Background: In addition to classical membranebound organelles, such as mitochondria and the Golgi apparatus, a variety of membraneless bodies harboring high concentrations of proteins and RNAs can be found in the nucleus, cytoplasm and on membranes of eukaryotic cells. Research over the past decade has revealed that many of these membraneless bodies, also known as biomolecular condensates, show liquid-like properties and form by liquid liquid phase separation . Their formation is driven by multivalent protein-protein or protein-RNA interactions, which often involve intrinsically disordered proteins (IDPs). Importantly, in several cases, similar droplets have been reconstituted in vitro using only one or two protein components. This approach can provide valuable insight into the molecular features behind the formation of intracellular condensates. However, for a full understanding of the forces and sequence features that drive these processes, there is a need for computational modeling.
This project: The aim of this project is to investigate the mechanisms of IDP phase separation by means of Monte Carlo simulations, based on an all-atom protein representation with an implicit solvent force field. The simulations will be carried out using our existing program PROFASI . Recently, we used this program to study the somewhat related problem of peptide folding in crowded environments [3,4]. The present project can be divided into two main parts:
(i) Force field development for IDPs. The force field used in PROFASI was originally developed through studies of folded peptides and proteins, at a time when limited data on IDPs were available. The force field is now being refined, to ensure a good description of IDPs. To this end, simulation data are compared against experimental data on IDPs relating to secondary-structure propensities and chain extension (primarily NMR and SAXS).
(ii) Investigation of IDPs that are involved in intracellular phase separation and have been shown to phase separate in vitro. Two well-known examples of such IDPs are the N-terminal regions of FUS and DDX4 with ~150 and ~250 residues, respectively . Using the above-mentioned model, the self-interaction of these IDPs will be investigated, to gain insight into the forces driving their phase separation. To this end, systems with up to 5-10 chains will be simulated. A long-term goal is to use these results to build fast, yet accurate coarse-grained models that permit the simulation of liquid condensation in larger systems.
1. For a review, see Y. Shin and C.P. Brangwynne, Liquid phase condensation in cell physiology and disease, Science 357, 1253 (2017).
2. A. Irbäck and S. Mohanty. PROFASI: A Monte Carlo simulation package for protein folding and aggregation. J. Comput. Chem. 27, 1548 (2006).
3. A. Bille, S. Mohanty and A. Irbäck. Peptide folding in the presence of interacting protein crowders. J. Chem. Phys. 144, 175105 (2016).
4. D. Nilsson, S. Mohanty and A. Irbäck. Markov modeling of peptide folding in the presence of protein crowders. J. Chem. Phys. 148, 055101 (2018).