Deciphering the Mechanism of Inhibition of SERCA1a by Sarcolipin Using Molecular Simulations

Abstract

SERCA1a is an ATPase calcium pump that transports Ca2+ from the cytoplasm to the sarco/endoplasmic reticulum lumen. Sarcolipin (SLN), a transmembrane peptide, regulates the activity of SERCA1a by decreasing its Ca2+ transport rate, but its mechanism of action is still not well-understood. To decipher this mechanism, we have performed normal mode analysis in the all-atom model, with the SERCA1a-SLN complex, or the isolated SERCA1a, embedded in an explicit membrane. The comparison of the results allowed us to provide an explanation at the atomic level for the action of SLN that is in good agreement with experimental observations. In our analyses, the presence of SLN locally perturbs the TM6 transmembrane helix and as a consequence modifies the position of D800, one of the key metal-chelating residues. Additionally, it reduces the flexibility of the gating residues, V304, and E309 in TM4, at the entrance of the Ca2+ binding sites, which would decrease the affinity for Ca2+. Unexpectedly, SLN has also an effect on the ATP binding site more than 35 Å away, due to the straightening of TM5, a long helix considered as the spine of the protein. The straightening of TM5 modifies the structure of the P-N linker that sits above it, and which comprises the 351DKTG354 conserved motif, resulting in an increase of the distance between ATP and the phosphorylation site. As a consequence, the turn-over rate could be affected. All this gives SERCA1a the propensity to go toward a Ca2+ low-affinity E2-like state in the presence of SLN and toward a Ca2+ high-affinity E1-like state in the absence of SLN. In addition to a general mechanism of inhibition of SERCA1a regulatory peptides, this study also provides an insight into the conformational transition between the E2 and E1 states.

Case report: Revealing the rare—a Brody Disease patient from Turkey expanding the phenotype

“… (A) Lolliplot diagram: SERCA1a is a transmembrane protein with a molecular weight of 110 kDa. The protein consists of a transmembrane (M) domain and a headpiece within the cytoplasm containing three domains: i) actuator (A) domain accounting for the dephosphorylation ii) phosphorylation (P) domain harboring a site for autophosphorylation, and iii) nucleotide-binding (N) domain which is the ATP binding site ( Wuytack et al, 2002 ; Barbot et al, 2021 ), created with BioRender.com . (B) Graphical illustration of cellular and physiological mechanisms in Brody Disease.…”

Sarcolipin alters SERCA1a interdomain communication by impairing binding of both calcium and ATP

“…This long-distance effect of SLN was recently detailed at molecular level using molecular simulations. In particular, a subtle straightening of M5 occurs in presence of SLN which leads to a reorientation of the loop containing the DKTG catalytic motif, thus perturbing binding of Mg.ATP 48…”

Sarcoplasmic Reticulum from Horse Gluteal Muscle Is Poised for Enhanced Calcium Transport

“…Although neither of these two biochemical assays provided information on molecular mechanism(s) that produce robust Ca 2+ transport by horse SR, both assays demonstrated the functional and structural similarities of SERCA orthologs from horse gluteus and rabbit muscles. 2+ Transport to ATP Hydrolysis Is Greater for Horse SR Vesicles Than Rabbit SR Vesicles SLN decreases the energetic efficiency of SERCA activity by partially uncoupling Ca 2+ transport from ATP hydrolysis, i.e., by decreasing the Ca 2+ /ATP coupling ratio below the maximum ratio of 2 Ca 2+ ions transported per ATP molecule hydrolyzed [18,[20][21][22][23]26]. Table 1 reports the Ca 2+ transport and ATP hydrolysis activities of horse and rabbit SR vesicles.…”

“…The general consensus is that SLN inhibits SERCA activity via multiple enzymatic mechanisms: by decreasing the maximal velocity (V max ), by decreasing the apparent Ca 2+ binding affinity (1/K Ca ), by decreasing ATP binding affinity (1/K ATP ), and by decreasing the number of Ca 2+ ions transported per ATP molecule hydrolyzed (coupling ratio) below the optimal Ca 2+ /ATP coupling ratio of two [17][18][19][20][21][22][23]. The SLN inhibition of SERCA activity is relieved in part by SLN phosphorylation or de-acylation [24][25][26].…”