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Journal of Biomolecular NMR

, Volume 38, Issue 4, pp 269–287 | Cite as

Empirical isotropic chemical shift surfaces

  • Eszter Czinki
  • Attila G. CsászárEmail author
Article

Abstract

A list of proteins is given for which spatial structures, with a resolution better than 2.5 Å, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles φ and ψ characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS(φ,ψ) surfaces obtained for the model peptides For–(l-Ala) n –NH2, with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the \(^{13}\hbox{C}^{\alpha}\) ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (αD), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical \(^{13}\hbox{C}^{\alpha}\)\(^{1}\hbox{H}^{\alpha}\) ICS(φ,ψ) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins.

Keywords

ICS surface Ramachandran map ICS-ICS correlation α-amino acid residue Alanine 

Notes

Acknowledgments

The work described has been supported by the Scientific Research Fund of Hungary (Grant No. OTKA T047185).

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.Laboratory of Molecular Spectroscopy, Institute of ChemistryEötvös UniversityBudapest 112Hungary

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