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  • 1
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 2
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; supercoiling ; structure prediction ; hemagglutinin ; mannose-binding protein ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The discontinuities found in heptad repeats of α-helical coiled-coil proteins have been characterized. A survey of 40 α-fibrous proteins reveals that only two classes of heptad breaks are prevalent: the stutter, corresponding to a deletion of three residues, and the newly identified “stammer,” corresponding to a deletion of four residues. This restriction on the variety of insertions/deletions encountered gives support to a unifying structural model, where different degrees of supercoiling accommodate the observed breaks. Stutters in the hemagglutinin coiled-coil region have previously been shown to produce an underwinding of the supercoil, and we show here how, in other cases, stammers would lead to overwinding. An analysis of main-chain structure also indicates that the mannose-binding protein, as well as hemagglutinin, contains an underwound coiled-coil region. In contrast to knobs-into-holes packing, these models give rise to non-close-packed cores at the sites of the heptad phase shifts. We suggest that such non-close-packed cores may function to terminate certain coiled-coil regions, and may also account for the flexibility observed in such long α-fibrous molecules as myosin. The local underwinding or overwinding caused by these specific breaks in the heptad repeat has a global effect on the structure and can modify both the assembly of the protein and its interaction properties. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 3
    ISSN: 0887-3585
    Keywords: α-keratin ; intermediate filaments ; epidermal keratin ; vimentin ; keratinopathies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In intermediate filaments (IF) both epidermal keratin and vimentin molecules have been shown to have an eight residue head to-tail overlap between the rod domains of similarly directed molecules. In the case of the epidermal keratins this region has also been shown to have particular structural/functional significance since it represents a hot-spot for mutations in the four keratinopathies characterized to date. While there is good evidence that this head-to-tail overlap is present in IF containing Type III, IV, and V chains, as well as in the epidermal keratin IF (Ib/IIb), there are no data currently available for the hard α-keratin IF (Ia/IIa). Using a variety of data derived from X-ray diffraction and crosslinking studies, as well as theoretical modeling, it is now possible to demonstrate that the overlap region is not a feature of hard α-keratin IF. Indeed, it is shown that there is a nine residue gap between consecutive parallel molecules in the IF. An explanation for this observation is presented in terms of compensating disulfide bonds that occur both within the IF, and between the IF and the matrix in which the IF are embedded. © 1995 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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  • 4
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
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  • 5
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Some 30 cytokine amino acid sequences (mainly interleukins, colony stimulating factors and tumor necrosis factors) have been examined for evidence of secondary structure as well as longer-range interactions of a type likely to lead to stable α-helical bundles. Most, though not all, of the cytokines examined have a high predicted α-helical content (40-60%) and quasi-repeating heptads containing i/i+3 apolar periodicities. This major subset of the cytokines is predicted to be characterized by molecules in which 4-α-helical bundles with an average length of 25Å are the most marked conformational features. Based on these conclusions, we suggest structures for huG-CSF, huGM-CSF and muIL-5 in which defined loop segments at the ends of helical bundles are the most likely sites for binding and recognition by specific cell receptors. As such, they provide a means for testing or refining the three working models we have defined, using currently available methods of site-directed substitution and deletion mutagenesis, as well as synthetic peptides corresponding to the proposed loop sequences and the use of monoclonal antibodies of defined epitopic specificity. The structure arrived at for huGM-CSF is consistent with the limited data currently available concerning the residues which are important for binding and activity.
    Additional Material: 1 Ill.
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  • 6
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Double ionization of the 1,1-dimethyl allene molecule to triplet electronic states of the dication has been studied using theoretical and experimental methods. Although the calculated data indicate a high density of states, suitable groupings of calculated double-ionization energies to those states agree well with values measured by double-charge-transfer spectroscopy. This indicates that the theoretical predictions provide an accurate indication of the composition of the triplet-state manifold for the 1,1-dimethyl allene dication between 25.2 eV and 39.6 eV.
    Additional Material: 2 Ill.
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  • 7
    ISSN: 0951-4198
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Physics
    Notes: Double-charge-transfer spectroscopy is routinely used to measure double-ionization energies of molecules to singlet and triplet electronic states of dications, but is experimentally difficult to apply because the yield of negative ions generated in the double-electron-capture reactions is low. The use of a data-acquisition system and repetitive scanning of a spectrum can increase signal-to-noise ratios, but the number of scans that can be acquired is limited by drifting in the spectrum position, which results in spectral-peak broadening. This limitation has been overcome in the present investigation by the application of a computer enhancement program that effectively superimposes successive spectra which are subject to slight drift. Spectra obtained for H+ projectile ions reacting with hexafluorobenzene (C6F6) molecules are presented; use of the program with such spectra reveals features in the computer-enhanced spectrum which are not clearly evident in the individual spectra.
    Additional Material: 4 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 4 (1991), S. 63-75 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The amino acid sequences of human and murine haemopoietins have been analysed using algorithms predictive for secondary structure. The results for 19 of these proteins (human and murine Interleukins 2, 3, 4, 5, 6, 7 and granulocyte, macrophage and granulocyte macrophage-colony stimulating factors as well as human erythropoietin) suggest that they each contain a 4-α-helical bundle, ca 25 Å long, as a common conformational feature. The most important predictive indicator was considered to be occurrence of quasi-repeating sequences of seven amino acids of the form (a-b-c-d-e-f-g)n with a polar side chains (usually leucine) lying alternately three and four residues apart in the a and d positions. As with other proteins of known secondary structure this periodicity favors the formation of α-helical elements, each with an a polar external strip, which interdigitate closely with one another when tested appropriately. Molecular models based on these putative 4-α-helical bundles are presented - with special references to human granulocyte macrophage-colony stimulating factor. The extent to which such models are consistent with experiments designed to delineate receptor binding sites is discussed.
    Additional Material: 5 Ill.
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  • 9
    ISSN: 1076-5174
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: Vertical double-ionization energies of ethylamine, propylamine and butylamine molecules to triplet electronic states of their dications were measured by double-charge-transfer spectroscopy. The energies to the lowest states of the dications were calculated using an ab initio method with four basis sets. The calculated values predicted fairly well the reduction in the lowest energy observed when the length of the substituted alkyl group increased. Double-ionization energies to the lowest and higher lying triplet states of the dications were calculated by application of a semi-empirical form of the multiple scattering Xα method. Even though several spectral peaks may only be identified with transitions to groups of closely lying states, the calculated data gave an insight into the electronic transitions which take place to give the double-charge-transfer spectra.
    Additional Material: 3 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Double-ionization energies, for transitions from the ground state of the neutral propyne molecule to both singlet and triplet states of its dication, are investigated theoretically with the ab initio second-order algebraic diagrammatic construction [ADC(2)] propagator method. The results are compared with a previous study which reported both experimental data obtained from double-charge-transfer (DCT) spectroscopy and their analysis with semiempirical theory. The ADC(2) predictions match almost all the experimental peaks well. In the lower-energy range, for transitions to dication states up to 7 eV above the ground state, ADC(2) predictions indicate that significant energy separations of those dication terms dominated by a common electronic configuration are responsible for previous difficulties in the assignment of peaks in that region. At higher energies, both configuration interaction and satellite ionizations are significant.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 64: 175-182, 1997
    Additional Material: 5 Tab.
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