Effects of Phosphorylation on Protein Backbone Dynamics and Conformational Preferences

Phosphorylations are the most common and extensively
studied post-translational
modification (PTM) of proteins in eukaryotes. They constitute a major
regulatory mechanism, modulating protein function, protein–protein
interactions, as well as subcellular localization. Phosphorylation
sites are preferably located in intrinsically disordered regions and
have been shown to trigger structural rearrangements and order-to-disorder
transitions. They can therefore have a significant effect on protein
backbone dynamics or conformation, but only sparse experimental data
are available. To obtain a more general description of how and when
phosphorylations have a significant effect on protein behavior, molecular
dynamics (MD) currently provides the only suitable framework to study
these effects at a large scale in atomistic detail. This study develops
a systematic MD simulation framework to explore the influence of phosphorylations
on the local backbone dynamics and conformational propensities of
proteins. Through a series of glycine-backbone peptides, we studied
the effects of amino acid residues including the three most common
phosphorylations (Ser, Thr, and Tyr), on local backbone dynamics and
conformational propensities. We further extended our study to investigate
the interactions of all such residues between position i to positions i + 1, i + 2, i + 3, and i + 4 in such peptides. The
final data set comprises structural ensembles for 3393 sequences with
more than 1 μs of sampling for each ensemble. To validate the
relevance of the results, the structural and conformational properties
extracted from the MD simulations are compared to NMR data from the
Biological Magnetic Resonance Data Bank. The systematic nature of
this study enables the projection of the gained knowledge onto any
phosphorylation site in the proteome and provides a general framework
for the study of further PTMs. The full data set is publicly available,
as a training and reference set.