Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis.
Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis.
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DOI：
10.7554/elife.76090
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发表时间：
2022-05-17
期刊：
影响因子：
7.7
通讯作者：
Steiner, Harald
中科院分区：
文献类型：
--
作者：
Feilen, Lukas P.;Chen, Shu-Yu;Fukumori, Akio;Feederle, Regina;Zacharias, Martin;Steiner, Harald
膜内蛋白酶对脂双层中膜蛋白的切割对于健康和疾病至关重要。虽然不同的脂质环境可以有效地调节它们的活性，但这与它们的结构动力学之间的联系尚不清楚。在这里，我们表明，羧肽酶样活性的古细菌膜内蛋白酶PSH，阿尔茨海默氏病相关的早老素/γ-分泌酶的同系物是受损的胶束和促进脂质双层。比较分子动力学模拟表明，重要的元素，如跨膜结构域6a的PSH底物结合更不稳定的胶束和稳定的脂质双层。此外，与PSH与过渡态类似物抑制剂的增强相互作用一致，双层促进了酶的催化活性位点几何形状的形成。我们的数据表明，膜内蛋白酶的脂质环境在酶-底物复合物的结构稳定和活性位点排列中起着关键作用，从而促进膜内蛋白水解。将蛋白质切割成碎片是细胞中的一个关键过程，允许几个重要过程发生，包括细胞分化（允许细胞发育成特定类型），细胞死亡，蛋白质质量控制，甚至蛋白质在细胞中的位置。然而，执行这一任务的专门蛋白质，称为蛋白酶，也可能参与疾病的发展。例如，在大脑中，一种称为γ-分泌酶的蛋白酶切割淀粉样β蛋白前体，产生被广泛认为是导致阿尔茨海默病的有毒形式的淀粉样β肽。像γ-分泌酶这样的蛋白酶在膜中发挥作用，膜是形成细胞外边界的脂肪层（也称为脂质）。细胞这一区域的环境可以影响蛋白酶的活性，但人们对这是如何发生的知之甚少。解决这个问题的一种方法是将γ-分泌酶在膜的脂质环境中的活性与其完全被不同分子（如去污剂分子）包围时的活性进行比较。不幸的是，当γ-分泌酶被去污剂从其脂质环境中除去时，它没有活性，使得难以进行这种比较。为了克服这个问题，Feilen等人选择研究PSH，这是一种类似于γ-分泌酶的蛋白酶，可以产生相同的淀粉样β肽，但在洗涤剂中保持活性。当Feilen等人将PSH与膜中发现的脂质分子和淀粉样蛋白-β前体蛋白混合时，PSH产生淀粉样蛋白-β肽，包括那些被认为导致阿尔茨海默氏症的肽。然而，当洗涤剂取代脂质分子时，这导致淀粉样β肽比通常更长，表明PSH不能有效地切割蛋白质。环境的变化似乎降低了PSH从肽中逐渐修剪小片段的能力。对脂质与洗涤剂中蛋白酶结构的计算机建模支持了实验结果：该模型预测，与洗涤剂相比，对识别和切割其他蛋白质很重要的PSH区域在膜中更稳定。这些结果表明，细胞膜在这种环境中裂解的蛋白酶活性区的稳定性中起着至关重要的作用。在未来，这可能有助于更好地了解膜中脂质分子的变化如何影响γ-分泌酶的活性及其在阿尔茨海默病中的作用。
Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here, we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer’s disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme’s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis. Cutting proteins into pieces is a crucial process in the cell, allowing several important processes to take place, including cell differentiation (which allows cells to develop into specific types), cell death, protein quality control, or even where in the cell a protein will end up. However, the specialized proteins that carry out this task, known as proteases, can also be involved in the development of disease. For example, in the brain, a protease called γ-secretase cuts up the amyloid-β protein precursor, producing toxic forms of amyloid-β peptides that are widely believed to cause Alzheimer’s disease. Proteases like γ-secretase carry out their role in the membrane, the layer of fats (also known as lipids) that forms the outer boundary of the cell. The environment in this area of the cell can influence the activity of proteases, but it is poorly understood how this happens. One way to address this question would be to compare the activity of γ-secretase in the lipid environment of the membrane to its activity when it is entirely surrounded by different molecules, such as detergent molecules. Unfortunately, γ-secretase is not active when it is removed from its lipid environment by a detergent, making it difficult to perform this comparison. To overcome this issue, Feilen et al. chose to study PSH, a protease similar to γ-secretase that produces the same amyloid-β peptides but remains active in detergent. When Feilen et al. mixed PSH with lipid molecules like those found in the membrane and amyloid-β precursor protein, PSH produced amyloid-β peptides including those that are thought to cause Alzheimer’s. However, when a detergent was substituted for the lipid molecules this led to longer amyloid-β peptides than usual, indicating that PSH was not able to cut proteins as effectively. The change in environment appeared to reduce PSH’s ability to progressively trim small segments from the peptides. Computer modelling of the protease’s structure in lipids versus detergent supported the experimental findings: the model predicted that the areas of PSH important for recognizing and cutting other proteins would be more stable in the membrane compared to the detergent. These results indicate that the cell membrane plays a vital role in the stability of the active regions of proteases that are cleaving in this environment. In the future, this could help to better understand how changes to the lipid molecules in the membrane may contribute to the activity of γ-secretase and its role in Alzheimer’s disease.