Piezo蛋白質家族的活化機制

Abstract

Piezo family為存在於哺乳類動物的蛋白質家族。主要包含兩類蛋白質：Piezo1與Piezo2。該蛋白質家族為鈣離子通道蛋白，鑲嵌於於細胞膜上。當細胞膜受一定大小之張力時，Piezo1與Piezo2的arm會由彎曲狀態轉為伸直扁平的狀態，因而提供足夠張力促使鈣離子通道由關閉狀態轉為開啟狀態。此過程稱為力活化。 近年來雖已有人使用超高速原子力顯微鏡、分子動態模擬等方法提出了Piezo1的力活化機制，並在奈米（nm）層級下Piezo1的力活化機制已清楚掌握，但解析度上還不夠精確。此外，在蛋白質資料庫中，並無力活化狀態下的Piezo1與Piezo2蛋白質構型。而模擬相關文獻並不能提出一個符合自然與實驗狀態下受張力影響的完整Piezo1力活化構型。 因此，本實驗目的即為利用分子動態模擬與ANM（anisotropic normal mode）等模擬方法模擬符合實驗情形下完整的力活化狀態Piezo family結構並比較其差異。另外，我們也創立一種圖形理論相關分群演算法PIROsaction搭配PRS（perturb response simulation）來比較Piezo1與Piezo2在異位調控上的差異，並檢附PIROsaction在社群網路上的應用，包含如何搭配人工智慧做分群。 實驗結果方面，我們一再確認Piezo2的力活化比Piezo1還要來得強烈。此外，PIROsaction搭配PRS（perturb response simulation）結果方面，我們發現比單純使用PRS（perturb response simulation）更能偵測Piezo1的異位調控完整位置（THU8~THU9）。另外，綜合所有結果分析，我們得知Piezo1傾向使用末端arm（THU1~THU3）與中端arm（THU4~THU6）做劇烈伸張運動促使pore開；而Piezo2只需使用末端arm（THU1~THU3）即可促使pore開。

Piezo family, which is a protein family, exists in mammals. It includes two types of proteins – Piezo1 and Piezo2. It is also a type of calcium gated ion channels imbedded in cell membrane. When the force acts on cell membrane enough, the arms of Pieoz1 and Piezo2 will be changed from curve shape to flatten and stretching shape. Hence, calcium gated ion channel will open from close state to open state by arms’ stretching force. This process is called mechanogating. In recent years, many scientists use high speed atomic force microscopy and molecular dynamics to offer the mechanism of Piezo1 mechanogating. Even though the mechanism of Piezo1 mechanogating at Nano-meter scale is well known, the resolution is not enough. Besides, the protein database has no open state proteins of Piezo1 and Piezo2. The simulation articles can’t also get the proper and nature states of activated and intact Piezo1. Hence, the goal of our research is using molecular dynamics and ANM (anisotropic normal mode) to simulate the open state and intact proteins of Piezo family at molecular scale (Åm), which meet with experimental result. Moreover, we develop graph theory algorithm – PIROsaction, which is local partitioning algorithm, to compare the mechanogating of Piezo1 and Piezo2 with PRS (perturb response simulation) method. We also append some social network applications of PIROsaction, including how to go with Artificial intelligence. In our result, we confirm that the mechanogating effect of Piezo2 is stronger than Piezo1. Otherwise, using PIROsaction with PRS (perturb response simulation) can determine more intact allosteric site of Piezo1 (THU8~THU9) in contrast to PRS (perturb response simulation). Besides, for all analysis, we conclude that Piezo1 prepher to use terminal arm (THU1~THU3) and middle arm (THU4~THU6) to vibrate and stretch fiercely to open the pore, but Piezo2 only need terminal arm to do so.