Abstract
Liquid–liquid phase separation (LLPS) of some IDPs/IDRs can lead to the formation of the membraneless organelles in vitro and in vivo, which are essential for many biological processes in the cell. Here we select three different IDR segments of chaperon Swc5 and develop a polymeric slab model at the residue-level. By performing the molecular dynamics simulations, LLPS can be observed at low temperatures even without charge interactions and disappear at high temperatures. Both the sequence length and the charge pattern of the Swc5 segments can influence the critical temperature of LLPS. The results suggest that the effects of the electrostatic interactions on the LLPS behaviors can change significantly with the ratios and distributions of the charged residues, especially the sequence charge decoration (SCD) values. In addition, three different forms of swc conformation can be distinguished on the phase diagram, which is different from the conventional behavior of the free IDP/IDR. Both the packed form (the condensed-phase) and the dispersed form (the dilute-phase) of swc chains are found to be coexisted when LLPS occurs. They change to the fully-spread form at high temperatures. These findings will be helpful for the investigation of the IDP/IDR ensemble behaviors as well as the fundamental mechanism of the LLPS process in bio-systems.
Highlights
In living cells, there is one special kind of organelles which are lack of the enclosing membrane
The membraneless organelles caused by liquid–liquid phase separation (LLPS) of Intrinsically disordered proteins (IDPs)/ intrinsically disordered regions (IDRs) are involved in a wide range of biological functions such as RNA processing, ribosome biogenesis, and sequestration of mRNA, proteins, and compacted chromatin
We focus on the histone H2A-H2B binding partner, Swc5 and investigate the effects of the temperature, sequence length and number of charged residues on the LLPS behaviors
Summary
There is one special kind of organelles which are lack of the enclosing membrane. They are named as membraneless organelles (MLOs) [1,2,3], such as nucleoli, stress granules, P bodies, pericentriolar material and germ granules [3,4,5,6]. LLPS can be found in the solution of one or more kinds of proteins, proteins and RNAs mixture, proteins with crowders in vitro [11] One class of these proteins is the folded proteins with multivalent interactions, including the signaling protein WASP [8]; the other class is the proteins with intrinsically disordered regions (IDRs), such as FUS [12], TDP-43 [13], hnRNPA1/hnRNPA2 [6, 14], Ddx4 [2], LAF-1 [15], etc. Protein sequence is important for the properties of LLPS
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