PDF(Pubmed)
Abstract：
Inositol-requiring enzyme 1 (IRE1) is a transmembrane sensor that is part of a trio of sensors responsible for controlling the unfolded protein response within the endoplasmic reticulum (ER). Upon the accumulation of unfolded or misfolded proteins in the ER, IRE1 becomes activated and initiates the cleavage of a 26-nucleotide intron from human X-box-containing protein 1 (XBP1). The cleavage is mediated by the RtcB ligase enzyme, which splices together two exons, resulting in the formation of the spliced isoform XBP1s. The XBP1s isoform activates the transcription of genes involved in ER-associated degradation to maintain cellular homeostasis. The catalytic activity of RtcB is controlled by the phosphorylation and dephosphorylation of three tyrosine residues (Y306, Y316, and Y475), which are regulated by the ABL1 tyrosine kinase and PTP1B phosphatase, respectively. This study focuses on investigating the mechanism by which the PTP1B phosphatase activates the RtcB ligase using a range of advanced in silico methods. Protein-protein docking identified key interacting residues between RtcB and PTP1B. Notably, the phosphorylated Tyr306 formed hydrogen bonds and salt bridge interactions with the \"gatekeeper\" residues Arg47 and Lys120 of the inactive PTP1B. Classical molecular dynamics simulation emphasized the crucial role of Asp181 in the activation of PTP1B, driving the conformational change from an open to a closed state of the WPD-loop. Furthermore, QM/MM-MD simulations provided insights into the free energy landscape of the dephosphorylation reaction mechanism of RtcB, which is mediated by the PTP1B phosphatase.
摘要：
需要肌醇的酶1（IRE1）是跨膜传感器，是负责控制内质网（ER）内未折叠蛋白质反应的三重奏传感器的一部分。在内质网中积累未折叠或错误折叠的蛋白质时，IRE1被激活并启动来自含有人X盒的蛋白质1（XBP1）的26个核苷酸的内含子的切割。切割是由RtcB连接酶介导的，将两个外显子拼接在一起，导致剪接的同工型XBP1s的形成。XBP1s同种型激活参与ER相关降解的基因的转录以维持细胞稳态。RtcB的催化活性受三个酪氨酸残基（Y306，Y316和Y475）的磷酸化和去磷酸化控制，由ABL1酪氨酸激酶和PTP1B磷酸酶调节，分别。本研究的重点是使用一系列先进的计算机模拟方法研究PTP1B磷酸酶激活RtcB连接酶的机制。蛋白质-蛋白质对接鉴定了RtcB和PTP1B之间的关键相互作用残基。值得注意的是,磷酸化Tyr306与无活性PTP1B的“看门人”残基Arg47和Lys120形成氢键和盐桥相互作用。经典的分子动力学模拟强调了Asp181在PTP1B活化中的关键作用,驱动构象变化从WPD环的开放状态到闭合状态。此外，QM/MM-MD模拟提供了对RtcB去磷酸化反应机制的自由能景观的见解，由PTP1B磷酸酶介导。
