Table1_Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs.DOCX

Ubiquitin is a small protein at the heart of many cellular processes, and several different protein domains are known to recognize and bind ubiquitin. A common motif for interaction with ubiquitin is the Ubiquitin Interacting Motif (UIM), characterized by a conserved sequence signature and often found in multi-domain proteins. Multi-domain proteins with intrinsically disordered regions mediate interactions with multiple partners, orchestrating diverse pathways. Short linear motifs for binding are often embedded in these disordered regions and play crucial roles in modulating protein function. In this work, we investigated the structural propensities of UIMs using molecular dynamics simulations and NMR chemical shifts. Despite the structural portrait depicted by X-crystallography of stable helical structures, we show that UIMs feature both helical and intrinsically disordered conformations. Our results shed light on a new class of disordered UIMs. This group is here exemplified by the C-terminal domain of one isoform of ataxin-3 and a group of ubiquitin-specific proteases. Intriguingly, UIMs not only bind ubiquitin. They can be a recruitment point for other interactors, such as parkin and the heat shock protein Hsc70-4. Disordered UIMs can provide versatility and new functions to the client proteins, opening new directions for research on their interactome.泛素（Ubiquitin）是一类核心参与诸多细胞进程的小分子蛋白质，目前已发现多种不同的蛋白质结构域（protein domain）能够识别并结合泛素。介导泛素结合的常见基序为泛素相互作用基序（Ubiquitin Interacting Motif, UIM），其具有保守的序列特征，且常存在于多结构域蛋白质中。带有内在无序区域（intrinsically disordered region）的多结构域蛋白质可介导与多种互作伴侣的相互作用，协同调控多样化的细胞通路。用于结合的短线性基序（short linear motif）通常嵌入于这类无序区域中，在调控蛋白质功能方面发挥关键作用。本研究利用分子动力学模拟（molecular dynamics simulation）与核磁共振化学位移（NMR chemical shift），探究了UIM的结构倾向性。尽管此前X射线晶体学（X-crystallography）揭示的UIM结构为稳定的螺旋构象，但本研究表明，UIM同时兼具螺旋构象与内在无序构象。本研究结果揭示了一类全新的无序UIM，该类无序UIM以共济失调蛋白3（ataxin-3）某一亚型的C端结构域，以及一组泛素特异性蛋白酶（ubiquitin-specific protease）作为代表范例。值得注意的是，UIM并非仅能结合泛素，还可作为招募其他互作分子的位点，例如帕金蛋白（parkin）与热休克蛋白Hsc70-4。无序UIM可为其靶蛋白赋予多功能性与全新功能，为相关互作组（interactome）的研究开辟了新方向。