Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors

Abstract

Ryanodine (Ryd) irreversibly targets ryanodine receptors (RyRs), a family of intracellular calcium release channels essential for many cellular processes ranging from muscle contraction to learning and memory. Little is known of the atomistic details about how Ryd binds to RyRs. In this study, we used all-atom molecular dynamics simulations with both enhanced and bidirectional sampling to gain direct insights into how Ryd interacts with major residues in RyRs that were experimentally determined to be critical for its binding. We found that the pyrrolic ring of Ryd displays preference for the RAGGG-F residues in the cavity of RyR1, which explain the effects of the corresponding mutations in RyR2 in experiments. Particularly, the mutant Q4933A (or Q4863A in RyR2) critical for both the gating and Ryd binding not only has significantly less interaction with Ryd than the wild-type, but also yields more space for Ryd and water molecules in the cavity. These results describe clear binding modes of Ryd in the RyR cavity and offer structural mechanisms explaining functional data collected on RyR blockade.

Role of cardiac ryanodine receptor calmodulin‐binding domains in mediating the action of arrhythmogenic calmodulin N‐domain mutation N54I

“…A hallmark of RyR2 channels is their binding to the agonist ryanodine . Ryanodine binds with high affinity to RyR2 channels in their open conformation, and the RyR2‐ryanodine association is therefore an indirect estimate of RyR2 open propensity .…”

“…A hallmark of RyR2 channels is their binding to the agonist ryanodine . Ryanodine binds with high affinity to RyR2 channels in their open conformation, and the RyR2‐ryanodine association is therefore an indirect estimate of RyR2 open propensity . To investigate the effect of CaM on this open propensity, we measured the time‐dependent binding of tritium ([ 3 H]) labeled ryanodine to lysates of RyR2‐expressing HEK293 cells, without or with addition of CaM.…”

Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies

“…As starting positions, we used the coordinates of the calcium and zinc ions, ATP and caffeine molecules, as previously determined by electron microscopy ( Georges et al, 2016 ). For ryanodine, we used a Ryd model provided by Ngo and the coordinates from their MD study of ligand placement ( Ngo et al, 2017 ). The models were created using YASARA.…”

The structural basis of ryanodine receptor ion channel function

“…Among the large number of drugs that affect SR Ca 2+ release ( Zucchi and Ronca-Testoni, 1997 ; Xu et al, 1998 ; Thomas and Williams, 2012 ), ryanodine and caffeine have been extensively used in the assessment of SR-controlling cytoplasmic Ca 2+ concentrations. Molecular dynamic simulations indicate that ryanodine interacts with residues in the cytosolic cavity of the closed RyR1 ( Ngo et al, 2017 ). Single-channel measurements with purified RyRs provide the most direct information on the action of ryanodine.…”