4D prediction of protein 1H chemical shifts
 

4D prediction of protein 1H chemical shifts


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 6â??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 0.17â??0.34 and 0.34â??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.

• Content Type Journal Article
• Pages 413-426
• DOI 10.1007/s10858-009-9384-1
• Authors
  • Juuso Lehtivarjo, University of Kuopio Department of Biosciences, Laboratory of Chemistry P.O.Box 1627 70211 Kuopio Finland
  • Tommi Hassinen, University of Kuopio Department of Biosciences, Laboratory of Chemistry P.O.Box 1627 70211 Kuopio Finland
  • Samuli-Petrus Korhonen, Perch Solutions Ltd. Hyrräkatu 3 A 1 70500 Kuopio Finland
  • Mikael Peräkylä, University of Kuopio Department of Biosciences, Laboratory of Biochemistry P.O.Box 1627 70211 Kuopio Finland
  • Reino Laatikainen, University of Kuopio Department of Biosciences, Laboratory of Chemistry P.O.Box 1627 70211 Kuopio Finland

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738
  • Journal Volume Volume 45
  • Journal Issue Volume 45, Number 4

Source: Journal of Biomolecular NMR