Molecular dynamics simulations of phosphorylated intrinsically disordered proteins: A force field comparison

Research output: Contribution to journalArticlepeer-review

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 phospho-rylation, 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.

Original languageEnglish
Article number10174
JournalInternational Journal of Molecular Sciences
Volume22
Issue number18
DOIs
Publication statusPublished - 2021 Sep

Bibliographical note

Funding Information:
Funding: Financial support was given by the Royal Physiographic Society in Lund and the Bertil Andersson foundation.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Subject classification (UKÄ)

  • Theoretical Chemistry

Keywords

  • Force fields
  • Intrinsically disordered proteins
  • Phosphorylation

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