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

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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.