Molecular Dynamics Simulations to Investigate the Thermal Unfolding Behaviors of the Tetramerization Domain of Shaker and Kv1.1 Potassium Channels

以分子動態模擬研究Shaker及Kv1.1鉀離子通道中T1 domain的受熱反摺疊行為

陳錦文(Chin-Wen Chen) ； 林進中(Jin-Chung Lin) ； 劉宣良(Hsuan-Liang Liu)

《Journal of the Chinese Institute of Chemical Engineers》 36卷6期 (2005/11) Pp. 649-660

https://doi.org/10.6967/JCICE.200511.0649

摘要

我們先前的研究利用Shake鉀離子通道T1 domain的X-射線繞射結晶結構作為模板，成功地建構真核生物Kv1.1-Kvl.6鉀離子通道的T1 domain結構模型。結果顯示Shake T1 domain和Kv通道之T1 domain有非常相似的摺疊構形。在本研究中，我們利用分子動態模擬預測Shake及Kv1.1 T1 domain在不同溫度下的動態行為。結果顯示，Shaker T1 domain在所有實驗溫度下的穩定性都比Kv1.1 T1 domain佳。另外，Shaker T1 domain開始發生瓦解的區域位於layer3。相較之下，layer 1及2有較佳的穩定性，那是因為layer 1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。Shake T1 domain中的Ile121在瓦解第4及第5螺旋之間的loop結構時扮演重要的角色。在熱瓦解模擬中，我們發現Ala120、Ile121、Leu122、Leu131以及Leu151將會形成新的疏水性作用力，導致破壞T1 domain中layer 2及3間的原始作用力。

並列摘要

In our previous study, a set of homology models of the tetramerization (T1) domain of six eukaryotic potassium channels Kv1.1-Kv1.6 from Homo Sapiens was constructed based on the crystal structure of the Shaker T1 domain from Aplysia californica. The results reveal that the T1 domains of these Kv channels exhibit similar folds as those of Shaker K(superscript +) channel. In this study, several molecular dynamics (MD) 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 Kvl.1 T1 domain at all temperatures examined. In addition, the thermal unfolding of the Shaker T1 domain begins at layer 3. In contrast, layers land 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 A1a120, Ile12l, Leu122, Leu13l, 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 ； Molecular dynamics simulations ； Thermal unfolding