Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca²⁺ Selectivity in Calcium Release-Activated Calcium Channels

Abstract

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca over Na. The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

Multiscale analysis of the effect of surface charge pattern on a nanopore’s rectification and selectivity properties: From all-atom model to Poisson-Nernst-Planck

“…Transport can be simulated directly using MD, Brownian Dynamics (BD) [70,71,72,73,74], or Dynamic Monte Carlo (DMC) [75,76,77], or computed with a transport equation. Direct simulation of ionic transport in the explicit-and implicit-water frameworks are done by MD and BD, respectively, by solving the Newton and the Langevin equations of motion, respectively.…”

Toward a Model for Activation of Orai Channel

“…It was previously proposed that residue E190 on TM3 of hOrai1 (equivalent to E262 in dOrai) regulates ion selectivity (Prakriya and Lewis, 2006, Yamashita et al., 2007), mainly by indirectly maintaining the geometry of the selectivity filter in the central pore (Zhou et al., 2010, Alavizargar et al., 2018). In the closed-state X-ray structure, the residue E262 forms hydrogen bonds with C198 and Y199, with the methyl group on Y199 pointing to TM1 (Hou et al., 2012); in the present putative open-state structure, although the residue C198 is dynamic, the hydrogen bonding between E262 and Y199 remains intact.…”

Critical parameters maintaining authentic CRAC channel hallmarks

“…Additionally, the residue E190 in TM3 controls high Ca 2+ selectivity of the Orai1 channel as its single-point mutation to a glutamine or alanine (E190Q/A) leads to an increased pore diameter of around 7 Å and thus, an increased permeation of Cs + ions (Zhou et al 2010b). New MD studies have proposed that dOrai W262Q (analogous position to hOrai1 E190Q) effects the hydration pattern of the pore and the dynamics of the surrounding residues in TM3 (Alavizargar et al 2018).…”