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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    ISSN: 1573-9023
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A full understanding of the way a drug interacts with its receptor, and thus of its function, relies on a complete description of the intermolecular interactions at atomic resolution. Besides X-ray crystallography, only nuclear magnetic resonance spectroscopy can provide the required structural data. NMR descriptions of drug-receptor complexes range from the plain identification of regions of the drug surface that contact the receptor to full characterizations of the three-dimensional structure of the complexes. In addition, NMR can be used for the detection of multiple conformations, the characterization of the presence and functional role of water molecules, and the measurement of internal dynamic processes that govern the binding and the action of a drug.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-5001
    Keywords: Nuclear magnetic resonance ; Protein structure determination ; Automated spectral analysis ; Software packageEASY ; Sequence-specific assignments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The programEASY supports the spectral analysis of biomacromolecular two-dimensional (2D) nuclear magnetic resonance (NMR) data. It provides a user-friendly, window-based environment in which to view spectra for interactive interpretation. In addition, it includes a number of automated routines for peakpicking, spin-system identification, sequential resonance assignment in polypeptide chains, and cross peak integration. In this uniform environment, all resulting parameter lists can be recorded on disk, so that the paper plots and handwritten notes which normally accompany manual assignment of spectra can be largely eliminated. For example, in a protein structure determination by 2D1H NMR,EASY accepts the frequency domain datasets as input, and after combined use of the automated and interactive routines it can yield a listing of conformational constraints in the format required as input for the calculation of the 3D structure. The program was extensively tested with current protein structure determinations in our laboratory. In this paper, its main features are illustrated with data on the protein basic pancreatic trypsin inhibitor.
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  • 3
    ISSN: 1573-5001
    Keywords: NMR structure determination ; Interactive computer graphics for support of NMR analysis ; Peak picking and integration ; Sequence-specific NMR assignments for biological macromolecules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes. Since the program utilizes the X-window system and the Motif widget set, it is portable on a wide range of UNIX workstations. The design objective was to provide maximal computer support for the analysis of spectra, while providing the user with complete control over the final resonance assignments. Technically important features of XEASY are the use and flexible visual display of ‘strips’, i.e., two-dimensional spectral regions that contain the relevant parts of 3D or 4D NMR spectra, automated sorting routines to narrow down the selection of strips that need to be interactively considered in a particular assignment step, a protocol of resonance assignments that can be used for reliable bookkeeping, independent of the assignment strategy used, and capabilities for proper treatment of spectral folding and efficient transfer of resonance assignments between spectra of different types and different dimensionality, including projected, reduced-dimensionality triple-resonance experiments.
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  • 4
    ISSN: 1573-5001
    Keywords: AIDS ; DYANA ; HIV-1 ; NMR structure ; ribonuclease H ; RNA-DNA hybrid ; torsion angle dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract A high-quality NMR solution structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) was determined using the program DYANA with its recently implemented new module FOUND, which performs exhaustive conformational grid searches for dinucleotides. To ensure conservative data interpretation, the use of 1H-1H lower distance limit constraints was avoided. The duplex comprises the tRNA–DNA junction formed during the initiation of HIV-1 reverse transcription. It forms an A-type double helix that exhibits distinct structural deviations from a standard A-conformation. In particular, the minor groove is remarkably narrow, and its width decreases from about 7.5 Å in the RNA/RNA stem to about 4.5 Å in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid duplexes of ∼11 Å and ∼8.5 Å, respectively, were previously reported. The present, new structure supports that reverse transcriptase-associated RNaseH specificity is related primarily to conformational adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex.
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  • 5
    ISSN: 1573-5001
    Keywords: NMR structure determination ; Automated sequence-specific resonance assignment ; Homologous proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The program GARANT (General Algorithm for Resonance AssignmeNT) for automated sequence-specific NMR assignment of proteins is based on the mapping of peaks predicted from the amino acid sequence onto the peaks observed in multidimensional spectra [C. Bartels, P. Güntert, M. Billeter and K. Wüthrich (1996) J. Comput. Chem., manuscript submitted for publication]. In this paper we demonstrate the potential of GARANT for the assignment of homologous proteins when either the three-dimensional structure or the chemical shifts of the parent protein are known. In these applications, GARANT utilizes supplementary information either in the form of interatomic distances derived from the three-dimensional structure, in order to add nuclear Overhauser effects reflecting the tertiary structure to the list of expected peaks, or in the form of the chemical shifts of the parent protein, in order to obtain a better estimate of the positions of the expected peaks. The procedure is illustrated with three different proteins: (i) a mutant form of Tendamistat (74 residues), using homonuclear 2D 1H NMR spectra and either the three-dimensional structure or the chemical shifts of the wild-type protein; (ii) the mutant Antp(C39S, W56S) homeodomain (68 residues), using homonuclear 2D 1H NMR spectra and the three-dimensional structure of the Antp(C39S) homeodomain; and (iii) free cyclophilin A (165 residues), using heteronuclear 3D NMR spectra and the three-dimensional structure of a cyclophilin A-cyclosporin A complex. In these three systems nearly complete assignment of the polypeptide backbone resonances and assignment of over 80% of the amino acid side-chain resonances was obtained without manual intervention.
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  • 6
    ISSN: 1573-5001
    Keywords: NMR structure determination ; distance restraints ; torsion angle restraints ; stereospecific assignment ; local conformation analysis ; grid search
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The new computer algorithm FOUND, which is implemented as an integrated module of the DYANA structure calculation program, is capable of performing systematic local conformation analyses by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based DYANA target function value. Sets of mutually dependent torsion angles, for example in ribose rings, are treated as a single degree of freedom. The results of the local conformation analysis include allowed torsion angle ranges and stereospecific assignments for diastereotopic substituents, which are then included in the input of a subsequent structure calculation. FOUND can be used for grid searches comprising up to 13 torsion angles, such as the backbone of a complete α-helical turn or dinucleotide fragments in nucleic acids, and yields a significantly higher number of stereospecific assignments than the precursor grid search algorithm HABAS.
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  • 7
    ISSN: 1573-5001
    Keywords: Vicinal spin-spin coupling constants ; J-modulated [15N,1H]-COSY ; Nonlinear fit of J-modulation ; Protein conformation ; NMR structure of proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Improved experimental schemes for the recently introduced J-modulated [15N,1H]-correlation experiment for measurements of the homonuclear amide proton-Cα proton vicinal coupling constants.3JHNα, in uniformly15N-labeled proteins are described, and a nonlinear fit procedure is presented for quantitative evaluation of3JHNα. The method was first tested with the N-terminal DNA-binding domain of the 434 repressor (M=7.3 kDa), where at 13 C precise values of3JHNα in the range 2.0–9.5 Hz were obtained for all residues with resolved15N-1H cross peaks. It was then applied to theAntennapedia homeodomain complexed to a synthetic 14-base pair DNA fragment (molecular weight of the complex ∼ 18 kDa). The3JHNα values measured were found to be in excellent agreement with those predicted from the secondary structure of this protein in the complex.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
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  • 9
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program for automatic resonance assignment of nuclear magnetic resonance (NMR) spectra of proteins, GARANT (General Algorithm for Resonance Assignment), is introduced. Three principal elements used in this approach are: (a) representation of resonance assignments as an optimal match of two graphs describing, respectively, peaks expected from combined knowledge of the primary structure and the magnetization transfer pathways in the spectra used, and experimentally observed peaks; (b) a scoring scheme able to distinguish between correct and incorrect resonance assignments; and (c) combination of an evolutionary algorithm with a local optimization routine. The score that evaluates the match of expected peaks to observed peaks relies on the agreement of the information available about these peaks, most prominently, but not exclusively, the chemical shifts. Tests show that the combination of an evolutionary algorithm and a local optimization routine yields results that are clearly superior to those obtained when using either of the two techniques separately in the search for the correct assignments. GARANT is laid out for assignment problems involving peaks observed in two- and three-dimensional homonuclear and heteronuclear NMR spectra of proteins. © 1997 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 10
    ISSN: 1546-170X
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] B-cell activation depends on the intensity of B-cell receptor cross-linking. Studies of haptenated antigens1 and vesicular stomatitis virus2 (VSV) have demonstrated a correlation between antigen repetitiveness and the degree to which B-cell activation is independent of T cells. Here, we compare ...
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