Conformational motions and ligand-binding underlying gating and regulation in IP3R channel

Abstract

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP3R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design

“…Arg568) directly impact hydrogen bond formation between IP 3 and its binding domain, 3,61 significantly reducing IP 3 -binding affinities and leading to dominant negative effects. These variants may respond to positive modulators of IP 3 R1 channel function.…”

“…1 Binding of IP 3 triggers conformational changes that are transmitted intramolecularly over a large distance to open the C-terminal channel pore. 3,8,9 Expression of ITPR1 (OMIM *147265) encoding the type 1 IP 3 R is ubiquitous, and IP 3 R1 is the predominant neuronal IP 3 receptor enriched in the Purkinje cells of the cerebellar cortex, [10][11][12][13] where it regulates Purkinje cell development and calcium homeostasis. 14,15 A knockout of the Itpr1 gene in mice results in very early lethality, severe ataxia, and epileptic seizures without an overt cellular phenotype.…”

Using mass spectrometry imaging to visualize age-related subcellular disruption

“…Ca 2+ is required in oxidative metabolism and acts as a cofactor of TCA enzymes (e.g., isocitrate dehydrogenase, a-ketoglutarate dehydrogenase, pyruvate dehydrogenase) and synthesis of reducing equivalents (e.g., NADH, FADH2). Whereas IP3R (IP3R1, IP3R2, IP3R3) modulates release of Ca 2+ stored in the ER/SR, VDACs mediates the flux of Ca 2+ into mitochondria ( Mikoshiba, 2015 ; Bartok et al, 2019 ; Fan et al, 2022 ; Schmitz et al, 2022 ). An additional MAM-enriched protein called SEPN1 has been identified at the ER/SR interface ( Filipe et al, 2021 ).…”

Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77

“…Enzymes achieve catalysis via a highly preorganized active site where catalytic residues are precisely arranged for their functions. Moreover, the conformational dynamics of enzymes can significantly impact their catalytic activity, and the conformations of enzymes can be modulated by some flexible domains or loops that are relatively far from the active site. − Therefore, the conformational dynamics are important for enzyme catalysis, including allosteric regulation, substrate binding, and product release. − …”