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Fluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction

Authors

  • Tuo Zhang,

    1. School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202
    2. Center for computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
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  • Eshel Faraggi,

    1. School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202
    2. Center for computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
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  • Yaoqi Zhou

    Corresponding author
    1. School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202
    2. Center for computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202
    • Center for computational Biology and Bioinformatics, Indiana University School of Medicine, 719 Indiana Ave., Walker Plaza Building Suite 319, Indianapolis, IN 46202
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Abstract

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures. Protein structural flexibility is often characterized by fluctuations in the Cartesian coordinate space. On the other hand, the protein backbone can be mostly defined by two torsion angles ϕ and ψ only. We introduce a new flexibility descriptor, backbone torsion-angle fluctuation derived from the variation of backbone torsion angles from different NMR models. The torsion-angle fluctuations correlate with mean-squared spatial fluctuations derived from the same collection of NMR models. We developed a neural-network based real-value predictor based on sequence information only. The predictor achieved ten-fold cross-validated correlation coefficients of 0.59 and 0.60, and mean absolute errors of 22.7° and 24.3° for the angle fluctuation of ϕ and ψ, respectively. This predictor is expected to be useful for function prediction and protein structure prediction when predicted torsion angles are used as restraints. Both sequence- and structure-based prediction of torsion-angle fluctuation will be available at http://sparks.informatics.iupui.edu within the SPINE-X package. Proteins 2010. © 2010 Wiley-Liss, Inc.

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