Cells harbour numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein- and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids, resulting in demixing via liquid–liquid phase separation. Proteins harbouring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modelling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.

细胞拥有许多中尺度无膜室，这些室容纳特定的生化过程并执行不同的细胞功能。这些富含蛋白质和RNA的体被认为是通过蛋白质和核酸之间的多价相互作用形成的，从而通过液-液相分离产生分层。含有本质无序区域（IDR）的蛋白质在无膜细胞器中占主导地位。然而，尚不清楚 IDR 序列是否可以单独决定不同凝聚相的形成。我们鉴定了一对 IDR，当在细胞中表达时能够形成空间上不同的凝聚物。当在体外重构时，这些模型蛋白不会共分配，这表明缩合特异性直接编码在多肽序列中。通过计算建模和诱变，我们确定了控制指导选择性缩合的同型和异型相互作用的氨基酸和链特性。这些结果构成了物理化学原理的基础，可以指导 IDR 的亚细胞组织形成特定的凝聚物，并揭示可以指导正交无膜室构建的 IDR 代码。