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4D prediction of protein 1H chemical shifts

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Abstract

A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6–7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17–0.34 and 0.34–0.65 ppm for the Hα and HN shifts, respectively. X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures. The 1H chemical shift prediction tool 4DSPOT is available from http://www.uku.fi/kemia/4dspot.

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Authors and Affiliations

  1. Department of Biosciences, Laboratory of Chemistry, University of Kuopio, P.O.Box 1627, 70211, Kuopio, Finland

    Juuso Lehtivarjo, Tommi Hassinen & Reino Laatikainen

  2. Department of Biosciences, Laboratory of Biochemistry, University of Kuopio, P.O.Box 1627, 70211, Kuopio, Finland

    Mikael Peräkylä

  3. Perch Solutions Ltd., Hyrräkatu 3 A 1, 70500, Kuopio, Finland

    Samuli-Petrus Korhonen

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  1. Juuso Lehtivarjo
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  2. Tommi Hassinen
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  3. Samuli-Petrus Korhonen
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  4. Mikael Peräkylä
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  5. Reino Laatikainen
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Correspondence to Juuso Lehtivarjo.

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Lehtivarjo, J., Hassinen, T., Korhonen, SP. et al. 4D prediction of protein 1H chemical shifts. J Biomol NMR 45, 413–426 (2009). https://doi.org/10.1007/s10858-009-9384-1

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  • DOI: https://doi.org/10.1007/s10858-009-9384-1

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