Saar Daniel, Lennartsson Caroline L E, Weidner Philip, Burgermeister Elke, Kragelund Birthe B
REPIN, University of Copenhagen, Copenhagen, Denmark.
The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Proteins. 2025 Apr;93(4):831-854. doi: 10.1002/prot.26774. Epub 2024 Nov 30.
Intrinsically disordered regions (IDRs) of proteins remain understudied with enigmatic sequence features relevant to their functions. Members of the myotubularin-related protein (MTMR) family contain uncharacterized IDRs. After decades of research on their phosphatase activity, recent work on the C-terminal IDRs of MTMR7 revealed new interactions and important new functions beyond the phosphatase function. Here we take a broader look at the C-terminal domains (CTDs) of 14 human MTMRs and use bioinformatic tools and biophysical methods to ask which other functions may be probable in this protein family. The predictions show that the CTDs are disordered and carry short linear motifs (SLiMs) important for targeting of MTMRs to defined subcellular compartments and implicating them in signaling, phase separation, interaction with diverse proteins, including transcription factors and are of relevance for cancer research and neuroscience. We also present experimental methods to study the CTDs and use them to characterize the coiled coil (CC) domains of MTMR7 and MTMR9. We show homo- and hetero-oligomerization with preference for MTMR7-CC to form dimers, while MTMR9-CC forms trimers. We relate the results to sequence features and make predictions for the structural landscape of other MTMRs. Our work gives a broad insight into the so far unrecognized features and SLiMs in MTMR-CTDs, and provides the basis for more in-depth experimental research on this diverse protein family and understudied IDRs in proteins in general.
蛋白质的内在无序区域（IDRs）仍未得到充分研究，其与功能相关的序列特征也很神秘。肌管素相关蛋白（MTMR）家族的成员含有未被表征的IDRs。在对其磷酸酶活性进行了数十年的研究之后，最近关于MTMR7 C端IDRs的研究揭示了磷酸酶功能之外的新相互作用和重要新功能。在这里，我们更广泛地研究了14种人类MTMR的C端结构域（CTDs），并使用生物信息学工具和生物物理方法来探究这个蛋白质家族中可能存在的其他功能。预测结果表明，CTDs是无序的，并带有短线性基序（SLiMs），这些基序对于将MTMR靶向特定的亚细胞区室很重要，并使它们参与信号传导、相分离、与多种蛋白质（包括转录因子）的相互作用，这与癌症研究和神经科学相关。我们还介绍了研究CTDs的实验方法，并使用这些方法来表征MTMR7和MTMR9的卷曲螺旋（CC）结构域。我们展示了MTMR7-CC和MTMR9-CC的同源和异源寡聚化，MTMR7-CC更倾向于形成二聚体，而MTMR9-CC形成三聚体。我们将结果与序列特征相关联，并对其他MTMR的结构格局进行预测。我们的工作深入揭示了MTMR-CTDs中迄今未被认识的特征和SLiMs，并为对这个多样化的蛋白质家族以及一般蛋白质中未充分研究的IDRs进行更深入的实验研究提供了基础。
