Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a potential drug target. Its binding partners carry a short linear motif (SLiM) known as the PCNA-interacting protein-box (PIP-box), but sequence-divergent motifs have been reported to bind to the same binding pocket. To investigate how PCNA accommodates motif diversity, we assembled a set of 77 experimentally confirmed PCNA-binding proteins and analyzed features underlying their binding affinity. Combining NMR spectroscopy, affinity measurements and computational analyses, we corroborate that most PCNA-binding motifs reside in intrinsically disordered regions, that structure preformation is unrelated to affinity, and that the sequence-patterns that encode binding affinity extend substantially beyond the boundaries of the PIP-box. Our systematic multidisciplinary approach expands current views on PCNA interactions and reveals that the PIP-box affinity can be modulated over four orders of magnitude by positive charges in the flanking regions. Including the flanking regions as part of the motif is expected to have broad implications, particularly for interpretation of disease-causing mutations and drug-design, targeting DNA-replication and -repair.

中文翻译：

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重新审视了PCNA交互主题：在PIP盒子外面思考。

增殖细胞核抗原（PCNA）是DNA代谢的细胞中心，也是潜在的药物靶标。它的结合伴侣带有一个短的线性基序（SLiM），称为PCNA相互作用蛋白盒（PIP-box），但是据报道序列有差异的基序可以与相同的结合袋结合。为了研究PCNA如何适应基序多样性，我们组装了77个实验确认的PCNA结合蛋白，并分析了其结合亲和力的特征。结合NMR光谱学，亲和力测量和计算分析，我们证实大多数PCNA结合基序位于本质上无序的区域中，结构的形成与亲和力无关，并且编码结合亲和力的序列模式基本上超出了PIP的边界-盒子。我们系统的多学科方法扩展了当前对PCNA相互作用的看法，并揭示了PIP-box亲和力可以通过侧翼区域中的正电荷在四个数量级上进行调节。预期将侧翼区域作为基序的一部分将具有广泛的意义，特别是对于以DNA复制和修复为目标的致病突变和药物设计的解释。