Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins

Quantum mechanics (QM) calculations
are applied to examine 1H, 13C, 15N, and 31P chemical
shifts of two phosphorylation sites in an intrinsically disordered
protein region. The QM calculations employ a combination of (1) structural
ensembles generated by molecular dynamics, (2) a fragmentation technique
based on the adjustable density matrix assembler, and (3) density
functional methods. The combined computational approach is used to
obtain chemical shifts (i) in the S19 and S40 residues of the nonphosphorylated
and (ii) in the pS19 and pS40 residues of the doubly phosphorylated
human tyrosine hydroxylase 1 as the system of interest. We study the
effects of conformational averaging and explicit solvent sampling
as well as the effects of phosphorylation on the computed chemical
shifts. Good to great quantitative agreement with the experiment is
achieved for all nuclei, provided that the systematic error cancellation
is optimized by the choice of a suitable NMR standard. The effect
of the standard reference on the computed 15N and 31P chemical shifts is demonstrated by employing three different
referencing methods. Error bars associated with the statistical averaging
of the computed 31P chemical shifts are larger than the
difference between the 31P chemical shift of pS19 and pS40.
The sequence trend of 31P shifts therefore could not be
reliably reproduced. On the contrary, the calculations correctly predict
the change of the 13C chemical shift for CB induced by
the phosphorylation of the serine residues. The present work demonstrates
that QM calculations coupled with molecular dynamics simulations and
fragmentation techniques can be used as an alternative to empirical
prediction tools in the structure characterization of intrinsically
disordered proteins.