Random coil chemical shifts for intrinsically disordered proteins

The following Javascript will calculate the random coil chemical shifts for any protein sequence. The chemical shifts and the general sequence correction factors are from [1] whereas the temperature coefficients and the glycine correction factors are from [2]. The principle behind the determination of the sequence correction factors is described in [3]. The correction factors for perdeuteration are from [4]. The Javascript was kindly coded by Alex Maltsev of the NIH.

Random coil chemical shifts for methyl groups obtained by similar methods can be obtained from [5]. For a discussion of the various different random coil chemical shift datasets see section 2.1 in [6].

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

Sample temperature (Celsius)      pH  

Using GGXGG-based neighbor correction for glycines
Perdeuterated protein

Protein sequence in one-letter code (incorrect symbols will be ignored)


Predicted chemical shifts

  

References: 

[1] 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

[2] 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.

[3] Schwarzinger, S., Kroon, G.J., Foss, T.R., Chung. J., Wright, P.E., Dyson, H.J. (2001) Sequence-dependent correction of random coil NMR chemical shifts. JACS 123(13):2970-8.

[4] Cavanagh, J., Fairbrother, W.J., Palmer, A.G., Rance, M. and Skelton, N.J. (2007) Protein NMR Spectroscopy - Principles and practice. 2nd edition. Academic Press

[5] 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

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