Computational Analysis of Binding Interactions between the Ryanodine Receptor Type 2 and Calmodulin

Abstract

Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to a variety of cardiac arrhythmias, such as catecholaminergic polymorphic ventricular tachycardia (CPVT). RyR2 is regulated by calmodulin (CaM), and mutations that disrupt their interaction can cause aberrant calcium release, leading to an arrhythmia. It was recently shown that increasing the RyR2–CaM binding affinity could rescue a defective CPVT-related RyR2 channel to near wild-type behavior. However, the interactions that determine the binding affinity at the RyR2–CaM binding interface are not well understood. In this study, we identify the key domains and interactions, including several new interactions, involved in the binding of CaM to RyR2. Also, our comparison between the wild-type and V3599K mutant suggests how the RyR2–CaM binding affinity can be increased via a change in the central and N-terminal lobe binding contacts for CaM. This computational approach provides new insights into the effect of a mutation at the RyR2–CaM binding interface, and it may find utility in drug design for the future treatment of cardiac arrhythmias.

Life-threatening arrhythmogenic CaM mutations disrupt CaM binding to a distinct RyR2 CaM-binding pocket

“…Deletion of the sequence 3583-3603aa in RyR2 resulted in disruption of CaM binding to RyR2 and reduced efficacy of CaM inhibition on RyR2 activity in single channel measurements [23]. Besides the 3583-3603aa region, other RyR2 regions have also been reported as potential CaMbinding sequences; however their exact contribution to CaM-binding remains to be fully elucidated [25,29]. Huang et al [30], based on previous binding studies with radio-labeled CaM where sequence 4303-4328 in RyR1 (4261-4286 in RyR2) was first detected as a CaM-binding sequence [4,31], investigated the 3581-3612aa and 4261-4286aa regions of mouse RyR2 as putative CaMBDs by cryo-EM and FRET experiments.…”

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

“…For this, we switched to a different method that we had used previously to study residue−residue binding interactions in the RyR2-CaM system. 62 S4S5L Interacts with the S6 Helix and the U-Motif. To provide a more detailed analysis of the interactions of the S4S5L with its surrounding environment, we located the primary residue−residue interactions involved in the binding of the S4S5L on a given subunit to its surrounding protein environment within the RyR2.…”

“…This similarity suggested that a more detailed analysis at the level of individual residue–residue binding interactions was required. For this, we switched to a different method that we had used previously to study residue–residue binding interactions in the RyR2-CaM system …”

“…For this, we switched to a different method that we had used previously to study residue–residue binding interactions in the RyR2-CaM system. 62 …”

Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin’s Calcium-Binding Properties

“…CaM has been a subject of interest from the computational community because of its coupling of structures and functions: folding, conformational changes, and Ca 2+ -binding. A few molecular dynamics simulations focus on separate incidences because each of these topics requires enormous computational resources and modeling efforts: CaM’s allostery, ,− the CaM-target binding, ,, or the coordination chemistry of Ca 2+ in the Ca 2+ -binding loops in CaM. ,− The energy landscape view for the interplay among folding, allostery, and binding of CaM domains was provided to investigate possible routes CaM might explore in response to external stimuli.…”