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A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data

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Abstract

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15N-T 1 and -T 2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15N-T 1, -T 2, and {1H}–15N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.

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Abbreviations

AIC:

Akaike’s information criteria.

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Acknowledgments

This research was supported by grants from the Canadian Institutes of Health Research (CIHR) and the Alberta Heritage Foundation for Medical Research (AHFMR). L.S. is an AHFMR Medical Research Senior Scholar. The author thanks Matt Crump (University of Bristol) for assistance with the spectral density mapping notebook. The Mathematica code for reading PDB coordinates was kindly provided by Brian Higgins (www.higgins.ucdavis.edu).

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Authors and Affiliations

  1. Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7

    Leo Spyracopoulos

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  1. Leo Spyracopoulos
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Correspondence to Leo Spyracopoulos.

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L. Spyracopoulos is an AHFMR Medical Research Senior Scholar

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Spyracopoulos, L. A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data. J Biomol NMR 36, 215–224 (2006). https://doi.org/10.1007/s10858-006-9083-0

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