Molecular Modeling and Structural Docking of a Ryanodine Receptor SPRY2 Domain

Abstract

Ryanodine receptors (RyRs) form a class of intracellular calcium release channels in various excitable tissues and cells such as muscles and neurons. SPRY domains are recognized as a protein interacting module and were so named because they were identified in a Dictyostelium discoidueumsplA kinase and in the mammalian RyR. There are 3 SPRY domains present in all the RyR isoforms. A particular interest has been raised for the SPRY2 domain, as it has been identified as the binding partner for the II-III loop from the α1S subunit of the dihydropyridine receptor, an interaction that is thought to be crucial for skeletal excitation-contraction coupling. In the present study, we have generated pseudo-atomic structures for RyR1 fragment 1,071-1,208 and homologous RyR2 fragment 1,084-1,221, both of which contain a SPRY2 domain. Both modeled SPRY2 fragments contain multiple β-sheets. Our initial rigid-body docking model in the sub-nanometer resolution cryo-EM map of RyR has placed the modeled fragment into a cytoplasmic domain adjacent to the N-terminal and central mutation region of RyR. Based on the modeled SPRY2 structure, we have designed a RyR2-GFP construct, with GFP inserted after residue Arg-1084, the N-terminus of the SPRY2 domain, to test our docking position by a 3D cryo-EM study. Our preliminary 2D analysis result supported the docking position.