Classifying Protein Structural Dynamics via Residual Dipolar Couplings

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Classifying Protein Structural Dynamics via Residual Dipolar Couplings (2004)

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by Ruben Valas , Christopher James Langmead

BibTeX

@MISC{Valas04classifyingprotein,
    author = {Ruben Valas and Christopher James Langmead},
    title = {Classifying Protein Structural Dynamics via Residual Dipolar Couplings},
    year = {2004}
}

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Abstract

Recent advances in Nuclear Magnetic Resonance (NMR) spectroscopy present new opportunities for investigating the conformational dynamics of proteins in solution. In particular, tensors for motions relevant to biological function can be obtained via experimental measurement of residual dipolar couplings (RDCs) between nuclei. These motion tensors have been used by others to characterize the magnitude and anisotropy of the dynamics of individual bond vectors. Here, we extend these results and demonstrate that RDCs can also be used to characterize the global nature of the protein’s motion (e.g., hinge motions, shear motions, etc.). In particular, we introduce the first method for classifying protein motions from RDC data. Our classifier consists of a discriminative model trained on 2,454 different molecular dynamics trajectories spanning seven categories of motion. The classifier achieves precision and recall accuracy of 90.6 % and 90.9%, respectively, using 10-fold cross-validation over these seven categories. 1

Keyphrases

residual dipolar coupling protein structural dynamic protein motion experimental measurement global nature 10-fold cross-validation hinge motion shear motion present new opportunity different molecular dynamic trajectory motion tensor nuclear magnetic resonance discriminative model recent advance rdc data individual bond vector conformational dynamic biological function first method

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