Calcium binding and permeation in TRPV channels: insights from molecular dynamics simulations

Abstract

Some calcium channels selectively permeate Ca2+, despite the high concentration of monovalent ions in the surrounding environment, which is essential for many physiological processes. Without atomistic and dynamical ion permeation details, the underlying mechanism of Ca2+ selectivity has long been an intensively studied, yet controversial, topic. This study takes advantage of the homologous Ca2+-selective TRPV6 and non-selective TRPV1 and utilizes the recently solved open-state structures and a newly developed multi-site calcium model to investigate the ion binding and permeation features in TRPV channels by molecular dynamics simulations. Our results revealed that the open-state TRPV6 and TRPV1 show distinct ion-binding patterns in the selectivity filter, which lead to different ion permeation features. Two Ca2+ ions simultaneously bind to the selectivity filter of TRPV6 compared with only one Ca2+ in case of TRPV1. Multiple Ca2+ binding at the selectivity filter of TRPV6 permeated in a concerted manner, which could efficiently block the permeation of Na+. Cations of various valences differentiate between the binding sites at the entrance of the selectivity filter in TRPV6. Ca2+ preferentially binds to the central site with a higher probability of permeation, repelling Na+ to a peripheral site. Therefore, we believe that ion binding competition at the selectivity filter of calcium channels, including the binding strength and number of binding sites, determines Ca2+ selectivity under physiological conditions. Additionally, our results showed that pore helix flexibility and the cytosolic domain of TRPV channels regulate ion permeability.

A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5

“…In the case of simulations containing Ca 2+ , the standard CHARMM36m Ca 2+ ions were then replaced with the multi-site Ca 2+ of Zhang et al Zhang et al ( 2020 ). This multi-site model has used been used to investigate Ca 2+ permeation in a number of channels, including including the type-1 ryanodine receptor Zhang et al ( 2020 ); Liu et al ( 2021 ), AMPA receptors Schackert et al ( 2022 ), the E protein of SARS-CoV-2 Antonides et al ( 2022 ), and TRPV channels Ives et al ( 2022 ); Liu and Song ( 2022 ).…”

“…( Zhang et al, 2020 ). This multi-site model has used been used to investigate Ca 2+ permeation in a number of channels, including including the type-1 ryanodine receptor Zhang et al ( 2020 ); Liu et al ( 2021 ), AMPA receptors ( Schackert et al, 2022 ), the E protein of SARS-CoV-2 ( Antonides et al, 2022 ), and TRPV channels ( Liu and Song, 2022 ; Ives et al, 2023 ).…”