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

Abstract

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.AbbreviationsIDPsintrinsically disordered proteinsREMDreplica exchange molecular dynamicsMSMMarkov state modelTADtransactivation domainPHpleckstrin homologyPRRproline-rich regionDBDDNA-binding domainTETTetramerization domainREGregulatory domainMDmolecular dynamicsPMEparticle-mesh EwaldTICAtime-lagged independent component analysisCKChapman–KolmogorovGMRQgeneralized matrix Rayleigh quotientSARWself-avoiding random walkKIDkinase-inducible domainMFPTmean first passage timeDSSPdefinition of secondary structure of proteinsRMSDroot mean square deviationRgradius of gyrationReeend to end distanceCommunicated by Ramaswamy H. Sarma