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arXiv 2001.06542physics.bio-phcond-mat.soft
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蛋白液滴形成的有限尺寸标度分析

Finite-size scaling analysis of protein droplet formation

Daniel Nilsson, Anders Irbäck

备注：
18 pages, 8 figures, to appear in Physical Review E
发表信息：
Phys. Rev. E 101, 022413 (2020)
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摘要：

细胞内生物分子凝聚体的形成通常涉及固有无序蛋白质（IDP），并且这些IDP中的几种还能够通过液-液相分离在其自身上形成液滴状致密组装体。当模拟热力学相变时，众所周知，有限尺寸标度分析可以是有价值的工具。然而，据我们所知，这种方法还没有被应用到具有挑战性的问题，建模序列依赖性的生物分子相分离的计算。在这里，我们实施有限尺寸标度方法来研究连续疏水/极性蛋白质模型中两个10-珠序列的相行为。结合可逆的显链蒙特卡罗模拟这些序列，有限尺寸标度分析证明是可行的和有益的，尽管依赖于渐近大系统的理论结果。虽然这两个序列在低温下形成致密的簇，但该分析表明，它们中只有一个经历液-液相分离。此外，在液滴形成设置的转变温度，观察到收敛缓慢与系统的大小，因此，即使对于我们最大的系统的转变是由约8%的移位。使用有限尺寸标度分析，可以估计和校正这种偏移。

英文摘要：

The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase separation. When modelings thermodynamic phase changes, it is well-known that finite-size scaling analysis can be a valuable tool. However, to our knowledge, this approach has not been applied before to the computationally challenging problem of modeling sequence-dependent biomolecular phase separation. Here, we implement finite-size scaling methods to investigate the phase behavior of two 10-bead sequences in a continuous hydrophobic/polar protein model. Combined with reversible explicit-chain Monte Carlo simulations of these sequences, finite-size scaling analysis turns out to be both feasible and rewarding, despite relying on theoretical results for asymptotically large systems. While both sequences form dense clusters at low temperature, this analysis shows that only one of them undergoes liquid-liquid phase separation. Furthermore, the transition temperature at which droplet formation sets in, is observed to converge slowly with system size, so that even for our largest systems the transition is shifted by about 8%. Using finite-size scaling analysis, this shift can be estimated and corrected for.

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