Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

By Chi W. Pak, Martyna Kosno, Alex S. Holehouse, S. Padrick, A. Mittal, Rustam Ali, A. Yunus, David R. Liu, Rohit V. Pappu, M. Rosen. Molecules and Cells, 2016

727 citations recorded by the source corpus.

Summary Liquid-liquid phase separation, driven by collective interactions among multivalent and intrinsically disordered proteins, is thought to mediate the formation of membrane-less organelles in cells. Using parallel cellular and in vitro assays we show that the Nephrin intracellular domain (NICD), a disordered protein, drives intracellular phase separation via complex coacervation, whereby the negatively charged NICD co-assembles with positively charged partners to form protein-rich dense liquid droplets. Mutagenesis reveals that the driving force for phase separation depends on the overall amino acid composition and not the precise sequence of NICD. Instead, phase separation is promoted by one or more regions of high negative charge density and aromatic/hydrophobic residues that are distributed across the protein. Many disordered proteins share similar sequence characteristics with NICD, suggesting that complex coacervation may be a widely used mechanism to promote intracellular phase separation.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4106287ad1a508784259cedbb67a49fc00700c53

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Citations in the corpus

CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins (2017, methodology): “The utility of an analysis package such as localCIDER comes from the ability to combine local and global sequence analysis with additional classiﬁcation tools and statistical methods to enable rapid, customized high-throughput analysis pipelines (26).”
Protein Phase Separation: A New Phase in Cell Biology (2018, background): “Additionally, disrupting alternating charge blocks [49,53] and mutating key residues in degenerate repeats [39,46] can also perturb phase separation.”
Liquid phase condensation in cell physiology and disease (2017, background): “resulting in the formation of liquid-like droplets (42).”
Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity (2017, neutral): “Low-complexity domains are well-established targets of post-translational modifications (Martin et al , 2016), and their sequences specify homotypic and heterotypic et al , 2015; Pak et al , 2016).”
Stress-triggered phase separation is an adaptive, evolutionarily tuned response (2017, background): “, 2014), charge-patch interactions (Pak et al., 2016) between multivalent RRMs enhanced by pH-modulated histidine protonation, and limited conformational change collaborate to cause phase separation.”
Pi-Pi contacts are an overlooked protein feature relevant to phase separation (2018, background): “While experimental data and computational work suggest other contributions (Yeo et al., 2011; Pak et al., 2016; Nott et al., 2015; Lin et al., 2016; Kim et al., 2016; Brangwynne et al., 2015), including the hydrophobic effect, electrostatics and multivalent binding of folded protein domains, our…”
Sequence determinants of protein phase behavior from a coarse-grained model (2017, background): “Multivalency has been shown to be important in driving LLPS in experiment [20, 35], in 415 which proteins with more repeated units begin to form droplets at lower concentrations.”
Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins (2016, methodology): “Such IDP phase behaviors are sequence-dependent [30,36] and may be regulated posttranslationally such as by phosphorylation of germ plasm component proteins in P granules [29] and by arginine methylation of Ddx4N1 organelles [30].”
Distinct stages in stress granule assembly and disassembly (2016, background): “This model is supported by observations in vitro wherein high concentrations of IDRs are sufficient to spontaneously form LLPS possibly through the interplay of weak electrostatic and hydrophobic homo- and heterotypic protein-protein interactions (Lin et al., 2015; Molliex et al., 2015; Murakami et ”
Intrinsically disordered regions contribute promiscuous interactions to RNP granule assembly (2017, background): “Scrambling these charges across the length of an IDR has been observed to impair LLPS both in vitro and in vivo (Nott et al., 2015; Pak et al., 2016).”
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins (2018, positive): “The role of tyrosine and arginine residues in driving phase separation of FUS family proteins provides support for recent studies that highlight the importance of cation-p interactions as drivers of phase separation (Nott et al., 2015; Pak et al., 2016; Lee et al., 2016; Boeynaems et al., 2017).”