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  • 1
    Electronic Resource
    Electronic Resource
    Pepto: An expert system for automatic peak assignment of two-dimensional nuclear magnetic resonance spectra of proteins (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 805-818 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two-dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110704
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  • 2
    Electronic Resource
    Electronic Resource
    Qualitative and quantitative analysis of the secondary structure of cytochrome C Langmuir-Blodgett films (1997)
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 227-237 
    Details
    ISSN: 0006-3525
    Keywords: fourier transform ir spectroscopy ; protein conformations ; cytochrome C ; Langmuir-Blodgett film ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A qualitative and quantitative analysis of the conformation of Langmuir-Blodgett (LB) dried films of cytochrome C on silicon wafers was performed by Fourier transform ir (FTIR) spectroscopy. A deconvolution procedure was applied to the amide I band analysis, in order to determine the percentage of the different secondary structures. Qualitative analysis was performed by examining difference spectra.Films obtained by spreading protein solutions at pH 7.4 and 1, dried at 25 and 100°C, on silicon wafers were also examined in order to detect spectral components associated with denatured protein domains, and to compare them with cytochrome C LB films.FTIR spectroscopy showed that the following important changes characterise LB film spectra: (a) the α-helix component is higher (its percentage is 57 and 54%) than the one estimated in dried film obtained by spreading the solutions at pH 7.4 on a silicon substrate (43%), (b) there is an increase in the intensity of bands attributed to protonated carboxy group bands, involved and not involved in the formation of hydrogen bonds, and a decrease in those attributed to deprotonated carboxy groups, (c) the intensity of several bands attributed to aromatic amino acids and aliphatic chains increases, and (d) bands due to O(SINGLEBOND)H stretching vibrations of crystallization water are present.These conformational changes could be induced by protein-protein interaction caused by the close packing of molecules that occurs during LB film formation; it cannot be excluded that they may be accompanied by partial changes in the tertiary structure of the protein. A preferential orientation of protein molecules in LB films is also a possibility. © 1997 John Wiley & Sons, Inc. Biopoly 42: 227-237, 1997
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Effects of histone acetylation on chromatin structure (1997)
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 64 (1997), S. 466-475 
    Details
    ISSN: 0730-2312
    Keywords: histone acetylation ; chromatin structure ; circular dichroism ; ethidium bromide intercalation ; differential scanning calorimetry ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: The effect of histone acetylation was monitored on CHO chromatin structure, following the addition of 7 mM Na-butyrate to the cell culture medium. The properties of both control and hyperacetylated chromatins and nuclei were investigated by circular dichroism, ethidium bromide intercalation, differential scanning calorimetry, and affinity chromatography. Our results are compatible with modest but significant alterations in the various levels of chromatin organization, as a result of the charge neutralization of some lysine residues within the N-terminal region of the histonic octamer. Namely, large statistically significant differences do exist in the heat capacity thermograms of native nuclei, where unfolding into single nucleofilament of the highly packed native chromatin superfiber appears associated with acetylation; at the same time CD, EB, and affinity chromatography point to modest but consistent differences in the compactness of isolated nucleosomes and polynucleosomes. J. Cell. Biochem. 64:466-475. © 1997 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Differential scattering of circularly polarized light by chromatin modeled as a helical array of dielectric ellipsoids within the born approximation (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 1301-1321 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Theoretical predictions within the Born approximation of the expected differential light scattering of circularly polarized light (CIDS) were made for the 300-Å chromatin fiber, modeled as a helical array of dielectric ellipsoids. Computed CIDS values were strongly dependent on the exact geometry of the solenoid model, depending particularly on parameters relaed to the chiral nature of the fiber and the orientation of the nucleosomes within the helix, in contrast to the values of the total light scattering, which mainly probed size and shape. In particular, both a superbead model and a strict linear 110-Å nucleosome filament would be predicted as giving rise to zero CIDS (in disagreement with the finite values observed). At the same time, helical models in which the normal vectors to the nucleosome faces were exactly parallel to the helical axis also yielded zero CIDS. Confirming earlier expectations, CIDS values were significantly less dependent on helical length than total light scattering. Finally, comparison of these calculated results from those extrapolated from available experimental data indicates that predicted CIDS values, based on currently accepted models of solenoid structure, are within an order of magnitude of those experimentally observed. Together, these results indicate the potential of differential light scattering measurements as a probe of chromatin higher-order structure, complementary to existing scattering measurements.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360240716
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  • 5
    Electronic Resource
    Electronic Resource
    Effect of cell trypsinization on nuclear proteins of WI-38 fibroblasts in culture (1975)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Cellular Physiology 86 (1975), S. 71-81 
    Details
    ISSN: 0021-9541
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: When resting confluent monolayers of WI-38 fibroblasts are trypsinized and replated at a lower density they are stimulated to proliferate again with an interval of 18 hours between replating and the onset of DNA synthesis. Trypsinization of resting cells causes a 40% loss of nuclear proteins as well as of cytoplasmic proteins. The amount of nuclear proteins remains low for the first six hours after the cells have been replated and then it increases rapidly, reaching the same level of non-trypsinized resting cells by ten hours after plating. The proteins that are lost from the nucleus immediately after trypsinization are chromatin-associated proteins and most of them are non-histone chromosomal proteins, although a modest loss of histones cannot be ruled out. The loss of non-histone chromosomal proteins from cells that have been trypsinized causes changes in the structure of chromatin that can be detected by circular dichroism and by viscosity measurements. These results show that cell trypsinization causes an extensive loss of proteins from chromatin and that the loss is restored only several hours after the cells have been replated at a lower density.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcp.1040860109
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