- 學位論文
以分子動力學模擬探討上皮角蛋白K5/K14之分子結構組裝及力學性質
Molecular Structure and Nanomechanical Properties of Human Epithelial Keratin K5/K14 Using Atomistic Simulation
摘要
上皮角蛋白是一種中間絲蛋白。它是維持人體最大器官皮膚表皮中細胞核穩定性的關鍵因素之一。它會吸收水分並承受外部壓力，從而影響皮膚的結構穩定性和機械性能。人的皮膚角蛋白由I型和II型角蛋白組成，通過鏈內氫鍵和鏈間的疏水作用能穩定地形成螺旋狀捲曲螺旋結構。K5/K14為本研究所探討的一種上皮角蛋白，關於此角蛋白的序列變異導致的遺傳疾病為遺傳性表皮分解水泡症，為普遍被大眾知道的泡泡龍疾病。根據文獻提出的角蛋白中間絲的組裝模型，在上皮角蛋白的結構之1B-1B區域之間旋鈕-口袋(Knob-Pocket)的交互作用會影響水平方向的組裝。另一方面發現在2B-2B結構域之間的ID1 接觸與中間絲的延長有關。目前X射線衍射實驗無法獲得全長中間絲的結構，因此不能全盤了解中間絲的組裝方式。本研究通過已知的蛋白質序列構建了完整的人體上皮角蛋白，應用全原子模型建構出角蛋白中間絲的模型並透過分子動力學模擬討論在1B以及2B結構域中二聚體及四聚體間的結構和氫鍵關係，以及透過拉伸分子動力學模擬獲得其力學特性，並且討論不同點位的錯義基因突變與其角蛋白組裝力學性質之間的相關性。我們發現在序列上不同位置的點突變會以不同方式影響1B區域的截斷四聚體結構，而對於2B區域相同位置的點突變並不一定影響異二聚體的結構，反之導致在四聚體的組裝差異。最後我們的結果與最新的實驗觀察結果進行進一步比較，連結基因造成的結構缺陷在分子尺寸上對於整體角蛋白中間絲的組裝情形以及力學性質的影響。
並列摘要
Epithelial keratin is an intermediate filament protein. It is one of the key factors to maintain the stability of the nucleus in the epidermis of the skin. It absorbs water and withstand external pressure, which affects the structural stability and mechanical properties of the skin. Human skin keratin is basically composed of one type I and one type II keratin, which can stably form a coiled-coil structure through the hydrogen bond and hydrophobic interaction of the core. K5/K14 is a kind of epithelial keratin discussed in this study. The genetic disease related to this keratin is Epidermolysis bullosa simplex. According to the previously proposed assembly model of keratin intermediate filaments, the knob-pocket interaction between 1B and 1B domains will affect the horizontal assembly. On the other hand, it is found that the ID1 contact between the 2B and 2B domains is related to the elongation of the intermediate filament. The crystal structure of keratin protein has not been fully resolved yet, so it is not possible to fully understand the assembly of the intermediate filament. Therefore, in this study, a complete human epithelial keratin is constructed through the known protein sequence, and the mechanics and assembly analysis of the intermediate filament were carried out. The full-atom molecular dynamics simulation is applied in this study. We discuss the structure and hydrogen bond relationship between dimers and tetramers in the 1B and 2B domains, as well as the mechanical properties obtained by steered molecular dynamics simulation and also discussed the gene mutations and keratin assembly mechanics at different positions. We further compare our results with the latest experimental measurements and discuss the relationship between the genotype of EBS disease and the atomic-level mutated structure.