Protein docking and steered molecular dynamics suggest alternative phospholamban-binding sites on the SERCA calcium transporter

• Published in: The Journal of biological chemistry 2020-08, Vol.295 (32), p.11262-11274
• Main Authors: Alford, Rebecca F., Smolin, Nikolai, Young, Howard S., Gray, Jeffrey J., Robia, Seth L.
• Format: Article
• Language: English
• Subjects: Animals; binding site; Binding Sites; calcium ATPase; calcium transport; Calcium-Binding Proteins - metabolism; Humans; Membrane Biology; membrane biophysics; membrane protein; micropeptides; molecular docking; molecular dynamics; Molecular Dynamics Simulation; phospholamban; Proteins - metabolism; protein–protein interaction; Sarcoplasmic Reticulum Calcium-Transporting ATPases - metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA120.012948

The transport activity of the sarco(endo)plasmic reticulum calcium ATPase (SERCA) in cardiac myocytes is modulated by an inhibitory interaction with a transmembrane peptide, phospholamban (PLB). Previous biochemical studies have revealed that PLB interacts with a specific inhibitory site on SERCA, and low-resolution structural evidence suggests that PLB interacts with distinct alternative sites on SERCA. High-resolution details of the structural determinants of SERCA regulation have been elusive because of the dynamic nature of the regulatory complex. In this study, we used computational approaches to develop a structural model of SERCA–PLB interactions to gain a mechanistic understanding of PLB-mediated SERCA transport regulation. We combined steered molecular dynamics and membrane protein–protein docking experiments to achieve both a global search and all-atom force calculations to determine the relative affinities of PLB for candidate sites on SERCA. We modeled the binding of PLB to several SERCA conformations, representing different enzymatic states sampled during the calcium transport catalytic cycle. The results of the steered molecular dynamics and docking experiments indicated that the canonical PLB-binding site (comprising transmembrane helices M2, M4, and M9) is the preferred site. This preference was even more stringent for a superinhibitory PLB variant. Interestingly, PLB-binding specificity became more ambivalent for other SERCA conformers. These results provide evidence for polymorphic PLB interactions with novel sites on M3 and with the outside of the SERCA helix M9. Our findings are compatible with previous physical measurements that suggest that PLB interacts with multiple binding sites, conferring dynamic responsiveness to changing physiological conditions.