A Dynamic Approach to Targeting Acid-Sensing Ion Channels: Computational simulations reveal key residues in ASICs

The current molecular dynamics (MD) research project employs virtual model building as a tool in elucidating the functions associated with key calcium binding sites of acid-sensing ion channels (ASICs). These integral membrane proteins, with neuronal proton-sensitive channels associated with pain and central nervous system diseases, represent novel therapeutic targets for these diseases. ASIC1 and ASIC3 are two subtypes of ASICs with highly conserved channel “pore” sequences, but play different roles in the development of hyperalgesia after inflammatory muscle injury. It has been proposed that the removal of calcium continues to allow the ASIC3 channel to open, but this is not the case for ASIC1. The objective of this project is to identify key residues responsible for the distinct gating mechanisms of ASIC1 and ASIC3, utilizing MD simulations. Model building through software, CHARMM-GUI membrane builder program, utilizing the RCSB-PDB (4KNY), has allowed the manipulation and examination of ASIC1’s amino acid sequence. Six simulation trajectories were carried out (accumulative 300 ns- 50 ns per trajectory) through remote access to TACC supercomputer center using NAMD simulation software. Previous experimental work has shown that unlike ASIC3, the ASIC1 channel cannot be opened by the removal of calcium. Despite ASICs' highly conserved channel sequence, this characteristic difference between these two subtypes may be defined by one key residue: a glutamic acid residue found in ASIC3, position 429, versus a glycine residue in ASIC1. Introduction of G429E mutation opens the ASIC1 channel. Consistent with experimental observation, analysis via VMD visualization software revealed the G429E mutant has a wider channel opening than the WT. We further identified that this opening is facilitated by the electrostatic interaction of glutamic acid 429 and asparagine 65 of lateral chains. We identified key residue responsible for the distinct gating mechanisms of ASIC1 and ASIC3. Located at the lipoprotein interface, this key “gating” region of the pore may prove useful in the identification of novel pharmacological targets and understanding the differences in channel gating between ASIC1 and ASIC3. Novel applications are sought for the selective targeting of ASICs channel subtypes, as well as, targeting ASICs within specific regions of the body.