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Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome
bioRxiv - Biochemistry Pub Date : 2020-07-28 , DOI: 10.1101/2020.07.27.223107
Sylvain D. Vallet , Martin N. Davis , Anna Barqué , Sylvie Ricard-Blum , Alexandra Naba

The extracellular matrix (ECM) protein SNED1 has been shown to promote breast cancer metastasis and control neural crest cell-specific craniofacial development, but the cellular and molecular mechanisms by which it does so remain unknown. ECM proteins exert their functions by binding to cell surface receptors, sequestering growth factors, and interacting with other ECM proteins, actions that can be predicted using knowledge of protein’s sequence, structure and post-translational modifications. Here, we combined in-silico and in-vitro approaches to characterize the physico-chemical properties of SNED1 and infer its putative functions. To do so, we established a mammalian cell system to produce and purify SNED1 and its N-terminal fragment, which contains a NIDO domain. We have determined experimentally SNED1’s potential to be glycosylated, phosphorylated, and incorporated into insoluble ECM produced by cells. In addition, we used biophysical and computational methods to determine the secondary and tertiary structures of SNED1 and its N-terminal fragment. The tentative ab-initio model we built of SNED1 suggests that it is an elongated protein presumably able to bind multiple partners. Using computational predictions, we identified 114 proteins as putative SNED1 interactors. Pathway analysis of the newly-predicted SNED1 interactome further revealed that binding partners of SNED1 contribute to signaling through cell surface receptors, such as integrins, and participate in the regulation of ECM organization and developmental processes. Altogether, we provide a wealth of information on an understudied yet important ECM protein with the potential to decipher its functions in physiology and diseases.

中文翻译:

新型ECM糖蛋白SNED1的计算和实验表征及其相互作用组的预测

细胞外基质(ECM)蛋白SNED1已被证明可促进乳腺癌转移并控制神经c细胞特异性颅面发育,但其细胞和分子机制尚不清楚。ECM蛋白质通过与细胞表面受体结合,隔离生长因子并与其他ECM蛋白质相互作用来发挥其功能,这些作用可以通过了解蛋白质的序列,结构和翻译后修饰来预测。在这里,我们结合了计算机内体外表征SNED1的理化性质并推断其推定功能的方法。为此,我们建立了一个哺乳动物细胞系统来生产和纯化SNED1及其N端片段,其中包含NIDO域。我们已经通过实验确定了SNED1被糖基化,磷酸化并整合到细胞产生的不溶性ECM中的潜力。此外,我们使用生物物理和计算方法来确定SNED1及其N端片段的二级和三级结构。暂定的从头开始我们基于SNED1构建的模型表明它是一种细长的蛋白,大概能够结合多个伴侣。使用计算预测,我们确定了114种蛋白质作为推定的SNED1相互作用因子。对新预测的SNED1相互作用组的路径分析进一步表明,SNED1的结合伴侣通过细胞表面受体(例如整合素)有助于信号传导,并参与ECM组织和发育过程的调控。总而言之,我们提供了关于尚未被研究但仍很重要的ECM蛋白的大量信息,这些信息可能会破译其在生理学和疾病中的功能。
更新日期:2020-07-30
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