Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison.

Ellen Rieloff,Marie Skepö

doi:10.3390/ijms221810174

Abstract

Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14–43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with experimental size estimates for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest separation between positively charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a reduction of the salt-bridging probability in the CHARMM36m simulations, implying that salt concentration has negligible effects in this study.

Highlights

Disordered proteins (IDPs) are characterized by a lack of a tertiary structure under physiological conditions [1,2], which means that they are better described by an ensemble of different conformations than a single structure
We recently showed that while the commonly used force fields CHARMM36m and Amber ff99SB-ILDN+TIP4P-D accurately captured the global dimensions of the 15-residue-long N-terminal fragment of Statherin in the nonphosphorylated state, it overestimated the compactness in the phosphorylated state [20]
In Tau1, the salt bridges pT175–K174 and pT181-K180 were formed without much effect on the overall conformation; an additional salt bridge between the N-terminus and pT175 decreased Rg and the end-to-end distance (Ree) and radius of gyration (Rg) in C36

Summary

Introduction

Disordered proteins (IDPs) are characterized by a lack of a tertiary structure under physiological conditions [1,2], which means that they are better described by an ensemble of different conformations than a single structure. This is reflected in their free energy landscapes, which normally are rather flat without a deep energy minimum as for globular proteins [3]. In proteins such as statherin and caseins, the phosphorylated residues are essential for their ability to bind to the tooth surface [6,7] or sequester calcium [8]

Methods

Results

Conclusion