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  • 1
    Electronic Resource
    Electronic Resource
    Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND (1998)
    Springer
    Journal of biomolecular NMR 12 (1998), S. 543-548 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008391403193
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  • 2
    Electronic Resource
    Electronic Resource
    The program XEASY for computer-supported NMR spectral analysis of biological macromolecules (1995)
    Springer
    Journal of biomolecular NMR 6 (1995), S. 1-10 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00417486
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Automated sequence-specific NMR assignment of homologous proteins using the program GARANT (1996)
    Springer
    Journal of biomolecular NMR 7 (1996), S. 207-213 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00202037
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  • 4
    Electronic Resource
    Electronic Resource
    [15N,1H]/[13C,1H]-TROSY for simultaneous detection of backbone 15N–1H, aromatic 13C–1H and side-chain 15N–1H2 correlations in large proteins (2000)
    Springer
    Journal of biomolecular NMR 17 (2000), S. 195-202 
    Details
    ISSN: 1573-5001
    Keywords: isotope-labeled proteins ; NMR structure determination ; transverse relaxation-optimized spectroscopy ; TROSY
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract This paper describes a [15N,1H]/[13C,1H]-TROSY experiment for the simultaneous acquisition of the heteronuclear chemical shift correlations of backbone amide 15N–1H groups, side chain 15N–1H2 groups and aromatic 13C–1H groups in otherwise highly deuterated proteins. The 15N–1H and 13C–1H correlations are extracted from two subspectra of the same data set, thus preventing possible spectral overlap of aromatic and amide protons in the 1H dimension. The side-chain 15N–1H2 groups, which are suppressed in conventional [15N,1H)-TROSY, are observed with high sensitivity in the 15N–1H subspectrum. [15N,1H]/[13C,1H]-TROSY was used as the heteronuclear correlation block in a 3D [1H,1H]-NOESY-[15N,1H]/[13C,1H]-TROSY experiment with the membrane protein OmpA reconstituted in detergent micelles of molecular weight 80 000 Da, which enabled the detection of numerous NOEs between backbone amide protons and both aromatic protons and side chain 15N–1H2 groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008399320576
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    Paper (German National Licenses)
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