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Computer modeling of nitroxide spin labels on proteins

Authors

  • Ma'mon M. Hatmal,

    1. Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089
    2. Department of Biochemistry, University of Southern California, Los Angeles, CA 90033-9151
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  • Yiyu Li,

    1. Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089
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  • Balachandra G. Hegde,

    1. Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033
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  • Prabhavati B. Hegde,

    1. Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033
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  • Christine C. Jao,

    1. Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033
    Current affiliation:
    1. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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  • Ralf Langen,

    1. Department of Biochemistry, University of Southern California, Los Angeles, CA 90033-9151
    2. Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033
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  • Ian S. Haworth

    Corresponding author
    1. Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089
    2. Department of Biochemistry, University of Southern California, Los Angeles, CA 90033-9151
    • Department of Biochemistry, University of Southern California, Los Angeles, CA 90033-9151
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com

Abstract

Electron paramagnetic resonance using site-directed spin labeling can be used as an approach for determination of protein structures that are difficult to solve by other methods. One important aspect of this approach is the measurement of interlabel distances using the double electron–electron resonance (DEER) method. Interpretation of experimental data could be facilitated by a computational approach to calculation of interlabel distances. We describe an algorithm, PRONOX, for rapid computation of interlabel distances based on calculation of spin label conformer distributions at any site of a protein. The program incorporates features of the label distribution established experimentally, including weighting of favorable conformers of the label. Distances calculated by PRONOX were compared with new DEER distances for amphiphysin and annexin B12 and with published data for FCHo2 (F-BAR), endophilin, and α-synuclein, a total of 44 interlabel distances. The program reproduced these distances accurately (r2 = 0.94, slope = 0.98). For 9 of the 11 distances for amphiphysin, PRONOX reproduced the experimental data to within 2.5 Å. The speed and accuracy of PRONOX suggest that the algorithm can be used for fitting to DEER data for determination of protein tertiary structure. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 35–44, 2012.

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