Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation

Authors

Ye, Q., Boyenle, I. D., Hemesath, H., Carillo, K. J., Manssuri, M., Zhang, L., Liu, Y.

Abstract

Sorcin is a dimeric penta-EF-hand Ca2+-binding protein that regulates intracellular Ca2+ homeostasis through Ca2+-dependent conformational activation and target recognition, and it has also been implicated in multidrug resistance in cancer. Although crystal structures have defined the apo inactive and Ca2+-bound active states of Sorcin, the transition pathways connecting these states and the conformational ensembles populated under each condition remain poorly understood. Here, we used long-timescale all-atom molecular dynamics simulations on Anton 3, totaling ~90 s, to define the Ca2+-coupled conformational landscape of dimeric human Sorcin at atomic resolution. Starting from the Ca2+-bound structure, we directly observed the transition from the active to the inactive state following Ca2+ removal, demonstrating that loss of Ca2+ coordination is sufficient to drive inactivation on the microsecond timescale. Simulations initiated from the Ca2+-bound crystal structure with retained ions unexpectedly revealed ultrafast Ca2+ dissociation and rebinding at all EF-hand sites, indicating weak intrinsic Ca2+ affinity and highly dynamic ion exchange. In complementary simulations initiated from the apo structure, Sorcin spontaneously sampled active-like conformations even in the absence of stable Ca2+ binding, supporting a conformational selection mechanism in which Ca2+ shifts the population toward pre-existing active states rather than inducing the transition de novo. Across all conditions, we also observed pronounced and persistent structural asymmetry between the two protomers, revealing that the Sorcin homodimer is dynamically heterogeneous despite its symmetric crystal structures. Together, these results support a coordination-biased conformational selection model for Sorcin activation, in which weak and rapidly exchanging Ca2+ binding stabilizes, rather than induces, the active state. This work provides a dynamic framework for understanding Sorcin function as a fast Ca2+ sensor and offers broader mechanistic insight into activation principles of EF-hand Ca2+-binding proteins.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 10 Jul 2026.

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