(747b) Role of Secondary Structure in Protein Liquid-Liquid Phase Separation Highlighted By a New Coarse-Grained Model | AIChE

(747b) Role of Secondary Structure in Protein Liquid-Liquid Phase Separation Highlighted By a New Coarse-Grained Model


Jovic, N. - Presenter, Lehigh University
Dignon, G. L., Lehigh University
Kim, Y. C., Naval Research Laboratory
Zheng, W., Arizona State University
Liquid-liquid phase separation (LLPS) has emerged as an important driving force in the formation of membraneless organelles [1]. In the recent years intrinsically disordered proteins (IDPs), have emerged as a major contributor to membraneless organelle formation [2]. Investigating the role of secondary structure on LLPS can be troublesome using experiments alone, due to the difficulty in obtaining structural properties as well as investigating the role of mutants in helix breaking or secondary structure stabilization. Due to computational efficiency, coarse-grained (CG) models can be used to directly simulate large liquid-like assemblies of proteins.

We present an extension to our original CG model [3], which now incorporates pseudo angle and pseudo dihedral potentials parametrized using experimental data and allows us to quantitatively capture the helical propensity. We show that the alpha helical and the PPII fractions obtained using CG simulations follow both the trend and the magnitude of the experimental NMR results. Using TDP-43 as a model system, we demonstrate the ability of this model to faithfully capture the role of secondary structure in LLPS. Particularly, we focus on the existence of a cooperative alpha helical region between the residues 331-340 [4], and show that designed, or ALS-related mutations in this region alter the local helical content, and LLPS of the full sequence.

[1] Brangwynne, Clifford P., et al. "Germline P granules are liquid droplets that localize by controlled dissolution/condensation." Science 324.5935 (2009): 1729-1732.

[2] Uversky, Vladimir N., et al. "Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates." FEBS letters 589.1 (2015): 15-22.

[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] Conicella, Alexander E., et al. "ALS mutations disrupt phase separation mediated by α-helical structure in the TDP-43 low-complexity C-terminal domain." Structure 24.9 (2016): 1537-1549.