Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose an innovative computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We apply it to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction. We find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence: the critical temperature can be enhanced by increasing the frequency of hydrophobic and aromatic residues, by changing the charge patterning, or by a combination of both. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the composition of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.

中文翻译：

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通过氨基酸序列的进化有针对性地调节蛋白质液-液相分离

合理而有效地修饰蛋白质的氨基酸序列以控制其按需进行液-液相分离（LLPS）的能力不仅是非常理想的，而且还可以帮助阐明哪些蛋白质特征对于LLPS很重要。在这里，我们提出了一种创新的计算方法，该方法将遗传算法与依赖于序列的粗粒蛋白质模型相结合，以发展相分离的固有无序蛋白质区域（IDR）的氨基酸序列，并有目的地增强或抑制它们的能力。相分离的。我们将其应用于三种天然存在的蛋白质（即FUS，hnRNPA1和LAF1）的相分离IDR，作为存在于细胞中并经历由不同类型的分子间相互作用驱动的同型LLPS的区域的原型。我们发现，在这三种情况中，除其他因素外，氨基酸序列向增强的LLPS的进化是由氨基酸平均大小的增加驱动的。但是，增强LLPS（例如疏水性，芳香性和电荷）的分子驱动力的变化方向取决于初始氨基酸序列：可以通过增加疏水性和芳香族残基的频率来提高临界温度。电荷图案化，或两者结合。最后，我们表明调节LLPS的氨基酸序列的进化与培养基的组成（例如RNA的存在或不存在）紧密相关，这可能对我们对多组分内相分离的理解具有重要意义。生物系统的混合物。