IDR
Several intrinsically disordered domains (IDRs) have been found to provide weak promiscuous interactions that can drive condensation of chimeric fusion proteins.
Commonly used IDRs include prion-like domains (PrLDs), cationic domains, or domains of alternating charge blocks.
IDRs are used both in vitro and in cells.
PROS:
+ common molecular grammar
+ compatible with endogenous MLO clients
+ material properties tunable
CONS:
- potential interference with endogenous MLOs
- generally requires nucleation domain
Example IDR sequences:
>FUS_PrLD (Wang et al., 2018)
MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPSYGGQQQSYGQQQSYNPPQGYGQQNQYNSSSGGGGGGGGGGNYGQDQSSMSSGGGSGGGYGNQDQSGGGGSGGYGQQDRGGRGRGGSGGGGGGGGGGYNRSSGGY
>TDP-43_PrLD (Schmidt et al., 2019)
FGGNPGGFGNQGGFGNSRGGGAGLGNNQGSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSS
>FLOE1_PrLD (Dorone et al., 2020)
HQIAPQPQVQPQPQPQQHQYYMPPPPTQLQNTPAPVPVSTPPSQLQAPPAQSQFMPPPPAPSHPSSAQTQSFPQYQQNWPPQPQARPQSSGGYPTYSPAPPGNQPPVESLPSSMQMQSPYSGPPQQSMQAYGYGAAPPPQAPPQQTKMSYSPQTGDGYLPSGPPPPSGYANAMYEGGRMQYPPPQPQQQQQQAHYLQGPQGG
GYSPQPHQAGGGNI
>polyPR (Boeynaems et al., 2018)
PRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPRPR
>DDX4_IDR (Nott et al., 2015)
MGDEDWEAEINPHMSSYVPIFEKDRYSGENGDNFNRTPASSSEMDDGPSRRDHFMKSGFASGRNFGNRDAGECNKRDNTSTMGGFGVGKSFGNRGFSNSRFEDGDSSGFWRESSNDCEDNPTRNRGFSKRGGYRDGNNSEASGPYRRGGRGSFRGCRGGFGLGSPNNDLDPDECMQRTGGLFGSRRPVLSGTGNGDTSQSRSGSGSERGGYKGLNEEVITGSGKNSWKSEAEGGES
How to tune IDR phase properties according to the sticker-spacer framework?
There are four ways on how to tune the phase diagram and/or material properties of IDR-based condensates. For the sake of illustration we will focus on prion-like IDRs.
Prion-like IDRs share sequence similarity with yeast prions (Alberti et al., 2009), which are naturally prone to phase separation and aggregation. The stickers in these domains are predominantly aromatic residues, but may include charged residues as well. Polar residues and glycine often serve as spacers.
1. Number of stickers: Simply increasing or decreasing the number of stickers has been shown to respectively decrease/increase the IDR saturation concentration. Additionally, differences in the number of stickers can make the condensates more gel-like or more liquid (Wang et al., 2018; Dorone et al., 2020). Commonly used approaches are changing the IDR length, or making specific sticker mutants (e.g., tyrosine-serine substitutions).
2. Sticker strength: Amino acid residues of the same class may have differential "stickiness" (Wang et al., 2018; Dorone et al., 2020).
Aromatic: tryptophan > tyrosine > phenylalanine
Basic: arginine > lysine
Aliphatic: methionine > (iso)leucine > valine
3: Sticker spacing: By playing with the spacing between stickers one can alter the material properties of IDRs. For example, reducing the spacing between aromatic stickers has been shown to drive gelation of PrLDs (Martin et al., 2020).
4: Spacer identity: Different spacers may promote more solid-like material properties of condensates. These include glutamine, serine and alanine (Wang et al., 2018).