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  • 1
    Electronic Resource
    Electronic Resource
    Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution (2001)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 558-570 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 Å resolution, the elements are reduced by two orders of magnitude for distances above 1.5 Å. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767301007656
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  • 2
    Electronic Resource
    Electronic Resource
    High-resolution neutron structure of nicotinamide adenine dinucleotide (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 981-989 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of the free-acid form of the coenzyme NAD+ was determined at 100 K from a single-crystal neutron experiment. NAD+ is the oxidized form of the coenzyme redox pair NAD+/NADH and plays an important role in the catalysis of biological processes. The molecule crystallizes in space group P1 with one NAD+ and four water molecules per unit cell. The structure is compared with the previous X-ray models of NAD+ [Reddy et al. (1981), J. Am. Chem. Soc. 103, 907–914; Parthasarathy & Fridey (1984b), Science, 226, 969–971; Guillot et al. (2000), Acta Cryst. C56, 726–728]. The crystal packing and the hydrogen-bond pattern are discussed as well as four short C—H\cdotsO contacts involving the pyridine and adenine rings. The structure displays stereochemical distortions owing to the hydrogen bonding and crystal-packing constraints, reflecting the adaptability of the NAD+ molecule in various chemical environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901007120
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  • 3
    Electronic Resource
    Electronic Resource
    Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1306-1318 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (\Delta B ∼ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998004466
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  • 4
    Electronic Resource
    Electronic Resource
    Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 Å resolution as a first test case (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 151-160 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The number of protein structures refined at a resolution higher than 1.0 Å is continuously increasing. Subatomic structures may deserve a more sophisticated model than the spherical atomic electron density. In very high resolution structural studies (d 〈 0.5 Å) of small peptides, a multipolar atom model is used to describe the valence electron density. This allows a much more accurate determination of the anisotropic thermal displacement parameters and the estimate of atomic charges. This information is of paramount importance in the understanding of biological processes involving enzymes and metalloproteins. The structure of the scorpion Androctonus australis Hector toxin II has been refined at 0.96 Å resolution using synchrotron diffraction data collected at room temperature. Refinement with a multipolar electron-density model in which the multipole populations are transferred from previous peptide studies led to the observation of valence electrons on covalent bonds of the most ordered residues. The refined net charges of the peptide-bond atoms were of the correct sign but were underestimated. Such protein-structure refinements against higher resolution data collected at cryogenic temperature will enable the calculation of experimental atomic charges and properties such as electrostatic potentials.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999014948
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  • 5
    Electronic Resource
    Electronic Resource
    Refinement of proteins at subatomic resolution with MOPRO (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 214-223 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Crystallography at subatomic resolution permits the observation and measurement of the non-spherical character of the atomic electron density. Charge density studies are being performed on molecules of increasing size. The MOPRO least-squares refinement software has thus been developed, by extensive modifications of the program MOLLY, for protein and supramolecular chemistry applications. The computation times are long because of the large number of reflections and the complexity of the multipolar model of the atomic electron density; the structure factor and derivative calculations have thus been parallelized. Stereochemical and dynamical restraints as well as the conjugate gradient algorithm have been implemented. A large number of the normal matrix off-diagonal terms turn out to be very small and the block diagonal approximation is thus particularly efficient in the case of large structures at very high resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889801001753
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  • 6
    Electronic Resource
    Electronic Resource
    Experimental charge density and electrostatic potential of glycyl-L-threonine dihydrate (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 155-165 
    Details
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The experimental electron density distribution in glycyl-L-threonine dihydrate has been investigated using single-crystal X-ray diffraction data at 110 K to a resolution of (sin θ/λ) = 1.2 Å−1. Multipolar pseudo-atom refinement was carried out against 5417 observed data and the molecular electron density was analyzed using topological methods. The experimental electrostatic potential around the molecule is discussed in terms of molecular interactions. Crystal data: C6H12N2O4.2H2O, Mr = 212.2, orthorhombic, P212121, Z = 4, F(000) = 456 e, T = 110 K, a = 9.572 (3), b = 10.039 (3), c = 10.548 (2) Å, V = 1013.6 (4) Å3, Dx = 1.3 g cm−3, µ = 1.2 cm−1 for λMo = 0.7107 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108768199014251
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  • 7
    Electronic Resource
    Electronic Resource
    Experimental and theoretical charge density of DL-alanyl-methionine (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 567-578 
    Details
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: X-ray diffraction data up to d = 0.50 Å resolution have been collected at 100 K for a DL-alanyl-methionine single crystal using a CCD area detector. Multipolar crystallographic refinement was carried out and the electron density of the molecule has been analyzed. The deformation electron density around the S atom reveals two lone pairs with an sp3 hybridization and agrees with the results of density functional theory calculations. The topological properties of the covalent bonds and of the hydrogen bonds have been investigated. Two weak polar intramolecular interactions of the type C5 (pentagonal cyclic structure) have unfavorable geometrical parameters for hydrogen bonds and are devoid of critical points. The two electron lone pairs of the carbonyl oxygen appear asymmetric in the experimental deformation density. This could be attributed to the different strength of the hydrogen bond and intramolecular polar interaction involving the carbonyl oxygen. In the ab-initio-derived deformation maps, the asymmetry of the electron doublets is reproduced only very partially.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108768101007212
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  • 8
    Electronic Resource
    Electronic Resource
    The oxidized form of nicotinamide adenine dinucleotide (2000)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 726-728 
    Details
    ISSN: 1600-5759
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the free acid form of NAD+ tetrahydrate (nicotinamide adenine dinucleotide tetrahydrate or 3-carbamoyl-1-β-D-ribofuranosylpyridinium hydroxide 5′-ester with adenosine 5′-pyrophosphate inner salt tetrahydrate, C21H27N7O14P2·4H2O) has been determined at 100 K. NAD+ is the coenzyme of several protein families and plays a dominant role in biological redox processes. In this study, the molecule shows a different conformation from the one usually found in holoenzyme complexes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108270100001220
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  • 9
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    Charge Density and Electrostatic Interactions of Fidarestat, an Inhibitor of Human Aldose Reductase (2009)
    American Chemical Society
    Details
    Publication Date: 2009-08-12
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society
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  • 10
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    Elucidation of the Phosphate Binding Mode of DING Proteins Revealed by Subangstrom X-ray Crystallography (2009)
    American Chemical Society
    Details
    Publication Date: 2009-06-10
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society
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