Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca2+ Pump SERCA

The tilting motion of the central core reveals the transport mechanism of the sarco/endoplasmic reticulum Ca2+-ATPase

The sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions per ATP hydrolyzed from the cytoplasm to the lumen. However, how the ATP hydrolysis remotely drives the Ca2+ transport is unclear. In the SERCA1a crystal structures, the ATP hydrolysis is accompanied by the notably increasing tilting angle of the central core (CC) and the Ca2+ transport, and the CC tilting angle dramatically decreases in the E2 to E1 transition. We demonstrated that the significantly increasing tilting motion of the CC drove the Ca2+ release in the molecular dynamics simulation of the R836A variant, and the dramatic spontaneous decrease in the CC tilting angle of the E2 state triggers the restart of the SERCA1a's transport cycle. The repulsion between the phosphorylated D351 and the phosphate groups in ADP triggers the release of ADP from the SERCA1a headpiece. We proposed a novel SERCA transport mechanism in which ATP hydrolysis drives a significant tilting motion of the CC, which drives Ca2+ transport and the A domain rotational motion in the E1P-ADP-2Ca2+ to E2P transition. The dramatic spontaneous decrease in the CC tilting angle of the E2 state drives the restart of the transport cycle.

Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials

We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The convergence is accelerated by a mapping function that increases the overlap between the target and the reference distributions. Building on recent work, we show that this map can be learned with a normalizing flow neural network, without requiring simulations with the expensive target potential but only a small number of single-point calculations, and, crucially, avoiding the systematic error that was found previously. We validate the method by numerically evaluating the free energy difference in a system with a double-well potential and by describing the free energy landscape of a simple chemical reaction in the gas phase.

Cryo-EM analysis provides new mechanistic insight into ATP binding to Ca2+ -ATPase SERCA2b

Sarco/endoplasmic reticulum Ca²⁺ -ATPase (SERCA) 2b is a ubiquitous SERCA family member that conducts Ca²⁺ uptake from the cytosol to the ER. Herein, we present a 3.3 Å resolution cryo-electron microscopy (cryo-EM) structure of human SERCA2b in the E1·2Ca²⁺ state, revealing a new conformation for Ca²⁺ -bound SERCA2b with a much closer arrangement of cytosolic domains than in the previously reported crystal structure of Ca²⁺ -bound SERCA1a. Multiple conformations generated by 3D classification of cryo-EM maps reflect the intrinsically dynamic nature of the cytosolic domains in this state. Notably, ATP binding residues of SERCA2b in the E1·2Ca²⁺ state are located at similar positions to those in the E1·2Ca²⁺ -ATP state; hence, the cryo-EM structure likely represents a preformed state immediately prior to ATP binding. Consistently, a SERCA2b mutant with an interdomain disulfide bridge that locks the closed cytosolic domain arrangement displayed significant autophosphorylation activity in the presence of Ca²⁺ . We propose a novel mechanism of ATP binding to SERCA2b.