電壓驅動型鉀離子通道Kv1.1-Kv1.6中T1 Domain之同源模型及分子動態模擬研究

Homology Models and Molecular Dynamics Simulations of the Tetramerization Domain of Voltage-Gated Potassium Channels Kv1.1-Kv1.6

陳錦文(Chin-Wen Chen)

指導教授 ： 劉宣良

國立臺北科技大學/工程學院/生物科技研究所/碩士(2005年)

https://doi.org/10.6841/NTUT.2005.00039

摘要

本研究利用Shaker鉀離子通道中T1 domain的結晶結構以及同源模擬技術架構真核生物鉀離子通道Kv1.1-Kv1.6之T1 domain的結構模型。根據胺基酸序列比對的結果指出鉀離子通道中T1 domain的守恆性相當高，在比較之後發現Shaker和Kv1.1的相似度僅為77%，而Kv1.6和Kv1.1及Kv1.2的相似度高達93%。藉由同源模型發現Kv和Shaker鉀離子通道中T1 domain具有相似的摺疊。這些模型顯示出T1 domain的單體在結構上可分為三層：第一層位於N端的細胞質側，而第三層位於C端的細胞膜側。針對每一個Kv通道，都是由四個相同的次單位所構成，並且藉由15個高度守恆的極性殘基間的氫鍵及鹽橋作用聚集成四聚體。在Shaker的T1 domain中，其孔洞最狹窄的地方由四個守恆的殘基Arg115所構成，而且這些同源性模型對於結構學上的研究將可以提供最詳細的結構資訊。
在1ns動態模擬過程中發現，結果顯示Shaker T1 domain和利用同源模擬技術架構出來的Kv通道之T1 domain有非常相似的摺疊構形。在本次的實驗裡，我們將利用分子動態模擬技術去預測Shaker及Kv1.1 T1 domain在不同溫度下的動態行為。我们的結果顯示，Shaker T1 domain在所有的溫度下的穩定性比Kv1.1 T1 domain佳。另外，Shaker T1 domain開始發生瓦解的區域位於layer 3。相較之下，layer 1及2有較佳的穩定性，那是因為layer1有較多的氫鍵作用力來維持其結構的穩定性而layer 2則位於高度守恆性的疏水性核心。Shaker T1 domain中的Ile121扮演重要的角色去瓦解螺旋4及5之間的loop結構。在熱瓦解模擬中，我们發現Ala120、Ile121、Leu122、Leu131以及Leu151將會形成新的疏水性作用力進而破壞T1 domain中layer2及3間的原始作用力。

關鍵字

T1 domain ； 鉀離子通道 ； 胺基酸序列比對 ； 同源模擬 ； 氫鍵 ； 鹽橋 ； 分子動態模擬 ； 熱瓦解

並列摘要

The homology models of the tetramerization (T1) domain of six eukaryotic potassium channels, Kv1.1-Kv1.6, were constructed based on the crystal structure of the Shaker T1 domain. The results of amino acid sequence alignment indicate that the T1 domains of these K+ channels are highly conserved, with the similarities varying from 77 % between Shaker and Kv1.6 to 93 % between Kv1.2 and Kv1.3. The homology models reveal that the T1 domains of these Kv channels exhibit similar folds as those of Shaker K+ channel. These models also show that each T1 monomer consists of three distinct layers, with N-terminal layer 1 and C-terminal layer 3 facing the cytoplasm and the membrane, respectively. Layer 2 exhibits the highest structural conservation because it is located around the central hydrophobic core. For each Kv channel, four identical subunits assemble into the homotetramer architecture around a four-fold axis through the hydrogen bonds and salt bridges formed by 15 highly conserved polar residues. The narrowest opening of the pore is formed by the four conserved residues corresponding to R115 of the Shaker T1 domain. The homology models of these Kv T1 domains provide particularly attractive targets for further structure-based studies.
Several molecular dynamics simulations towards the Shaker and Kv1.1 T1 domains were conducted at various temperatures. Our results show that the Shaker T1 domain exhibit higher structural integrity than the Kv1.1 T1 domain at all temperatures examined. In addition, the thermal unfolding of the Shaker T1 domain begins at layer 3. In contrast, layers 1and 2 exhibit higher structural stability because layer 1 remains more hydrogen bonding interactions at elevated temperatures and layer 2 is located in the highly conserved hydrophobic core. Ile121 in the Shaker T1 domain plays an important role in disrupting the loop between helices 4 and 5. During the thermal unfolding process, the newly formed hydrophobic interactions between Ala120, Ile121, Leu122, Leu131, and Leu151 may distort the native contact between layers 2 and 3 of the T1 domain.

並列關鍵字

tetramerization (T1) domain ； potassium channel ； amino acid sequence alignment ； homology ； hydrogen bond ； salt bridge ； molecular dynamics simulation ； thermal unfolding

參考文獻

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