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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 11 (1998), S. 241-263 
    ISSN: 1573-5001
    Keywords: conformation filter ; distance geometry ; parallel computing ; systematic search
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Two complementary approaches for systematic search in torsion angle space are described for the generation of all conformations of polypeptides which satisfy experimental NMR restraints, hard-sphere van der Waals radii, and rigid covalent geometry. The first procedure is based on a recursive, tree search algorithm for the examination of linear chains of torsion angles, and uses a novel treatment to propagate the search results to neighboring regions so that the structural consequences of the restraints are fully realized. The second procedure is based on a binary combination of torsion vector spaces for connected submolecules, and produces intermediate results in Cartesian space for a more robust restraint analysis. Restraints for NMR applications include bounds on torsion angles and internuclear distances, including relational and degenerate restraints involving equivalent and nonstereoassigned protons. To illustrate these methods, conformation search results are given for the tetrapeptide APGA restrained to an idealized β-turn conformation, an alanine octapeptide restrained to a right-handed helical conformation, and the structured region of the peptide SYPFDV.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 14 (1999), S. 197-198 
    ISSN: 1573-5001
    Keywords: glutaredoxin ; oxidoreductase ; thiol-disulfide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 16 (2000), S. 9-21 
    ISSN: 1573-5001
    Keywords: dipolar couplings ; domain orientation ; transcription factor III A ; zinc fingers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Residual dipolar coupling constants measured in anisotropic solution contain information on orientations between internuclear vectors and the magnetic field, providing long-range information that may help determine the relative orientations of distinct domains in biomolecules. Here we describe the measurement and use of residual dipolar coupling restraints in the refinement of the structure of the complex of DNA with three zinc fingers of transcription factor IIIA (TFIIIA), measured in a DMPC/DHPC bicelle solution. These dipolar restraints were applied on a variety of orientations of the zinc finger domains (derived from crystallography, previous NMR studies, and systematic modeling) in order to examine the validity and sensitivity of using residual dipolar splittings to study interdomain orientations. The spread in interdomain angles between zinc fingers is reduced from 24° to 9° upon incorporation of dipolar restraints. However, the results also show that the ability to determine relative orientations is strongly dependent on the structural accuracy of the local domain structures.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 5 (1995), S. 14-24 
    ISSN: 1573-5001
    Keywords: ‘Random coil’ chemical shifts ; Temperature coefficient ; Trifluoroethanol ; Peptide proton chemical shifts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D 1H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chain assignments in previous studies to be resolved. An additional benefit of the temperature data is that they can be used to obtain ‘random coil’ amide proton chemical shifts at any temperature between 278 and 318 K by interpolation. Changes of chemical shift as a function of trifluoroethanol concentration have also been determined at a variety of temperatures for a subset of peptides. Significant changes are found in backbone and side-chain amide proton chemical shifts in these ‘random coil’ peptides with increasing amounts of trifluoroethanol, suggesting that caution is required when interpreting chemical shift changes as a measure of helix formation in peptides in the presence of this solvent. Comparison of the proton chemical shifts obtained here for H-Gly-Gly-X-Gly-Gly-OH with those for H-Gly-Gly-X-Ala-OH [Bundi, A. and Wüthrich, K. (1979) Biopolymers, 18, 285–297] and for Ac-Gly-Gly-X-Ala-Gly-Gly-NH2 [Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81] generally shows good agreement for CH protons, but reveals significant variability for NH protons. Amide proton chemical shifts appear to be highly sensitive to local sequence variations and probably also to solution conditions. Caution must therefore be exercised in any structural interpretation based on amide proton chemical shifts.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 12 (1998), S. 51-71 
    ISSN: 1573-5001
    Keywords: binding ; chemical shift ; complex ; DNA ; structure ; TFIIIA ; Zinc Finger
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone1 HN, 15N,13 Cα and13 Cβ and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 12 (1998), S. 1-23 
    ISSN: 1573-5001
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 13 (1999), S. 387-391 
    ISSN: 1573-5001
    Keywords: bicelle ; ether-lipid ; liquid crystal ; protein alignment ; residual dipolar coupling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract We have prepared and characterized a novel bicelle system composed of 1,2-di-O-dodecyl-sn-glycero-3-phos- phocholine (DIODPC) and 3-(chloramidopropyl)dimethylammonio-2-hydroxyl-1-propane sulfonate (CHAPSO). At the optimal DIODPC/CHAPSO molar ratio of 4.3:1, this medium becomes magnetically oriented from pH 6.5 down to pH 1.0. Unlike previously reported bicelle preparations, these bicelles are chemically stable at low pH and are capable of inducing protein alignment, as illustrated by the large residual dipolar couplings measured for rusticyanin from Thiobacillus ferrooxidans at pH 2.1. The DIODPC/CHAPSO system is particularly useful for measuring residual dipolar couplings of macromolecules that require very acidic conditions.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 16 (2000), S. 271-272 
    ISSN: 1573-5001
    Keywords: assignments ; inserted domain ; integrin ; LFA-1 ; metal binding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 16 (2000), S. 349-350 
    ISSN: 1573-5001
    Keywords: assignments ; backbone ; DHFR ; enzyme ; NADPH
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 18 (2000), S. 43-48 
    ISSN: 1573-5001
    Keywords: chemical shift ; CSI ; denaturant ; NMRView ; peptide ; random coil
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best.
    Type of Medium: Electronic Resource
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