Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
IMPMC - UMR 7590, CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
BMC Mol Cell Biol. 2022 Sep 10;23(1):39. doi: 10.1186/s12860-022-00437-2.
The AAA + ATPase p97 is an essential unfoldase/segragase involved in a multitude of cellular processes. It functions as a molecular machine critical for protein homeostasis, homotypic membrane fusion events and organelle biogenesis during mitosis in which it acts in concert with cofactors p47 and p37. Cofactors assist p97 in extracting and unfolding protein substrates through ATP hydrolysis. In contrast to other p97's cofactors, p37 uniquely increases the ATPase activity of p97. Disease-causing mutations in p97, including mutations that cause neurodegenerative diseases, increase cofactor association with its N-domain, ATPase activity and improper substrate processing. Upregulation of p97 has also been observed in various cancers. This study aims towards the characterization of the protein-protein interaction between p97 and p37 at the atomic level. We defined the interacting residues in p97 and p37. The knowledge will facilitate the design of unique small molecules inhibiting this interaction with insights into cancer therapy and drug design.
The homology model of human p37 UBX domain was built from the X-ray crystal structure of p47 C-terminus from rat (PDB code:1S3S, G) as a template and assessed by model validation analysis. According to the HDOCK, HAWKDOCK, MM-GBSA binding free energy calculations and Arpeggio, we found that there are several hydrophobic and two hydrogen-bonding interactions between p37 UBX and p97 N-D1 domain. Residues of p37 UBX predicted to be involved in the interactions with p97 N-D1 domain interface are highly conserved among UBX cofactors.
This study provides a reliable structural insight into the p37-p97 complex binding sites at the atomic level though molecular docking coupled with molecular dynamics simulation. This can guide the rational design of small molecule drugs for inhibiting mutant p97 activity.
AAA+ATPase p97 是一种必需的展开酶/分离酶，参与多种细胞过程。它作为一种分子机器，对于蛋白质的动态平衡、同源膜融合事件和有丝分裂期间的细胞器发生至关重要，在此期间，它与辅助因子 p47 和 p37 协同作用。辅助因子通过 ATP 水解协助 p97 提取和展开蛋白底物。与其他 p97 的辅助因子不同，p37 独特地增加了 p97 的 ATP 酶活性。p97 的致病突变，包括导致神经退行性疾病的突变，增加了辅助因子与其 N 结构域、ATP 酶活性和不当底物加工的结合。在各种癌症中也观察到 p97 的上调。本研究旨在从原子水平上描述 p97 和 p37 之间的蛋白质-蛋白质相互作用。我们确定了 p97 和 p37 中的相互作用残基。这一知识将有助于设计独特的小分子抑制剂，通过对癌症治疗和药物设计的深入了解来抑制这种相互作用。
从大鼠 p47 C 末端的 X 射线晶体结构（PDB 代码：1S3S，G）构建了人 p37 UBX 结构域的同源模型，并通过模型验证分析进行了评估。根据 HDOCK、HAWKDOCK、MM-GBSA 结合自由能计算和 Arpeggio，我们发现 p37 UBX 与 p97 N-D1 结构域之间存在几个疏水相互作用和两个氢键相互作用。预测参与 p37 UBX 与 p97 N-D1 结构域界面相互作用的残基在 UBX 辅助因子中高度保守。
通过分子对接结合分子动力学模拟，本研究从原子水平上提供了 p37-p97 复合物结合位点的可靠结构见解。这可以指导抑制突变 p97 活性的小分子药物的合理设计。
