Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters

被引:92
作者
Das, Suman [1 ]
Amin, Alan N. [1 ]
Lin, Yi-Hsuan [1 ,2 ]
Chan, Hue Sun [1 ,3 ]
机构
[1] Univ Toronto, Dept Biochem, Med Sci Bldg 5th Fl,1 Kings Coll Circle, Toronto, ON M5S 1A8, Canada
[2] Hosp Sick Children, Mol Med, Toronto, ON M5G 0A4, Canada
[3] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada
基金
加拿大自然科学与工程研究理事会; 加拿大健康研究院;
关键词
LIQUID PHASE-SEPARATION; MOLECULAR-DYNAMICS SIMULATIONS; HYDROPHOBIC INTERACTIONS; INTRINSIC DISORDER; FORCE-FIELD; GRANULES; BEHAVIOR; BINDING; COACERVATION; EQUILIBRIA;
D O I
10.1039/c8cp05095c
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Biomolecular condensates undergirded by phase separations of proteins and nucleic acids serve crucial biological functions. To gain physical insights into their genetic basis, we study how liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) depends on their sequence charge patterns using a continuum Langevin chain model wherein each amino acid residue is represented by a single bead. Charge patterns are characterized by the blockiness measure and the sequence charge decoration (SCD) parameter. Consistent with random phase approximation (RPA) theory and lattice simulations, LLPS propensity as characterized by critical temperature T-cr* increases with increasingly negative SCD for a set of sequences showing a positive correlation between and -SCD. Relative to RPA, the simulated sequence-dependent variation in T-cr* is oftenthough not alwayssmaller, whereas the simulated critical volume fractions are higher. However, for a set of sequences exhibiting an anti-correlation between and -SCD, the simulated T-cr*'s are quite insensitive to either parameter. Additionally, we find that blocky sequences that allow for strong electrostatic repulsion can lead to coexistence curves with upward concavity as stipulated by RPA, but the LLPS propensity of a strictly alternating charge sequence was likely overestimated by RPA and lattice models because interchain stabilization of this sequence requires spatial alignments that are difficult to achieve in real space. These results help delineate the utility and limitations of the charge pattern parameters and of RPA, pointing to further efforts necessary for rationalizing the newly observed subtleties.
引用
收藏
页码:28558 / 28574
页数:17
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