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Photo Marie Skepö

Marie Skepö

Professor

Photo Marie Skepö

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

Author

  • Ellen Rieloff
  • Marie Skepö

Summary, in English

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.

Department/s

  • Computational Chemistry
  • LINXS - Institute of advanced Neutron and X-ray Science
  • eSSENCE: The e-Science Collaboration

Publishing year

2021-09

Language

English

Publication/Series

International Journal of Molecular Sciences

Volume

22

Issue

18

Document type

Journal article

Publisher

MDPI AG

Topic

  • Theoretical Chemistry (including Computational Chemistry)

Keywords

  • Force fields
  • Intrinsically disordered proteins
  • Phosphorylation

Status

Published

ISBN/ISSN/Other

  • ISSN: 1661-6596