(607f) A Coarse-Grained Model to Elucidate the Regulation of Protein Phase Behavior By Post Translational Modifications

Perdikari, T. M., Brown University
Dignon, G. L., Lehigh University
Mittal, J., Lehigh University
Fawzi, N., Brown University
Proteins can undergo liquid-liquid phase separation (LLPS), a physicochemical process that stimulates the generation of high local concentrations of multicomponent protein-RNA complexes in cells, known as biocondensates. Enriching the repertoire of the 20 natural amino acids through post-translational modifications (PTMs) can change the electrochemical properties of the sequences and unlock new modes of inter-protein interactions that can either enable or disrupt the phase-separation of multicomponent granules[1]. Although recent advances in synthetic chemistry have enabled the study of PTMs in-vitro[2], these strategies are often limited by the inability to generate homogeneously modified samples. Therefore, there exists a critical need to develop a transferable approach to investigate the phase separation of proteins and the assembly of biocondensates under the influence of PTMs.

Here, we expand upon our amino acid resolution coarse-grained model[3] to represent the biomolecular interactions exerted among non-canonical, and post-translationally modified amino acids in order to investigate how the position and the number of post-translationally modified sites can alter the phase behavior of proteins. To do so, we use a slab-geometry molecular dynamics method to calculate the phase diagram [3]. We investigate the most-frequently occurring post-translational modifications seen in the modulation of LLPS, including phosphorylation, methylation, acetylation and ubiquitination. Being in agreement with experimental observations[4], our model is able to capture that arginine dimethylation of hnRNPA2 protein decreases the phase separation whereas tyrosine phosphorylation causes a drop in the critical temperature, thus enhancing phase separation.

[1] Monahan, Zachary, et al. "Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity." The EMBO journal 36.20 (2017): 2951-2967.

[2] Chin, Jason W. "Expanding and reprogramming the genetic code." Nature 550.7674 (2017): 53.

[3] Dignon, Gregory L., et al. "Sequence determinants of protein phase behavior from a coarse-grained model." PLoS computational biology 14.1 (2018): e1005941.

[4] Ryan, Veronica H., et al. "Mechanistic view of hnRNPA2 low-complexity domain structure, interactions, and phase separation altered by mutation and arginine methylation." Molecular cell 69.3 (2018): 465-479.