%0 Journal Article
%T Relationship between chemical shift value and accessible surface area for all amino acid atoms
%A Wim F Vranken
%A Wolfgang Rieping
%J BMC Structural Biology
%D 2009
%I BioMed Central
%R 10.1186/1472-6807-9-20
%X We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA) in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html webcite.Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.Nuclear Magnetic Resonance (NMR) spectroscopy provides structural information on an atomic level and is, together with X-ray crystallography, the leading technique for structure elucidation: about 15% of all the protein and nucleic acid structures deposited at the wwPDB [1,2] were solved by NMR. The most prevalent NMR information used to calculate these structures are inter-atomic distances determined by the Nuclear Overhauser Effect (NOE). However, it has long been known that the chemical shift value of an atom is highly sensitive to its local chemical environment [3], and that it could be a highly informative NMR parameter when determining or validating structures. This effect has been exploited using the chemical shifts of backbone atoms to determine protein secondary structure elements [4-6] and dihedral angles [7-9]. More recently, databases that contain chemical shifts from the BioMagResBank (BMRB) [10] were used in conjuction with their corresponding atomic coordinates from the wwPDB to determine tertiary protein structures from chemical shifts [11-13], and to determine protein flexibility [14,15]. Methods to determine chemical shift values from a sequence or coordinates [16-18]
%U http://www.biomedcentral.com/1472-6807/9/20