Molecular Dynamics Simulation of SERCA and PLB Oligomers

Abstract

On a cellular level, the cardiac cycle is orchestrated by release of Ca2+ into the cytosol during systole (contraction) and subsequent reuptake of Ca2+ into internal stores by an ion-motive ATPase during diastole (relaxation). This pump, the sarco(endo)plasmic reticulum calcium ATPase (SERCA), undergoes large conformational changes between enzymatic substates during calcium transport. Recently, we quantified SERCA structural dynamics using intramolecular fluorescence resonance energy transfer (FRET). Here, we extend this work to investigate SERCA conformational changes in atomic detail using molecular dynamics simulations. Specifically, we tested a hypothesis generated from FRET experiments: Open conformations of SERCA are more dynamic than compact, closed structures. Our molecular dynamics simulations showed that larger amplitude cytoplasmic domain motions for open conformations compare to compact structures. The data suggest that the open conformation of SERCA is more dynamically disordered than the closed state. We also performed a molecular dynamics simulation on PLB, a homopentameric regulator of SERCA. Previous studies have suggested that a naturally occurring human heart failure mutation of PLB, L39Stop, disrupts membrane localization. Molecular dynamics simulations showed that L39Stop-PLB was unstable compared to WT PLB. In particular, we observed that the interactions between protomers of the L39Stop PLB pentamer were disrupted within 10 ns, resulting in collapse of the pentamer structure. L39Stop-PLB monomers were subsequently extruded from the bilayer, becoming soluble in the aqueous phase. We determined that the instability of the L39Stop PLB pentamers is partially due to lack of van der Waals interactions between truncated PLB monomers.