Molecular mechanism of the sea anemone toxin ShK recognizing the Kv1.3 channel explored by docking and molecular dynamic simulations
Molecular mechanism of the sea anemone toxin ShK recognizing the Kv1.3 channel explored by docking and molecular dynamic simulations
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DOI：
10.1021/ci700178w
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发表时间：
2007-09-01
影响因子：
5.6
通讯作者：
Wu, Yingliang
中科院分区：
文献类型：
--
作者：
Jin, Ling;Wu, Yingliang
用计算方法模拟了海葵毒素ShK与小鼠电压门控钾通道Kv13.3的相互作用。为了提高ZDOCK刚性蛋白质对接的性能，考虑了蛋白质数据库中所有可用的20种ShK结构。通过聚类分析、专家知识筛选、能量最小化和分子动力学模拟，在大量预测的络合物中获得了传统的和新颖的结合模式。通过500ps分子动力学模拟和计算丙氨酸扫描技术结合自由能的变化，进一步评价了所得络合物的质量和有效性，以确定有利的络合物结构。通过使用Lys22残基封闭通道孔，发现了新颖合理的ShK-Kv1.3复合体结构与传统模型不同。从得到的ShK-Kv1.3复合体的结构来看，ShK主要将通道外前庭与其第二螺旋段联系在一起。结构分析首先发现ShK多肽的Lys22残基侧链仅悬挂在Kv 1.3通道的C和D链之间，而不是物理上堵塞通道孔。ShK Ser20Ala和Tyr23Ala突变体与Kv1.3通道结合能力的明显丧失是由构象变化引起的。ShK中的Arg24与Kv1.3中的H404(A)和d402(D)之间的5个氢键使Arg24成为与Kv1.3通道结合最关键的氢键。除了ShK与Kv1.3在原子水平上的详细相互作用外，ShK肽与Kv1.3通道相互作用引起的显著构象变化，伴随着结合自由能的逐渐降低，强烈暗示ShK肽与Kv1.3通道的结合是一个构象重排和能量稳定的动态过程。所有这些都可以加速ShK结构免疫抑制剂的发展。
Computational methods are employed to simulate the interaction of the sea anemone toxin ShK in complex with the voltage-gated potassium channel Kvl.3 from mice. All of the available 20 structures of ShK in the Protein Data Bank were considered for improving the performance of the rigid protein docking of ZDOCK. The traditional and novel binding modes were obtained among a large number of predicted complexes by using clustering analysis, screening with expert knowledge, energy minimization, and molecular dynamic simulations. The quality and validity of the resulting complexes were further evaluated to identify a favorable complex structure, by 500 ps molecular dynamic simulations and the change of binding free energies with a computational alanine scanning technique. The novel and reasonable ShK-Kv1.3 complex structure was found to be different from the traditional model by using the Lys22 residue to block the channel pore. From the resulting structure of the ShK-Kv1.3 complex, ShK mainly associates the channel outer vestibule with its second helical segment. Structural analysis first revealed that the Lys22 residue side chain of the ShK peptide just hangs between C and D chains of the Kv 1.3 channel instead of physically blocking the channel pore. The obvious loss of the ShK Ser20Ala and Tyr23Ala mutant binding ability to the Kv1.3 channel is caused by the conformational change. The five hydrogen bonds between Arg24 in ShK and H404(A) and D402(D) in Kv1.3 make Arg24 the most crucial for its binding to the Kv1.3 channel. Besides the detailed interaction between ShK and Kv 1.3 at the atom level, the significant conformational change induced by the interaction between the ShK peptide and the Kv1.3 channel, accompanied by the gradual decrease of binding free energies, strongly implies that the binding of the ShK peptide toward the Kv1.3 channel is a dynamic process of conformational rearrangement and energy stabilization. All of these can accelerate the development of ShK structure-based immunosuppressants.