Molecular Level Details of Compositional and Domain Dependence in Assembly and Condensate Formation of Intrinsically Disordered Proteins

Abstract

Intrinsically disordered proteins (IDPs), which lack a stable tertiary structure, have emerged as a significant player in the formation of membraneless organelles (MLOs) which include nucleoli, stress granules, processing bodies and have been found to be involved in neurodegenerative diseases such as ALS, Alzheimer’s, dementia as well as biological functions such as DNA repair and cellular signaling. We study how different disordered domains as well as binding partners affect phase separation ability of Fused in Sarcoma (FUS), a RNA and DNA binding protein that regulates transcription, splicing and mRNA transport and show compositional. FUS has been implicated into neurodegenerative diseases such as diseases amyotrophic lateral sclerosis and frontotemporal dementia. We study the impacts of carefully selected mutations shown to be of high interest in perturbing the phase behavior of in the intrinsically disordered low complexity domain of FUS. We explore the role different interaction modes play in stabilizing the condensed phase and the contributions of individual residue types to atomic interaction modes. We show how these mutations affect protein partitioning in the condensed phase and probe difference in inter and intra-molecular interactions accounting for the abundance of an amino acid in the protein sequence to highlight the intrinsic contact propensity of amino acids. We also study compositional features of another class of IDPs, resilin-like polypeptides (RLPs) and could enable control of their liquid-liquid phase separation (LLPS). Evaluation of the phase separation of RLPs in solutions of ammonium sulfate offers insights into the sequence-dependent LLPS of the RLP solutions, and atomistic simulations, along with experimental techniques, suggest specific amino acid interactions that may mediate this phase behavior. Finally, we elucidate the role of phosphorylation on assembly of HP1ɑ (Heterochromatin Protein 1), a protein found in the heterochromatin complex responsible for compaction and silencing of genetic material within the genome. By using a transferable physics based coarse grained (CG)model we are able to propose a mechanism of assembly suggesting that competition between different disordered domains is responsible for the observed phase behavior. These results should pave the way for a greater understanding of sequence determinants of protein phase separation.