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In plant cells, proteins marked with ubiquitin are degraded via the ESCRT machinery. This process is tightly regulated, for instance by ubiquitylating and deubiquitylating enzymes. One of these is OTU11, a deubiquitylating enzyme found in Arabidopsis thaliana [1]. Proteomics studies have identified six phosphorylation sites on the N-terminal frame of OTU11. Posttranslational modifications like phosphorylation can have variant effects on the function of proteins. To better understand these effects, the influence on the conformational ensemble of the respective proteins needs to be understood. We are interested in the impact of the phosphorylation on the structural stability of OTU11. Therefore we study the protein’s dynamics with a combined all-atom and coarse-grained approach. We performed the molecular dynamics (MD) simulations using the GROMACS engine version 2024.4. [2] For the all-atom reference dataset we performed in total 12 simulations of 1 µs (timestep: 2 fs) length started from the same starting configuration of a single solvated OTU11 protein. To improve our coarse-grained model of OTU11 we perfomed multiple coarse-grained MD simulations with varying lengths up to 20 µs (timestep: 20 fs).
[1] K. Vogel, et al. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat. Commun. 2022, 13, 1, 6897. https://doi.org/10.1038/s41467-022-34637-3
[2] M. J. Abraham, et al. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX. 2015, 1, 19-25. https://doi.org/10.1016/j.softx.2015.06.001