4D prediction of protein (1)H chemical shifts.
A 4D approach for protein (1)H 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 Halpha and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17-0.34 and 0.34-0.65 ppm for the Halpha 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 (1)H chemical shift prediction tool 4DSPOT is available from http://www.uku.fi/kemia/4dspot .
Lehtivarjo
Juuso
J
Department of Biosciences, University of Kuopio, Kuopio, Finland. juuso.lehtivarjo@uku.fi
Hassinen
Tommi
T
Korhonen
Samuli-Petrus
SP
Peräkylä
Mikael
M
Laatikainen
Reino
R
D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006859:Hydrogen; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins; D006859:Hydrogen