|Title||Relationship between chemical shift value and accessible surface area for all amino acid atoms.|
|Publication Type||Journal Article|
|Year of Publication||2009|
|Authors||Vranken, W. F., and W. Rieping|
|Journal||BMC Struct Biol|
|Keywords||Amino Acids, Databases, Protein, Nuclear Magnetic Resonance, Biomolecular, Protein Structure, Secondary, Proteins, Surface Properties|
BACKGROUND: Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes.RESULTS: 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.CONCLUSION: 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.
|Alternate Journal||BMC Struct. Biol.|
|PubMed Central ID||PMC2678133|
|Grant List||WT GR075968MA / / Wellcome Trust / United Kingdom|
Relationship between chemical shift value and accessible surface area for all amino acid atoms.