Competition between Intramolecular Hydrogen Bonds and Solvation in Phosphorylated Peptides:  Simulations with Explicit and Implicit Solvent

Abstract

The atomic-level mechanisms of protein regulation by post-translational phosphorylation remain poorly understood, except in a few well-studied systems. Molecular mechanics simulations can in principle be used to help understand and predict the effects of protein phosphorylation, but the accuracy of the results will of course depend on the quality of the force field parameters for the phosphorylated residues as well as the quality of the solvent model. The phosphorylated residues typically carry a -2 charge at physiological pH; however, the effects of phosphorylation can sometimes be mimicked by substituting Asp or Glu for the phosphorylated residue. Here we examine the suitability of explicit and implicit solvent models for simulating phospho-serine in both the -1 and -2 charge states. Specifically, we simulate a capped phosphorylated peptide, Ace-Gly-Ser-pSer-Ser-Nme, and compare the results to each other and to experimental observables from an NMR experiment. The first major conclusion is that explicit water models (TIP3P, TIP4P and SPC/E) and a Generalized Born implicit solvent model provide reasonable agreement with the experimental observables, given appropriate partial charges for the phosphate group. The Generalized Born results, however, show greater hydrogen bonding propensity than the explicit solvent results. Distance dependent dielectric treatments perform poorly. The second major conclusion is that many ensemble-averaged properties obtained for the phosphopeptide in the -1 and -2 charge states are strikingly similar; the -1 species has a slightly higher propensity to form internal hydrogen bonds. All of the results can be rationalized by quantifying the strength of the P-O/H-N hydrogen bond, which depends on a sensitive balance between strongly favorable charge/dipole and dipole/dipole interactions and strongly unfavorable desolvation.

Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation

“…The atomic partial charges for the phosphorylated amino acid side chains were adjusted slightly from the default values by performing quantum chemistry calculations. The partial charges for phosphoserine (pSer) and phosphothreonine (pThr) were taken from previous work by Wong et al [65], whereas charges for phosphotyrosine (pTyr) and phosphoaspartate (pAsp) were determined in their À2 and À1 charge states by performing quantum mechanical calculations with the software program Jaguar [66]. Methyl-benzyl-phosphate was used to represent the pTyr side chain, and acetyl phosphate was used for pAsp.…”

Multisite Phosphorylation Disrupts Arginine-Glutamate Salt Bridge Networks Required for Binding of Cytoplasmic Linker-associated Protein 2 (CLASP2) to End-binding Protein 1 (EB1)

“…To further elucidate the mechanism by which phosphorylation regulates CLASP2-EB1 binding, we performed in silico molecular dynamics simulations of the same SKIP peptide as used in the in vitro binding experiments. Starting from an extended conformation, multiple independent 40 -50-ns molecular dynamics simulations of either the non-phosphorylated or triple-phosphorylated peptide were carried out in explicit solvent, which yields good agreement with experimental results for phosphopeptide simulations (38). Although the simulation of disordered proteins in explicit solvent suffers from a potential under-sampling problem, the simulations did explore a sufficiently large conformational space to allow interactions between arginine and phosphoserine side chains.…”

Elastic deformation and failure in protein filament bundles: Atomistic simulations and coarse-grained modeling

“…The Nose-Hoover thermostat [31] was used to allow sampling from the canonical ensemble, and the GBSW implicit solvent model [32] was used to approximate energetic effects of water. GBSW has been shown to agree well with Poisson-Boltzmann solvers [33] and with experimental observables [34].…”