Relationship between chemical shift value and accessible surface area for all amino acid atoms.

TitleRelationship between chemical shift value and accessible surface area for all amino acid atoms.
Publication TypeJournal Article
Year of Publication2009
AuthorsVranken, W. F., and W. Rieping
JournalBMC Struct Biol
Volume9
Pagination20
Date Published2009
ISSN1472-6807
KeywordsAmino Acids, Databases, Protein, Nuclear Magnetic Resonance, Biomolecular, Protein Structure, Secondary, Proteins, Surface Properties
Abstract

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.

DOI10.1186/1472-6807-9-20
Alternate JournalBMC Struct. Biol.
PubMed ID19341463
PubMed Central IDPMC2678133
Grant ListWT GR075968MA / / Wellcome Trust / United Kingdom
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