Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation

Phosphorylation of protein is critical for various cell processes, which preferentially happens in intrinsically disordered proteins (IDPs). How phosphorylation modulates structural ensemble of disordered peptide remains largely unexplored. Here, using replica exchange molecular dynamics (REMD) and Markov state model (MSM), the conformational distribution and kinetics of p53 N-terminal transactivation domain (TAD) 2 as well as its dual-site phosphorylated form (pSer46, pThr55) were simulated. It reveals that the dual phosphorylation does not change overall size and secondary structure element fraction, while a change in the distribution of hydrogen bonds induces slightly more pre-existing bound helical conformations. MSM analysis indicates that the dual phosphorylation accelerates conformation exchange between disordered and order-like states in target-binding region. It suggests that p53 TAD2 after phosphorylation would be more apt to bind to both the human p62 pleckstrin homology (PH) domain and the yeast tfb1 PH domain through different binding mechanism, where experimentally it exhibits an extended and α-helix conformation, respectively, with increased binding strength in both complexes. Our study implies except binding interface, both conformation ensemble and kinetics should be considered for the effects of phosphorylation on IDPs.
AbbreviationsIDPs
intrinsically disordered proteins
REMDreplica exchange molecular dynamics
MSMMarkov state model
TADtransactivation domain
PHpleckstrin homology
PRRproline-rich region
DBDDNA-binding domain
TETTetramerization domain
REGregulatory domain
MDmolecular dynamics
PMEparticle-mesh Ewald
TICAtime-lagged independent component analysis
CKChapman–Kolmogorov
GMRQgeneralized matrix Rayleigh quotient
SARWself-avoiding random walk
KIDkinase-inducible domain
MFPTmean first passage time
DSSPdefinition of secondary structure of proteins
RMSDroot mean square deviation
Rgradius of gyration
Reeend to end distance

intrinsically disordered proteins
replica exchange molecular dynamics
Markov state model
transactivation domain
pleckstrin homology
proline-rich region
DNA-binding domain
Tetramerization domain
regulatory domain
molecular dynamics
particle-mesh Ewald
time-lagged independent component analysis
Chapman–Kolmogorov
generalized matrix Rayleigh quotient
self-avoiding random walk
kinase-inducible domain
mean first passage time
definition of secondary structure of proteins
root mean square deviation
radius of gyration
end to end distance
Communicated by Ramaswamy H. Sarma