title: 4D prediction of protein (1)H chemical shifts.
abstract: 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 .
authors.affiliation: Department of Biosciences, University of Kuopio, Kuopio, Finland. juuso.lehtivarjo@uku.fi
authors.forename: Juuso
authors.initials: J
authors.lastname: Lehtivarjo
authors.forename: Tommi
authors.initials: T
authors.lastname: Hassinen
authors.forename: Samuli-Petrus
authors.initials: SP
authors.lastname: Korhonen
authors.forename: Mikael
authors.initials: M
authors.lastname: Peräkylä
authors.forename: Reino
authors.initials: R
authors.lastname: Laatikainen
mesh_terms: 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*
chemical_list: D011506:Proteins; D006859:Hydrogen