Journal of Biomolecular NMR

, 45:413 | Cite as

4D prediction of protein 1H chemical shifts

  • Juuso Lehtivarjo
  • Tommi Hassinen
  • Samuli-Petrus Korhonen
  • Mikael Peräkylä
  • Reino Laatikainen


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


Protein Proton Chemical shift Prediction Molecular dynamics 

Supplementary material

10858_2009_9384_MOESM1_ESM.pdf (132 kb)
Supplementary material 1 (PDF 131 kb)


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Juuso Lehtivarjo
    • 1
  • Tommi Hassinen
    • 1
  • Samuli-Petrus Korhonen
    • 3
  • Mikael Peräkylä
    • 2
  • Reino Laatikainen
    • 1
  1. 1.Department of Biosciences, Laboratory of ChemistryUniversity of KuopioKuopioFinland
  2. 2.Department of Biosciences, Laboratory of BiochemistryUniversity of KuopioKuopioFinland
  3. 3.Perch Solutions Ltd.KuopioFinland

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