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  • 1. Helgstrand, M
    et al.
    Allard, Peter
    KTH, Tidigare Institutioner, Bioteknologi.
    QSim, a program for NMR simulations2004Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 30, nr 1, s. 71-80Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present QSim, a program for simulation of NMR experiments. Pulse sequences are implemented and analyzed in QSim using a mouse driven interface. QSim can handle almost any modern NMR experiment, using multiple channels, shaped pulses, mixing, decoupling, phase-cycling and pulsed field gradients. Any number of spins with any spin quantum number can, in theory, be used in simulations. Relaxation is accounted for during all steps of pulse sequences and relaxation interference effects are supported. Chemical kinetics between any numbers of states can be simulated. Both classical and quantum mechanical calculations can be performed. The result of a simulation can be presented either as magnetization as a function of time or as a processed spectrum.

  • 2.
    Wahlberg, Elisabet
    et al.
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Lendel, Christofer
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Helgstrand, Magnus
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Allard, Peter
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Dincbas-Renqvist, Vildan
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Hedqvist, Anders
    Berglund, Helena
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Nygren, Per-Åke
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Härd, Torleif
    KTH, Tidigare Institutioner                               , Bioteknologi.
    An affibody in complex with a target protein: Structure and coupled folding.2003Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 100, nr 6, s. 3185-3190Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z(SPA-1) affibody has been selected from a phage-displayed library as a binder to protein A. Z(SPA-1) also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z(SPA-1) affibody in its uncomplexed state and determined the solution structure of a Z:Z(SPA-1) protein-protein complex. Uncomplexed Z(SPA-1) behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z(SPA-1). We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z(SPA-1) and Ig Fc, respectively, suggesting that the Z(SPA-1) affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.

  • 3.
    Woestenenk, Esmeralda A.
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Allard, Peter
    KTH, Tidigare Institutioner, Bioteknologi.
    Gongadze, G. M.
    Moskalenko, S. E.
    Shcherbakov, D. V.
    Rak, A. V.
    Garber, M B
    Härd, Torleif
    KTH, Tidigare Institutioner, Bioteknologi.
    Berglund, Helena
    KTH, Tidigare Institutioner, Bioteknologi.
    Assignment and secondary structure identification of the ribosomal protein L18 from Thermus thermophilus2000Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 17, nr 3, s. 273-274Artikkel i tidsskrift (Fagfellevurdert)
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