Molecular Dynamics Simulations of the Cardiac Ryanodine Receptor Type 2 (RyR2) Gating Mechanism

Abstract

Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to fatal cardiac arrhythmias such as catecholaminergic polymorphic ventricular tachycardia (CPVT). While many CPVT mutations are associated with an increase in Ca 2+ leak from the sarcoplasmic reticulum, the mechanistic details of RyR2 channel gating are not well understood, and this poses a barrier in the development of new pharmacological treatments. To address this, we explore the gating mechanism of the RyR2 using molecular dynamics (MD) simulations. We test the effect of changing the conformation of certain structural elements by constructing chimera RyR2 structures that are derived from the currently available closed and open cryo-electron microscopy (cryo-EM) structures, and we then use MD simulations to relax the system. Our key finding is that the position of the S4−S5 linker (S4S5L) on a single subunit can determine whether the channel as a whole is open or closed. Our analysis reveals that the position of the S4S5L is regulated by interactions with the U-motif on the same subunit and with the S6 helix on an adjacent subunit. We find that, in general, channel gating is crucially dependent on high percent occupancy interactions between adjacent subunits. We compare our interaction analysis to 49 CPVT1 mutations in the literature and find that 73% appear near a high percent occupancy interaction between adjacent subunits. This suggests that disruption of cooperative, high percent occupancy interactions between adjacent subunits is a primary cause of channel leak and CPVT in mutant RyR2 channels.

Structure-based mechanism of RyR channel operation by calcium and magnesium ions

“…The importance of the U-motif residues I4218 and F4219, which we observed in the allosteric networks of most RyR1 and RyR2 model structures is underlined by the finding that the corresponding RyR2 residues I4172 and F4173 were found important for the interaction of the U-motif with the C-terminal domain and S6 helix, respectively (Kobayashi et al, 2022), and their alanine substitution led to the gain of function for RyR2 (Murayama et al, 2011). Greene et al (2022) observed in molecular dynamics simulations that the S45 linker of all monomers has to assume the "open" position for the channel to be open, suggesting their intimate involvement with the transitions between macrostates. The residues T4825, I4826, S4828, and S4829, present in several branches of the activation and inhibition networks, were shown to be involved in RyR1 gating (Murayama et al, 2011), and the mutation T4825I was shown to weaken RyR1 inhibition by Ca 2+ (Gomez et al, 2016).…”

OpiCa1-PEG-PLGA nanomicelles antagonize acute heart failure induced by the cocktail of epinephrine and caffeine

“…3 D) and left ventricular fractional shortening rate (FS) ( Fig. 3 E) indicators, which showed that OpiCa1 and OpiCa1-PEG-PLGA were completely restored to normal, and PEG-PLGA had a gentle trend of partial recovery [ 49 , 50 ]. In all, The results from survival rate and echocardiography indicated that OpiCa1-PEG-PLGA nanoparticles retain the activity of OpiCa1 and have the effect of antagonizing the lethal acute heart failure induced by Caff and Epi.…”