary electrophoresis ; ion-exchange high-performance liquid chromatography ; high-performance liquid chromatography ; oligodeoxyribonucleotides ; oligoribonucleotides ; oligonucleotides ; polymerization processes ; chemical synthesis ; dynamics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we put forward improved mathematical methods for detecting synthesis parameters in connection with analyzing crude products of chemically synthesized oligonucleotides. The crude products experimentally sampled are separated by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography. The measured separation profiles of experimental syntheses can be expressed as target and nontarget yields; they are characterized by a few parameters. These parameters account for nonlinear synthesis equations that are solvable by employing iteration procedures. We provide here a theoretical as well as computational analysis based upon specific models for stepwise chain growth.Under nonconstant (nonuniform) conditions we use here an exponential form of growth, with different expressions for calculating the fractal dimension of the biochemical process under study. Step lengths of parameter variations in an interval of finite length have to be adjusted properly to find convergent solutions in a mathematical, regularly four-dimensional parameter space. It is conceivable to have most, if not all, of the calculating and plotting carefully done by a computer.This analysis represents the experimental situation up to 65-mer target oligonucleotides analyzed so far. We thus obtain the dynamics of the polymerization process limited in number by fractal models. The advantage, calculating these new methods as compared to qualitatively judged experimental methods, lies in the satisfactory evaluation of crude products, also of large amounts, of syntheses of these biopolymers. © 1998 John Wiley & Sons, Inc. Biopoly 45: 361-379, 1998
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  • 10
    ISSN: 0006-3525
    Keywords: protein folding ; proteins ; Type VI turn ; cis proline ; nmr ; ring current shifts ; equilibrium constants ; Van't Hoff enthalpy ; isomerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the native state of proteins there is a marked tendency for an aromatic amino acid to precede a cis proline. There are also significant differences between the three aromatic amino acids with Tyr exhibiting a noticeably higher propensity than Phe or Trp to precede a cis proline residue. In order to study the role that local interactions play in these conformation preferences, a set of tetrapeptides of the general sequence acetyl-Gly-X-Pro-Gly-carboxamide (GXPG), where X = Tyr, Phe, Trp, Ala, or cyclohexyl alanine, were synthesized and studied by nmr. Analysis of the nmr data shows that none of the peptides adopt a specific backbone structure. Ring current shifts, the equilibrium constants, the Van't Hoff enthalpy, and the measured rate of cis-trans isomerization all indicate that the cis proline conformer is stabilized by favorable interactions between the aromatic ring and the proline residue. Analysis of the side chain conformation of the aromatic residue and analysis of the chemical shifts of the pyrrolidine ring protons shows that the aromatic side chain adopts a preferred conformation in the cis form. The distribution of rotamers and the effect of an aromatic residue on the cis-trans equilibrium indicate that the preferred conformation is populated to approximately 62% for the Phe containing peptide, 67% for the Tyr containing peptide, and between 75 and 80% for the Trp containing peptide. The interaction is unaffected by the addition of 8M urea. These local interactions favor an aromatic residue immediately preceding a cis proline, but they cannot explain the relative propensities for Phe-Pro, Tyr-Pro, and Trp-Pro cis peptide bonds observed in the native state of proteins. In the model peptides the percentage of the cis proline conformer is 21% GYPG while it is 17% for GFPG. This difference is considerably smaller than the almost three to one preponderance observed for cis Tyr-Pro peptide bonds vs cis Phe-Pro peptide bonds in the protein database. © 1998 John Wiley & Sons, Inc. Biopoly 45: 381-394, 1998
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  • 11
    ISSN: 0006-3525
    Keywords: temperature dependence ; thermodynamics ; partitioning ; substance P ; neuropeptide ; dodecylphosphocholine micelles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The temperature dependence of the partition of a neuropeptide, Substance P (SP), and its [Tyr8] analogue in a widely used membrane mimic, dodecylphosphocholine micelles, was studied by using a pulsed field gradient nmr diffusion technique. The partition coefficient was found to decrease when the temperature is increased, indicating a favorable (negative) enthalpy change upon partitioning of the peptides. Thermodynamic functions of the partitioning were determined. The enthalpy of partition ΔHpart, was found to be in the -2.5 to -3.0 kcal/mol range, which is between 2 and 3 times higher than the entropic term -TΔSpart. The free energy of partitioning is consistent with a model in which the SP peptides interact with the micelles mainly through the hydrophobic side chains of the residues Phe7, Phe8 (or Tyr8), Leu10, and Met11, and without the insertion of a major portion of the peptide into the hydrophobic core of the micelles. © 1998 John Wiley & Sons, Inc. Biopoly 45: 395-403, 1998
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  • 12
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 469-478 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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  • 13
    ISSN: 0006-3525
    Keywords: islet amyloid peptide ; amylin peptide ; human amylin ; molecular dynamics ; simulated annealing ; conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular dynamics simulations and simulated annealing in vacuum, model aqueous solution, and simulated membrane were used to analyze the conformational preferences of a segment spanning 20-29 residues of human islet amyloid polypeptide, [referred to as IAPPH(20-29)]. Molecular dynamics simulations were conducted at 300 K on IAPPH(20-29). The minimum energy conformers obtained in model aqueous solution and vacuum exhibited similar structures. Even in the absence of any constraints on peptide bonds, trans conformation was preferred consistently by all the peptide bonds. Analysis of the minimum energy conformers indicated that IAPPH(20-29) showed a strong preference for turn structures in all the environments. These turn structures were stabilized by the formation of hydrogen bonds between the backbone amide and carbonyl groups. A good agreement was found between the results obtained from the molecular dynamics simulation and solid-state nmr experimental studies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 9-20, 1998
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  • 14
    ISSN: 0006-3525
    Keywords: cyclic analogues ; Saccharomyces cerevisiae ; α-factor ; pheromone ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Analogues of the α-factor mating pheromone (WHWLQLKPGQPMY) from Saccharomyces cerevisiae in which the side chains of residues 7 and 10 were joined by lactam bonds were studied by nmr and molecular modeling. These investigations were carried out to discern the effect of lactam ring size on conformation and to ascertain whether the side chain i to i + 3 cyclized tetramers [H. R. Marepalli et al. (1996) Journal of the American Chemical Society, Vol. 118, pp. 6531-6539] can be considered as conformation-constraining building blocks when introduced into a long peptide chain. Nuclear Overhauser effect constraints, temperature coefficients, and backbone torsional angles were derived from 1H-nmr spectra measured in DMSO-d6. Modeling studies using the above constraints indicate that the lactam regions of the tridecapeptides assume various combinations of type II β-turns, γ-turns, and γ′-turns, but never type I β-turns. These investigations provide evidence that the tetrapeptide building blocks retain their preferred conformations in larger molecules and can be used to control the architecture of regions of such peptides. © 1998 John Wiley & Sons, Inc. Biopoly 45: 21-34, 1998
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  • 15
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
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  • 16
    ISSN: 0006-3525
    Keywords: salivary histatins ; antifungal agents ; candidacidal peptides ; peptide conformation ; nmr ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of human salivary histatin 5 (D-S-H-A-K-R-H-H-G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) was examined in water (pH 3.8) and dimethyl sulfoxide solutions using 500 MHz homo- and heteronuclear two-dimensional (2D) nmr. The resonance assignment of peptide backbone and side-chain protons was accomplished by 2D total correlated spectroscopy and nuclear Overhauser effect (NOE) spectroscopy. The high JNH-CαH values (≥7.4 Hz), absence of any characteristic NH-NH(i, i + 1) or CαH-CβH(i, i + 3) NOE connectivities, high dδ/dT values (≥0.004 ppm K-1) and the fast 1H/2H amide exchange suggest that histatin 5 molecules remain unstructured in aqueous solution at pH 3.8. In contrast, histatin 5 prefers largely α-helical conformation in dimethyl sulfoxide solution as evident from the JNH-CαH values (≤6.4 Hz), slow 1H/2H exchange, low dδ/dT values (≤0.003 ppm K-1) observed for amide resonances of residues 6-24, and the characteristic NH-NH(i, i + 1) and CαH-CβH(i, i +3) NOE connectivities. All backbone amide 15N-1H connectivities fall within 6 ppm on the 15N scale in the 2D heteronuclear single quantum correlated spectrum, and the restrained structure calculations using DIANA suggest the prevalence of α-helical conformations stabilized by 19 (5 → 1) intramolecular backbone amide hydrogen bonds in polar aprotic medium such as dimethyl sulfoxide. The interside-chain hydrogen bonding and salt-bridge type interactions that normally stabilize the helical structure of linear peptides in aqueous solutions are not observed. Histatin 5, unlike other naturally occurring antimicrobial polypeptides such as magainins, defensins, and tachyplesins, does not adopt amphiphilic structure, precluding its insertion into microbial membranes and formation of ion channels across membranes. Electrostatic (ionic type) and hydrogen bonding interactions of the positively charged and polar residues with the head groups of microbial membranes or with a membrane-bound receptor could be the initial step involved in the mechanism of antimicrobial activity of histatins. © 1998 John Wiley & Sons, Inc. Biopoly 45: 51-67, 1998
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  • 17
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 31-37 
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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  • 18
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 39-51 
    ISSN: 0006-3525
    Keywords: fluorescent dye ; thiazole orange ; nucleic acids ; double-stranded DNA ; single-stranded polypurines ; single-stranded polypyrimidines ; monomer ; dimer ; asymmetric cyanines ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorescent dye thiazole orange (TO) with nucleic acids is characterized. It is found that TO binds with highest affinity to double-stranded (ds) DNA [log(K) ≈ 5.5 at 100 mM salt], about 5-10 times weaker to single-stranded polypurines, and further 10-1000 times weaker to single-stranded polypyrimidines. TO binds as a monomer to dsDNAs and poly(dA), both as a monomer and as a dimer to poly(dG) and mainly as a dimer to poly(dC) and poly(dT). The fluorescence quantum yield of TO free in solution is about 2 · 10-4, and it increases to about 0.1 when bound to dsDNA or to poly(dA), and to about 0.4 when bound to poly(dG). Estimated quantum yields of TO bound to poly(dC) and poly(dT) are about 0.06 and 0.01, respectively. The quantum yield of bound TO depends on temperature and decreases about threefold between 5 and 50°C. © 1998 John Wiley & Sons, Inc. Biopoly 46: 39-51, 1998
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  • 19
    ISSN: 0006-3525
    Keywords: human plasma protein S ; activated protein C ; blood coagulation ; coagulation factors Va and VIIIa ; thrombin-sensitive region ; first epidermal growth factor module ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Human plasma protein S is a nonenzymatic cofactor for activated protein C (APC) in the inactivation of coagulation factors Va and VIIIa, and helps to provide an essential negative feedback on blood coagulation. Previous indirect evidence suggested that the thrombin-sensitive region (TSR:residues 47-75, 1 disulfide) and the first epidermal growth factorlike region (EGF1: residues 76-116, 3 disulfides) of protein S may be functionally important for expression of its APC cofactor activity. To study the functional importance of these modules directly, access to the isolated TSR and EGF1 modules would be preferred. Recombinant expression of protein S intact TSR and correctly folded EGF1 has not been possible. Here we describe the synthesis of both TSR and EGF1 modules by stepwise solid phase peptide synthesis using the in situ neutralization/2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate activation procedure for tert-butoxycarbonyl chemistry. For the TSR, correct intramodular disulfide bonding was confirmed. To overcome folding difficulties with the EGF1, a two-step oxidation procedure was used in which the cysteines involved in the middle, crossing, disulfide bond (Cys85-Cys102) remained protected with acetamidomethyl (Acm) groups after hydrogen fluoride treatment of the peptide resin. Selective formation of the first two disulfide bonds (Cys80-Cys93 and Cys104-Cys113) was followed by release of the Acm groups and subsequent formation of the third disulfide bond (Cys85-Cys102). CD studies revealed 54% of β-sheet/turn in the EGF1 that is characteristic for EGF modules. Deuterium exchange studies suggested a very tightly packed core in EGF1 that is not accessible to the bulk solvent, likely a result from the compact structure caused by its three disulfide bonds. The 30% β-sheet structure observed in the TSR involved amide protons that could be readily exchanged by deuterons, likely reflecting a more flexible structure of the TSR loop in contrast to the rigid structure of EGF1. The establishment of synthetic access to the TSR and EGF1 of protein S provides a versatile tool to study interactions of these modules with the blood coagulation components of the anticoagulant plasma protein C pathway. © 1998 John Wiley & Sons, Inc. Biopoly 46: 53-63, 1998
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  • 20
    ISSN: 0006-3525
    Keywords: gurmarin ; gurmarin analogues ; sweetness suppression ; synthetic peptide ; chorda tympani nerve ; gurmarin missing disulfide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sweetness-suppressing polypeptide gurmarin isolated from Gymnema sylvestre consists of 35 amino acid residues and includes three intramolecular disulfide bonds. The roles of the three disulfide bonds were investigated by replacing each with two alanine residues by solid-phase synthesis. Nine analogues of [Ala3,18]gurmarin, [Ala10,23]gurmarin, and [Ala17,33]-gurmarin were obtained. Three analogues had native disulfide bonds, while the other six had non-native disulfide bonds. The three analogues with native disulfide bonds suppressed the response to sucrose, but not those to glucose, fructose, saccharin, or glycine in rats. In contrast, the six analogues with non-native disulfide bonds did not suppress the responses to any of these sweeteners. These results suggest that the native disulfide bonds of gurmarin are necessary for interaction with the receptor protein, and that the sucrose-specific receptor site is present in rats. © 1998 John Wiley & Sons, Inc. Biopoly 46: 65-73, 1998
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  • 21
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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  • 22
    ISSN: 0006-3525
    Keywords: hydrophobic free energy eigenfunction ; peptide hydrophobic wavelets ; peptide power spectra ; hydrophobic modes ; dopamine D2 receptor ; dopamine transporter (DAT) ; neurotensin ; cholecystokinin ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dominant statistical hydrophobic free energy inverse frequencies, amino acid wavelengths as hydrophobic modes, of neurotensin (NT), cholescystokinin (CCK), the human dopamine D2 receptor [(DA)D2], and the human dopamine transporter (DAT) were determined using orthogonal decomposition of the autocovariance matrices of their amino acid sequences as hydrophobic free energy equivalents in kcal/mol. The leading eigenvalues-associated eigenvectors were convolved with the original series to construct eigenfunctions. Eigenfunctions were further analyzed using discrete trigonometric wavelet and all poles, maximum entropy power spectral transformations. This yielded clean representations of the dominant hydrophobic free energy modes, most of which are otherwise lost in the smoothing of hydropathy plots or contaminated by end effects and multimodality in conventional Fourier transformations. Mode matches were found between NT and (DA)D2 and between CCK and DAT, but not the converse. These mode matches successfully predicted the nonlinear kinetic interactions of NT-(DA)D2 in contrast with CCK-(DA)D2 on 3H-spiperone binding to (DA)D2, and by CCK-DAT but not NT-DAT on [N-methyl-3H]-WIN 35,428 binding to DAT in (DA)D2 and DAT cDNA stably transfected cell lines without known NT or CCK receptors. Computation of the dominant modes of hydrophobic free energy eigenfunctions may help predict functionally relevant peptide-membrane protein interactions, even across neurotransmitter families. © 1998 John Wiley & Sons, Inc. Biopoly 46: 89-101, 1998
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  • 23
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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  • 24
    ISSN: 0006-3525
    Keywords: conformational space ; 20-residue membrane-bound portion of melittin ; conformational space annealing ; Empirical Conformational Energy Program for Peptides ; global minimum-energy conformation ; lowest energy conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational space of the 20-residue membrane-bound portion of melittin has been investigated extensively with the conformational space annealing (CSA) method and the ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm. Starting from random conformations, the CSA method finds that there are at least five different classes of conformations, within 4 kcal/mol, which have distinct backbone structures. We find that the lowest energy conformation of this peptide from previous investigations is not the global minimum-energy conformation (GMEC); but it belongs to the second lowest energy class of the five classes found here. In four independent runs, one conformation is found repeatedly as the lowest energy conformation of the peptide (two of the four lowest energy conformations are identical; the other two have essentially identical backbone conformations but slightly different side-chain conformations). We propose this conformation, whose energy is lower than that found previously by 1.9 kcal/mol, as the GMEC of the ECEPP/3 force field. The structure of the proposed GMEC is less helical and more compact than the previous one. It appears that the CSA method can find several classes of conformations of a 20-residue peptide starting from random conformations utilizing only its amino acid sequence information. The proposed GMEC has also been found with a modified electrostatically driven Monte Carlo method [D. R. Ripoll, A. Liwo, and H.A. Scheraga (1998) “New Developments of the Electrostatically Driven Monte Carlo Method: Test on the Membrane-Bound Portion of Melittin,” Biopolymers, Vol. 46, pp. 117-126]. © 1998 John Wiley & Sons, Inc. Biopoly 46: 103-115, 1998
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  • 25
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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  • 26
    ISSN: 0006-3525
    Keywords: α-MSH ; [D-Phe7]α-MSH ; isomerism ; cyclic analogues ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Results of energy calculations for α-MSH (α-melanocyte stimulating hormone, Ac-Ser1-Tyr2-Ser3-Met4-Glu5-His6-Phe7-Arg8-Trp9-Gly10-Lys11-Pro12-Val13-NH2) and [D-Phe7]α-MSH were used for design of cyclic peptides with the general aim to stabilize different conformational isomers of the parent compound. The minimal structural modifications of the conformationally flexible Gly10 residue, as substitutions for L-Ala, D-Ala, or Aib (replacing of hydrogen atoms by methyl groups), were applied to obtain octa- and heptapeptide analogues of α-MSH(4-11) and α-MSH(5-11), which were cyclized by lactam bridges between the side chains in positions 5 and 11. Some of these analogues, namely those with substitutions of the Gly10 residue with L-Ala or Aib, showed biological activity potencies on frog skin comparable to the potency of the parent tridecapeptide hormone. Additional energy calculations for designed cyclic analogues were used for further refinement of the model for the biologically active conformations of the His-Phe-Arg-Trp “message” sequence within the sequences of α-MSH and [D-Phe7]α-MSH. In such conformations the aromatic moieties of the side chains of the His6, L/D-Phe7, and Trp9 residues form a continuous hydrophobic “surface,” presumably interacting with a complementary receptor site. This feature is characteristic for low-energy conformers of active cyclic analogues, but it is absent in the case of inactive analogues. This particular spatial arrangement of functional groups involved in the message sequence is very close for α-MSH and [D-Phe7]α-MSH, as well as for biologically active cyclic analogues despite differences of dihedral angle values for corresponding low-energy conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 155-167, 1998
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  • 27
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 145-154 
    ISSN: 0006-3525
    Keywords: cytochrome c ; conformational change ; polyanion binding ; coulombic interaction ; hydrophobic interaction ; microcalorimetry ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The properties of the complexes of ferricytochrome c with two different polyanions - poly(vinylsulfate) and poly(4-styrene-sulfonate) - with a comparable charge density but with the different size of the uncharged part of their molecules have been studied by means of optical spectroscopy, differential scanning calorimetry, and gel chromatography. Ferriccytochrome c formed a complex with the former one through coulombic interactions and remained in a native-like state. The addition of the second polyanion to a solution of ferric cytochrome c at a low ionic strength, pH 7.0, resulted in profound conformational change in the hydrophobic core of protein (opening of the heme crevice with a perturbation of the methionine 80-heme iron bond and the hydrophobic core of the protein). These may be understood as an involvement of noncoulombic (hydrophobic, H-bonding) interactions of the uncharged part of the polyanion molecule. Conformational changes and the observed shift in acidic transition from low spin to high spin state of ferric cytochrome c detected in the presence of the polyanions may have biological implication in understanding the origin of conformational changes in proteins induced in the course of their interaction with membrane lipids and membrane proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 145-154, 1998
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  • 28
    ISSN: 0006-3525
    Keywords: Raman tensor ; polarized Raman spectrum ; adenine ; uracil, uridylyl(3′-5′)adenosine ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polarized Raman scattering measurements have been made of a single crystal of uridylyl(3′-5′)adenosine (UpA) by the use of a Raman microscope with 488.0 nm excitation. The UpA crystal belongs to space group P21 (monoclinic), and Raman intensities Iaa, Ibb, and Ic′c′, have been determined for each Raman band. These intensities correspond to the aa, bb, and c′c′ components of the crystal Raman tensor, where c′ is defined as an axis perpendicular to the crystallographic a axis in the ac plane. From these experimental data, and by taking the known crystal structure into account, anisotropic and isotropic molecular Raman tensors have been calculated for the following 11 normal modes: ring stretching modes of the adenine residue (protonated) at 1560, 1516, 1330, and 715 cm-1; ring stretching modes of the uracil residue at 1696, 1657, 1615, 1228, and 790 cm-1; PO-2 symmetric stretching mode at 1080 cm-1; P( - )O single bond stretching mode at 801 cm-1. These pieces of information of the Raman tensors are considered to be useful for estimating the orientations of the DNA and RNA strands in a biological complex from a polarized Raman spectroscopic measurement of such a complex. © 1998 John Wiley & Sons, Inc. Biopoly 45: 135-147, 1998
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  • 29
    ISSN: 0006-3525
    Keywords: conformational transition ; aqueous solutions ; chain association ; ι-carrageenan ; microcalorimetry ; optical activity ; enthalpy of mixing ; polysaccharide ; polyelectrolytes ; thermodynamics ; counterion condensation theory ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Isothermal microcalorimetry, differential scanning calorimetry (DSC), and chirooptical data obtained for ι-carrageenan in NaCl, LiCl, and NaI aqueous solutions are presented. The experiments have been performed as a function of concentration both for the polymer and for the simple salt as a cosolute. The experimental findings consistently show the occurrence of a salt-induced disorder-to-order transition. From microcalorimetric experiments the exothermic enthalpy of transition ΔHtr is obtained as the difference between the theoretical, purely electrostatic ΔHel enthalpy change and the actual mixing enthalpy ΔHmix, measured when a ι-carrageenan salt-free solution at constant polymer concentration is mixed with a 1:1 electrolyte solution of variable concentration. In the case of added NaCl, the absolute values of enthalpy changes |ΔHtr| are in good agreement with those obtained for the opposite process, at comparable polymer and salt concentrations, from DSC melting curves. The microcalorimetric results show that the negative maximum value of ΔHtr corresponding to the interaction of Li+ counterion with ι-carrageenan polyion results to be significantly lower than the corresponding values obtained for Na+ counterion. At variance with the microcalorimetric data, chirooptical results show that the salt-induced disorder-to-order transition, occurring in the 0.02-0.2M salt concentration range, appears to be complete at a concentration of about 0.08-0.1M of the simple ion, irrespective of the polymer concentration and of the nature of added electrolyte. © 1998 John Wiley & Sons, Inc. Biopoly 45: 105-117, 1998
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  • 30
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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  • 31
    ISSN: 0006-3525
    Keywords: malonamide ; diaminomethane ; retropeptide ; retro-glycine ; peptide conformation ; Ramachandran plot ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Malonic and diaminomethane residues, equivalent to the two possible retro modifications of a glycine unit, with an inverted peptide group, present particular conformations that differ from those found in glycine and, in general, in α-amino acids. In both cases the ϕi and ψi torsional angles have restricted values as deduced from inspection of the Cambridge Structural Data Bank and from compounds studied by us. Thus, both ψi angles tend to be equal to 115° (or -115°) in the malonyl residues, whereas the ϕi angles tend to be equal to 88° (or -88°) in the diaminomethane residues. These results are in agreement with previous experimental data on polymers, but in the case of malonyl residues they differ from theoretical calculations on isolated molecules. The experimental data for both residues can be represented in a way similar to the usual Ramachandran plot, which will be useful in analyzing the incorporation of these residues into proteins. When side chains are present in either type of residue, they are similar to conventional α-amino acids, although the orientation of the peptide groups is different. In such cases they acquire conformations similar to those found in peptide residues in the α-helix and β-sheet conformations, although other conformations are also possible. © 1998 John Wiley & Sons, Inc. Biopoly 45: 149-155, 1998
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  • 32
    ISSN: 0006-3525
    Keywords: photoswitchable peptide antigens ; solid surfaces ; anti-trans azobene monoclonal antibody ; lipid monolayer ; trans p-phenylazophenylalanine ; atomic force microscope technique ; hapten-specific binding ; lipid bilayers ; quartz crystal microbalance technique ; cis-trans photoisomerization ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The anti-trans azobenzene monoclonal antibody was found to bind to a lipid monolayer carrying peptides containing a trans p-phenylazophenylalanine group on a mica surface. The binding of the antibody was directly observed by an atomic force microscope technique. The hapten-specific binding was also followed on lipid bilayers containing azobenzene groups developed on a quartz surface by using the quartz crystal microbalance technique. The binding was controlled by the cis-trans photoisomerization of the azobenzene group. © 1998 John Wiley & Sons, Inc. Biopoly 47: 159-165, 1998
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  • 33
    ISSN: 0006-3525
    Keywords: bacterial polysaccharide ; (1 → 4)-β-D-glucuronan ; Rhizobium meliloti ; molecular modeling ; fructose ; sucrose ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mutant strain M5N1 CS of Rhizobium meliloti produces, in a Rhizobium complete medium supplemented with fructose and sucrose, a partially acetylated homopolymer of D-glucuronic acid residues linked β-(1 → 4). This polysaccharide forms thermoreversible gels with monovalent salts and thermally stable gels with divalent salts.In order to define the different levels of structural characterization, modeling simulations were performed for both the regular (1 → 4)-β-D-glucuronan and the acetylated derivatives. This required the evaluation of the accessible conformational space for the 16 disaccharides. Detailed conformational analysis was accomplished using the flexible residue of the MM3 molecular mechanics procedure and the results were used to access the configurational statistics of representative polysaccharide chains. Within the potential energy surfaces calculated for each disaccharide, several low energy conformers can be identified. When these conformations are extrapolated to regular polysaccharide structures, they generate polymers with right- and left-handed chirality along with a 2-fold axis. This later arrangement (n = 2, h = 5.16 Å) closely corresponds to that derived from a fiber x-ray diffraction investigation. The insertion of acetyl groups induces changes in the helical features of the polymer. As for the simulation of the configurational properties of (1 → 4)-β-D-glucuronan, an extended disordered chain having a persistence length of 105 Å (corresponding to 22 monomers) is predicted. This agrees with previous conclusions derived from solution study. The inclusion of varying amounts of acetyl groups only slightly perturbs the calculated persistence length. © 1998 John Wiley & Sons, Inc. Biopoly 45: 165-175, 1998
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  • 34
    ISSN: 0006-3525
    Keywords: conformational interconversions ; peptide β-turns ; enantiomeric conformations ; chiral perturbations ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of the model tripeptide Boc-Aib-Gly-Leu-OMe (1) reveals two independent molecules in the asymmetric unit that adopt “enantiomeric” type I and type I′ β-turn conformations with the Aib and Gly residues occupying the corner (i + 1 and i + 2) positions. 13C cross polarization and magic angle sample spinning spectra in the solid state also support the coexistence of two conformational species. 13C-nmr in CDCl3 establishes the presence of a single species or rapid exchange between conformations. 400 MHz 1H-nmr provides evidence for conformational exchange involving a major and minor species, with β-turn conformations supported by the low solvent exposure of Leu(3) NH and the observation of NiH ↔ Ni+1H nuclear Overhauser effects. CD bands in the region 190-230 nm are positive, supporting a major population of type I′ β-turns. The isomeric peptide, Boc-Gly-Leu-Aib-OMe (2), adopts an “open” type II′ β-turn conformation in crystals. Solid state and solution nmr support population of a single conformational species. Chiral perturbation introduced outside the folded region of peptides may provide a means of modulating screw sense in achiral sequences. © 1998 John Wiley & Sons, Inc. Biopoly 45: 191-202, 1998
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  • 35
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 197-223 
    ISSN: 0006-3525
    Keywords: protein tyrosine kinases (PTK) ; PTK structure ; substrate specificity ; drug discovery ; cell regulation ; substrate motifs ; protein kinase assays ; protein kinase inhibitors ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Protein tyrosine kinases (PTKs) play a crucial role in many cell regulatory processes. It is therefore not surprising to see that functional perturbation of PTKs results in many diseases. Despite the diverse primary structure organization of various PTKs, the catalytic or kinase domains of various PTKs as well as that of Ser/Thr kinases are generally conserved. The high resolution crystal structure of a few PTKs has been solved in the last few years. In contrast to the well-defined linear peptide substrate motifs recognized by specific Ser/Thr kinases, the identification of specific substrate motifs for PTK has been slow. It is not until recently that through the use of combinatorial peptide library methods that specific recognition motifs for specific PTKs have begun to emerge. Efficient and specific peptide substrates for some PTKs with Km at the mid μM range have been identified. Based on these peptide substrates, relatively potent (IC50 at the low μM range) and highly selective pseudosubstrate-based peptide inhibitors have been developed. There has been enormous effort in the development of PTK inhibitors for diseases such as cancer, psoriasis, and osteoporosis. Several new high-throughput PTK assay technologies have recently been described. Small molecules against specific PTK have been developed. Most of them are competitive inhibitors at the ATP binding site. Some of these inhibitors have already been in clinical trial. © 1998 John Wiley & Sons, Inc. Biopoly 47: 197-223, 1998
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  • 36
    ISSN: 0006-3525
    Keywords: signal transduction ; Src homology domain ; Grb2 ; Zap70 ; phosphopeptide ; phosphotyrosine ; protein-protein interactions ; peptidomimetic ; nonpeptide ; structure-based drug design ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Src homology-2 (SH2) domains and their associated catalytic or noncatalytic proteins constitute critical signal transduction targets for drug discovery. Such SH2 proteins are found in the regulation of a number of cellular processes, including growth, mitogenesis, motility, metabolism, immune response, and gene transcription. From the relationship of tyrosine phosphorylation and intracellular regulation by protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs), the dynamic and reversible binding interactions of SH2 domain containing proteins with their cognate phosphotyrosine (pTyr) containing proteins provide a third dimensionality to the orchestration of signal transduction pathways that exist as a result of pTyr formation, degradation, and molecular recognition events. This review highlights several key research achievements impacting our current understanding of SH2 structure, mechanisms, and drug discovery that underlie the role(s) of SH2 domains in signal transduction processes, cellular functions, and disease states. © 1998 John Wiley & Sons, Inc. Biopoly 47: 243-261, 1998
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  • 37
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 263-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 38
    ISSN: 0006-3525
    Keywords: structure-based design ; Vascular Cell Adhesion Molecule ; α4β1 ; integrins ; epitope transfer ; peptides ; receptor ; antagonists ; nmr spectroscopy ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Results from protein mutagenesis and x-ray crystallographic studies of the multidomain protein Vascular Cell Adhesion Molecule (VCAM) were used to design cyclic octapeptides that retain the critical structural and binding elements of the epitope of VCAM in the interaction with the integrin α4β1 (VLA-4). Changes in the activities of peptide analogues correlated with the relative activities of protein mutants of VCAM, and predicted the properties of two new mutants that bound α4β1 with improved affinity vs wild type protein. The nmr structures of two peptides revealed a high degree of similarity to the structure of the VCAM binding epitope. These results demonstrate that a compact binding epitope identified via protein structure-function studies may be transferred to a synthetically accessible small peptide with the key structure-activity relationships intact. © 1998 John Wiley & Sons, Inc. Biopoly 47: 265-275, 1998
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  • 39
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
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  • 40
    ISSN: 0006-3525
    Keywords: fertilization ; fertilin ; epidermal growth factor-like ; peptide synthesis ; mouse ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A key step leading to fertilization is the binding of sperm to the egg plasma membrane. When a mammalian sperm reaches the egg plasma membrane, fertilin, an extracellular sperm membrane protein, is believed to bind to an egg plasma membrane receptor mediating fusion. Fertilin is composed of two subunits, and each subunit contains several domains, i.e., metalloprotease, disintegrin, epidermal growth factor (EGF)-like and fusion domains. This investigation examined the role of the EGF-like domains of mouse fertilinα and fertilinβ. Peptides corresponding to the N-terminal subdomain, containing four cysteines, and the C-terminal subdomain, containing two cysteines, were synthesized by solid-phase synthesis methods. Disulfide bonds were formed regioselectively according to the canonical EGF-like disulfide pattern. The activity of these peptides and their linear counterparts were tested for activity in a mouse in vitro fertilization assay. One peptide, 4a, corresponding to the cystine-constrained N-terminal subdomain of fertilinβ, had an activating effect on fertilization. The fertilization rate (number of eggs fertilized), fertilization index (number of sperm fused per egg), and level of polyspermy (three or more sperm fused per egg) increased in the presence of 500 μM 4a (12, 56, and 190%, respectively). Its linear counterpart, 4b, had no effect on in vitro fertilization. These data suggest that the EGF-like domain of fertilinβ has a function in sperm-egg binding and fusion. Previously, it has been shown that the fertilinβ disintegrin domain has a role in sperm-egg binding. Considered together, these studies suggest that fertilin is a modular, multidomain protein with more than one mechanism of action. This modularity may be used to design inhibitors of fertilin-receptor interactions that have high specificities for the fertilization process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 299-307, 1998
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  • 41
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    Biopolymers 47 (1998), S. 353-363 
    ISSN: 0006-3525
    Keywords: safety-catch linkers ; multiply cleavable linkers ; solid-phase synthesis ; combinatorial chemistry ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This review article focuses on concepts that incorporate safety-catch and multiply cleavable linkers in solid-phase synthesis. Discussed are specific applications of such linkers in the synthesis of peptides, peptide mimetics, and “small” organic molecules, as well as their limitations for particular chemistries and reaction conditions. © 1999 John Wiley & Sons, Inc. Biopoly 47: 353-363, 1998
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  • 42
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    Biopolymers 47 (1998), S. 311-351 
    ISSN: 0006-3525
    Keywords: solid-phase organic synthesis ; drug discovery ; supports ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid-phase synthesis of small organic molecules has received renewed attention since the first reports of the polymer-supported synthesis of compounds of therapeutic interest. Solid-phase synthesis is now a key component of the high-throughput synthesis and screening approach to drug discovery. The recent rapid growth in the number of organic transformations that have been successfully demonstrated on solid supports has involved both the use of the established amine, halide, and hydroxyl supports developed originally for peptide synthesis, and the design and synthesis of new supports to permit the anchoring and releasing of other functional groups. In this article, resins and linkers are subdivided according to the functional group on the solid support to which the first building block is anchored. The chemistry of these supports is illustrated by a relatively small but representative selection from the many recent examples of potential therapeutic agents synthesized on solid supports. © 1999 John Wiley & Sons, Inc. Biopoly 47: 311-351, 1998
    Additional Material: 88 Ill.
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  • 43
    ISSN: 0006-3525
    Keywords: solid-phase peptide synthesis ; solid-phase combinatorial chemistry ; chemical libraries ; polyethylene glycol-polystyrene (PEG-PS) ; polymeric supports ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The choice of a polymeric support is a key factor for the success of solid-phase methods for syntheses of organic compounds and biomolecules such as peptides and oligonucleotides. Classical Merrifield solid-phase peptide synthesis (SPPS), performed on low cross-linked hydrophobic polystyrene (PS) beads, sometimes suffers from sequence-dependent coupling difficulties. The concept of incorporating polyethylene glycol (PEG) into supports for solid-phase synthesis represents a successful approach to alleviating such problems. Previous reports from our laboratories have shown the advantages of “low-load” PEG-PS (0.15-0.25 mmol/g) for SPPS. Herein, we demonstrate that the beneficial aspects of the PEG-PS concept can be extended with resins that have higher loadings (0.3-0.5 mmol/g). © 1999 John Wiley & Sons, Inc. Biopoly 47: 365-380, 1998
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  • 44
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    Biopolymers 47 (1998), S. 381-396 
    ISSN: 0006-3525
    Keywords: solid-phase synthesis ; dendrimer ; hyperbranched polymers ; polyamidoamine ; bead loading amplification ; multiple antigen peptide system ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dendrimers are highly ordered, hyperbranched polymers with potential for a whole range of chemical applications. Solution-phase synthesis of dendrimers is often challenging, requiring long reaction times and nontrivial purification; solid-phase methodology, on the other hand, enables reactions to be driven to completion by using a large excess of reagents with trivial purification. In this paper we show that polyamidoamine dendrimers may be synthesized conveniently and efficiently on a solid support, and that these molecules are of good homogeneity as characterized by 1H- and 13C-nmr and electrospray mass spectrometry. These solid-phase dendrimers were used as a bead loading amplification tool in the synthesis of a hexapeptide library (Xaa-Gly-Gly-Phe-Leu-Lys) to allow single bead analysis as well as allowing the efficient synthesis of two dendrimer conjugates (Leu-enkephalin-Lys and Chlorambucil). This demonstrated that peptides and small drug molecules can be grown directly onto the dendrimer or onto a linker attached to the dendrimer periphery, enhancing general dendrimer utility. © 1999 John Wiley & Sons, Inc. Biopoly 47: 381-396, 1998
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  • 45
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    Biopolymers 47 (1998), S. 397-404 
    ISSN: 0006-3525
    Keywords: solid-phase synthesis ; planar supports ; cotton ; continuous synthesis ; libraries ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Planar supports represent a unique opportunity in designing novel approaches to solid-phase synthesis of peptides and small organic molecules. Published work includes assembly on cellulose paper sheets, cotton strips, or membranes, as well as ultrahigh-density synthesis on glass supports. Planar carriers allow for the synthesis to be performed without any reaction vessels (inclusion volume chemistry), construction of libraries with only one representation of each structure, or for continuous synthesis (replacing sequence in time by sequence in space). © 1999 John Wiley & Sons, Inc. Biopoly 47: 397-404, 1998
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  • 46
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    Biopolymers 47 (1998), S. 435-450 
    ISSN: 0006-3525
    Keywords: antimicrobial peptides ; amphibian skin ; innate immunity ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Amphibian skin secretions contain many biologically active compounds, such as biogenic amines, complex alkaloids, or peptides. Within the latter class of molecules, a large number of peptide antibiotics has been isolated and characterized from different amphibian species. Antimicrobial peptides are considered the effector molecules of innate immunity, acting as a first line of defense against bacterial infections, by perturbing the phospholipid bilayer of the target cell membrane. These gene-encoded molecules are synthesized as inactive precursors and in several cases their proparts were shown to have highly conserved structures. It has also been demonstrated that the promoter regions of inducible peptide antibiotics are often regulated by the transcriptional control machinery NF-κB/IκBα. In amphibia of Rana and Bombina genera, inhibition of transcription of the genes encoding antimicrobial peptides has been obtained by glucocorticoid treatment, which causes an increase of IκBα synthesis. Moreover, determination of the structure of a number of genes coding for antimicrobial peptides in amphibia has actually shown that their promoter regions contain recognition sites for nuclear factors. © 1999 John Wiley & Sons, Inc. Biopoly 47: 435-450, 1998
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  • 47
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    Biopolymers 47 (1998), S. 465-477 
    ISSN: 0006-3525
    Keywords: antimicrobial peptides ; insects ; innate immunity ; bacterial infections ; fungal infections ; invertebrates ; arthropods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Antimicrobial peptides are pivotal elements of the innate immune defense against bacterial and fungal infections. Within the impressive list of antimicrobial peptides available at present, more than half have been characterized in arthropods. Cysteine-rich antimicrobial peptides represent the most diverse and widely distributed family among arthropods and, to a larger extent, among invertebrates. Proeminent groups of cysteine-rich peptides are peptides with the CSαβ motif and peptides forming an hairpin-like β-sheet structure. Although these substances exhibit a large structural diversity and a wide spectrum of activity, they have in common the ability to permeabilize microbial cytoplasmic membranes. Drosophila has proved a remarkable system for the analysis of the regulation of expression of gene encoding antimirobial cysteine-rich peptides. These studies have unraveled the striking parallels that exist between insect immunity and innate immunity in mammals that point to a common ancestry of essential aspects of innate immunity. © 1999 John Wiley & Sons, Inc. Biopoly 47: 465-477, 1998
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  • 48
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    Biopolymers 47 (1998), S. 451-463 
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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  • 49
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    Biopolymers 47 (1998), S. 479-491 
    ISSN: 0006-3525
    Keywords: antimicrobial peptides ; plant defense peptides ; thionin ; defensin ; lipid transfer protein ; hevein- and knottin-like peptides ; MBP1 ; IbAMP ; snakin ; disulfide bridge ; pathogen ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Eight families of antimicrobial peptides, ranging in size from 2 to 9 kD, have been identified in plants. These are thionins, defensins, so-called lipid transfer proteins, hevein- and knottin-like peptides, MBP1, IbAMP, and the recently reported snakins. All of them have compact structures that are stabilized by 2-6 disulfide bridges. They are part of both permanent and inducible defense barriers. Transgenic overexpression of the corresponding genes leads to enhanced tolerance to pathogens, and peptide-sensitive pathogen mutants have reduced virulence. © 1999 John Wiley & Sons, Inc. Biopoly 47: 479-491, 1998
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  • 50
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    Biopolymers 48 (1998), S. 1-2 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 51
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    Biopolymers 48 (1998), S. 3-17 
    ISSN: 0006-3525
    Keywords: desolvation ; hydrogen bonding ; Watson-Crick pairing ; mispairing ; fidelity ; geometry ; Klenow fragment ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recent experiments have presented evidence that Watson-Crick hydrogen bonds in a base pair are not absolute requirements for efficient synthesis of that pair by DNA polymerase enzymes. Here we examine quantitative steady-state kinetic data from several published studies involving poorly hydrogen-bonding DNA base analogues and adducts, and analyze the results in terms of solvation, hydrogen bonding, and steric effects. We propose a mechanism that can explain the surprising lack of hydrogen-bonding requirement accompanied by significant selectivity in pairing. This hypothesis makes use of steric matching, enforced both by the tightly confined polymerase active site and by the DNA backbone, as a chief factor determining nucleotide selection during DNA synthesis. The results also suggest that hydrogen bonds from bases to water (solvation) may be important in increasing the effective size of DNA bases, which may help prevent misinsertion of small bases opposite each other. © 1998 John Wiley & Sons, Inc. Biopoly 48: 3-17, 1998
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  • 52
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    Biopolymers 48 (1998), S. 29-37 
    ISSN: 0006-3525
    Keywords: amide synthase ; catalytic antibodies ; Diels-Alderase ; ideal catalyst platform ; in vitro selection ; Lewis acid ; modified uridines ; modified RNA ; ribozymes ; SELEX ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this manuscript the catalytic ability of RNA is examined and compared to other biopolymers. Despite having considerably fewer catalytically enabling properties when compared to proteins, the power of in vitro selection has allowed for RNA and DNA catalysts to be isolated. RNA catalysis has been expanded by incorporating modified bases to enrich the structural and functional diversity of RNA. Successful examples of new RNA chemistry using base modifications include carbon-carbon bond forming reactions and creation of highly specific active sites that are capable of recognizing small organic molecules without the need for nucleic acid templating or intercalation. In fact, the scope of functional modifications available for use in the RNA platform may eventually surpass those that are found in proteins and there are already hints that well chosen modifications allow nucleic acid catalysts to take advantage of mechanisms not available to selected protein catalysts for similar reactions. The chemical versatility of RNA is just emerging and future research directions will likely entail more creative methods for functional modification that will lead to new catalysts. © 1998 John Wiley & Sons, Inc. Biopoly 48: 29-37, 1998
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  • 53
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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  • 54
    ISSN: 0006-3525
    Keywords: Aib peptides ; crystal state structure ; helical peptides ; peptide helices ; x-ray crystallography ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal-state preferred conformations of six Nα-blocked pentapeptide esters, each containing four helicogenic, achiral α-aminoisobutyric acid (Aib) residues followed by one chiral L-valine (L-Val) or Cα-methyl-L-valine [(αMe)Val] residue at the C-terminus, have been assessed by x-ray diffraction analysis. In all of the compounds the —(Aib)4— sequence is folded in a regular 310-helical conformation. In the four pentapeptides characterized by the L-(αMe)Val residue two conformationally distinct molecules occur in the asymmetric unit. Conversely, only one molecule is observed in the asymmetric unit of two pentapeptides with the C-terminal L-Val residue. In the L-Val based peptides the helical screw sense of the —(Aib)4— sequence is right-handed, whereas in the L—(αMe)Val— analogues both right- and left-handed helical screw senses concomitantly occur in the two crystallographically independent molecules. © 1998 John Wiley & Sons, Inc. Biopoly 46: 433-443, 1998
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  • 55
    ISSN: 0006-3525
    Keywords: fluorescein-oligonucleotide conjugates ; local electrostatic potential ; local pH ; protolytic equilibrium ; FITC fluorescence energy transfer ; dye labeled oligonucleotides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The properties of fluorescein are substantially altered upon conjugation to nucleic acids, affecting not only the molar absorptivities and fluorescence quantum yields but also the protolytic equilibrium constant and fluorescence lifetimes. Around neutral pH, the fluorescein moiety is present as both mono- and dianion, and the pKa relating them is increased from 6.43 for free fluorescein to about 6.90 for fluorescein attached to both single- and double-stranded oligonucleotides of at least 12 bases/base pairs. This difference reflects the local electrostatic potential around the nucleic acid, which is calculated to -28 mV. The molar absorptivities and spectral responses of the conjugated fluorescein protolytic species are also determined, from which the concentrations of fluorescein-oligonucleotide conjugates can be calculated by assuming: ε494 = 62000/[1 + 10-(pH-6.90)] + 12000/[1 + 10(pH-6.90)] (M-1 cm-1). The fluorescence quantum yield of the conjugates depends, in a complex way, on temperature, environment and oligonucleotide length, sequence and conformation, and must be determined for each experimental situation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 445-453, 1998
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  • 56
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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  • 57
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    Biopolymers 46 (1998), S. 493-501 
    ISSN: 0006-3525
    Keywords: large-scale dynamics ; proteins ; bovine pancreatic trypsin inhibitor ; Newton equations ; anharmonic modes ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We study a dynamical model for the large-scale motions of bovine pancreatic trypsin inhibitor in vacuum. The model is obtained by projecting Newton equations onto some set of anharmonic modes. We compare the statistics of the so-obtained trajectories with those obtained by standard techniques, and conclude that our dynamical model is able to reproduce fairly well the average properties of the large-scale motions of this protein. Moreover, it allows for time steps one order of magnitude larger than the standard ones. © 1998 John Wiley & Sons, Inc. Biopoly 46: 493-501, 1998
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  • 58
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    Biopolymers 48 (1998), S. 83-96 
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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  • 59
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    Biopolymers 48 (1998), S. 137-153 
    ISSN: 0006-3525
    Keywords: RNA ; pseudoknot ; Turnip Yellow Mosaic Virus ; Mouse Mammary Tumor Virus ; Beet Western Yellows Virus ; Simian Retrovirus type-1 ; Hepatitis Delta Virus ; translational frameshifting ; ribozyme ; nmr ; x-ray diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, several high-resolution structures of RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs. © 1999 John Wiley & Sons, Inc. Biopoly 48: 137-153, 1998
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