Probing Domain Interactions in a Large Multimeric Protein: Molecular Dynamics and Bioinformatic Analysis of Closed and Open States of RyR1.

Abstract

The ryanodine receptor isoform-1 (RyR1) is a large intracellular calcium release channel essential for skeletal muscle contraction. While cryo-electron microscopy (cryo-EM) has revealed structural snapshots of RyR1 in closed and open states, the dynamic features associated with calcium-dependent gating remain incompletely understood. In this study, we integrated all-atom molecular dynamics (MD) simulations with domain-level bioinformatic analyses to characterize and compare the structural dynamics of RyR1 in its closed and open conformations. Our simulations revealed distinct structural differences, including domain flexibility patterns, solvent accessibility, and hydrogen bonding networks, between the closed and open states. The closed state exhibited more extensive inter-subunit contacts and stable hydrogen-bonding networks, supporting a compact architecture characterized by inter-subunit domain engagement and intra-subunit domain loosening. In contrast, the open state showed increased solvent exposure and reduced inter-subunit interactions, reflecting inter-subunit domain loosening coupled with intra-subunit domain engagement, particularly in regions connecting the cytoplasmic and pore-forming domains. The comparative approach provides structural perspectives on how calcium binding may contribute to RyR1's conformational organization relevant to gating function. Our findings highlight the utility of integrating MD simulations with domain-scale analyses to investigate large protein complexes and generate hypotheses for future experimental validation.