Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling

Abstract

The ryanodine receptors (RyRs) are a family of calcium (Ca) channels that regulate Ca release by undergoing a closed-to-open gating transition in response to action potential or Ca binding. The allosteric mechanism of RyRs gating, which is activated/regulated by ligand/protein binding >200 Å away from the channel gate, remains elusive for the lack of high-resolution structures. Recent solution of the closed-form structures of the RyR1 isoform by cryo-electron microscopy has paved the way for detailed structure-driven studies of RyRs functions. Toward elucidating the allosteric mechanism of RyRs gating, we performed coarse-grained modeling based on the newly solved closed-form structures of RyR1. Our normal mode analysis captured a key mode of collective motions dominating the observed structural variations in RyR1, which features large outward and downward movements of the peripheral domains with the channel remaining closed, and involves hotspot residues that overlap well with key functional sites and disease mutations. In particular, we found a key interaction between a peripheral domain and the Ca-binding EF hand domain, which may allow for direct coupling of Ca binding to the collective motions as captured by the above mode. This key mode was robustly reproduced by the normal mode analysis of the other two closed-form structures of RyR1 solved independently. To elucidate the closed-to-open conformational changes in RyR1 with amino-acid level of details, we flexibly fitted the closed-form structures of RyR1 into a 10-Å cryo-electron microscopy map of the open state. We observed extensive structural changes involving the peripheral domains and the central domains, resulting in the channel pore opening. In sum, our findings have offered unprecedented structural and dynamic insights to the allosteric mechanism of RyR1 via modulation of the key collective motions involved in RyR1 gating. The predicted hotspot residues and open-form conformation of RyR1 will guide future mutational and functional studies.

Keywords: channel gating; elastic network model; flexible fitting; hotspot residues; normal mode analysis; ryanodine receptor.