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

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


Perdikari, T. M. - Presenter, Brown University
Dignon, G. L., 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.