Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins.

ABSTRACT

Phosphorylation of proteins plays an important regulatory role at almost all levels of cellular organization. Molecular dynamics (MD) simulation is a promising tool to reveal the mechanism of how phosphorylation regulates many key biological processes at the atomistic level. MD simulation accuracy depends on force field precision, while the current force fields for phospho-amino acids have resulted in notable inconsistency with experimental data. Here, a new force field parameter (named FB18CMAP) is generated by fitting against quantum mechanics (QM) energy in aqueous solution with φ/ψ dihedral potential-energy surfaces optimized using CMAP parameters. MD simulations of phosphorylated dipeptides, intrinsically disordered proteins (IDPs), and ordered (folded) proteins show that FB18CMAP can mimic NMR observables and structural characteristics of phosphorylated dipeptides and proteins more accurately than the FB18 force field. These findings suggest that FB18CMAP performs well in both the simulation of ordered and disordered states of phosphorylated proteins.