A COMBINED COMPUTATIONAL AND PHYSIOLOGICAL STUDY ON THE LIGAND-GATING IN CNG AN

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 CAMP和cGMP是两个重要的细胞内第二信使，介导着广泛的细胞过程。除了直接激活蛋白激酶，cAMP和cGMP还通过直接与环核苷酸门控(CNG)和超极化激活阳离子(HCN)通道的环核苷酸结合域(CNBD)结合来调节几种类型的离子通道的功能。这些离子通道在人类的感觉、心血管和中枢神经系统中发挥着重要作用。每个通道亚基包含一个六跨膜结构域，在C末端有一个CNBD，在其间有一个连接区。正如大家所注意到的，最近发表的离子通道相关结构揭示了对通道功能的许多机械性见解。然而，来自静态图片的信息总是有限的。通道相关结构的可获得性和最近计算方法的改进为将实验和理论技术相结合来研究通道蛋白功能的性质创造了绝佳的机会。目前，我们一直在应用分子动力学模拟和自由能计算来解释生理数据，得到了一些关于环核苷酸与HCN通道结合域结合的有趣结果。研究中使用了GROMACS、VMD、APBS、MOLARIS等用于分子动力学模拟和能量计算的模拟软件。此外，基于同源蛋白结构，包括Kv1.2的跨膜区和HCN2的CNBD，构建CNG和HCN通道的完整通道结构，以更深入地了解门控机制，特别是与配体结合相关的构象变化以及配体门控与电压门控通路的耦合。我们相信，分配适当的计算时间将极大地促进当前对CNG和HCN通道蛋白生物物理性质的研究。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. cAMP and cGMP are two important intracellular second messengers mediating a wide range of cellular processes. Other than direct activating protein kinases, cAMP and cGMP also modulate the function of several types of ion channels through the direct binding to the intracellular cyclic-nucleotide binding domain (CNBD) of cyclic-nucleotide gated (CNG) and hyperpolarization-activated cation (HCN) channels. These ion channels play important roles in the human sensory, cardiovascular and central nervous systems. Each channel subunit contains a six-transmembrane domain, a CNBD in the C-terminus and a linker region in between. As everyone noticed, recently published ion channel related structures have revealed so much mechanistic insights into the channel function. However, the information from a static picture is always limited. The availability of channel-related structures and the recent improvement in computational methodologies create a prefect opportunity to combine the experimental and theoretical techniques to study the nature of channel protein function. Currently, we have been applying molecular dynamics simulation and free energy calculations to interpret the physiological data and got some interesting results about the binding of cyclic-nucleotides to the binding domain of HCN channel. Several simulation packages for MD simulation and energetic calculations, such as GROMACS, VMD, APBS, MOLARIS etc., are involved in the research. Furthermore, it is also interesting to build the whole channel structures for CNG and HCN channels, based on the homologous protein structures, including the transmembrane domain of Kv1.2 and the CNBD of HCN2, to gain more insights into the gating mechanisms, especially the conformation changes related to ligand binding and the coupling of ligand-gating to voltage-gating pathways. We believe that the allocation of appropriate amount of computational time would facilitate the current research of the biophysical properties of the CNG and HCN channel proteins dramatically.