Potential cation and H+ binding sites in acid sensing ion channel-1

Acid sensing ion channels (ASICs) are cation-selective membrane channels activated by H(+) binding upon decrease in extracellular pH. It is known that Ca(2+) plays an important modulatory role in ASIC gating, competing with the ligand (H(+)) for its binding site(s). However, the H(+) or Ca(2+) binding sites involved in gating and the gating mechanism are not fully known. We carried out a computational study to investigate potential cation and H(+) binding sites for ASIC1 via all-atom molecular dynamics simulations on five systems. The systems were designed to test the candidacy of some acid sensing residues proposed from experiment and to determine yet unknown ligand binding sites. The ion binding patterns reveal sites of cation (Na(+) and Ca(2+)) localization where they may compete with protons and influence channel gating. The highest incidence of Ca(2+) and Na(+) binding is observed at a highly acidic pocket on the protein surface. Also, Na(+) ions fill in an inner chamber that contains a ring of acidic residues and that is near the channel entrance; this site could possibly be a temporary reservoir involved in ion permeation. Some acidic residues were observed to orient and move significantly close together to bind Ca(2+), indicating the structural consequences of Ca(2+) release from these sites. Local structural changes in the protein due to cation binding or ligand binding (protonation) are examined at the binding sites and discussed. This study provides structural and dynamic details to test hypotheses for the role of Ca(2+) and Na(+) ions in the channel gating mechanism.