Random Coil Chemical Shifts – Section for Biomolecular Sciences - University of Copenhagen

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Random coil chemical shifts for intrinsically disordered proteins

Alex Maltsev has kindly coded a Javascript that automatically calculates the sequence-corrected random coil chemical shifts of a protein, while taking the effects of pH and temperature into consideration. The backbone chemical shifts are based peptide studies in SBiNLab [1,2]. The dataset is designed for intrinsically disordered proteins (also know as natively unfolded proteins), but should work equally well for folded proteins or denatured proteins. The javascript for calculation of backbone random coil chemical shifts can be found here. Random coil chemical shifts for methyl groups obtained by similar methods can be obtained from [3]. For a discussion of the various different random coil chemical shift datasets see section 2.1 in [4].

Note: Table 3 in [2] contains a typo. The pKa values for His is 1.5 x 10-7.

References: 

[1] Kjaergaard, M., Brander, S. and Poulsen, F.M. (2011) Random coil chemical shifts for intrinsically disordered proteins: Effects of temperature and pH J. Biomol. NMR 49(2):139-49.

[2] Kjaergaard, M. and Poulsen, F.M. (2011) Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution J. Biomol. NMR 50(2):157-165

[3] Kjaergaard, M., Iešmantavičius, V. and Poulsen F.M. (2011) The interplay between transient α-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts. Protein Sci. 20(12):2023-34

[4] Kjaergaard, M. and Poulsen F.M. (2012) Disordered proteins studied by chemical shifts. Prog Nucl Magn Reson Spectrosc. 60:42-51.