Complementary in vitro functional studies and in silico alchemical free energy simulations of the sarco-endoplasmic reticulum calcium pump (SERCA) and phospholamban (PLN) complex.

Abstract

SERCA is ubiquitously expressed in all eukaryotic cells and is responsible for actively transporting calcium ions from the cytoplasm into the SR/ER lumen. PLN is a small transmembrane peptide that regulates SERCA's calcium transport activity in cardiac muscle. Human genetic variants of PLN have been implicated in cardiomyopathies. PLN is a 52 amino acid peptide with an N-terminal cytoplasmic helix (residues 1-17), a short linker region (residues 18-27) and a C-terminal transmembrane helix (residues 28-52). Previous structural studies have identified the binding groove for PLN formed by transmembrane segments M2, M6, and M9 of SERCA (PDB: 4KYT). The structure of the SERCA-PLN complex consists of SERCA in a calcium-free, E1-like state and includes the linker region and transmembrane helix of PLN (residues 20-52). Here, we carry out in vitro functional studies and in silico free energy calculations to examine the effects of alanine scanning mutations in PLN (residues 20-52) on SERCA regulation. From the functional studies, changes in kinetics parameters such as calcium affinity (KCa) and maximal activity (VMax) of SERCA are determined for each of the alanine substitutions. From the in silico alchemical free energy simulations (using Compute Canada supercomputing resources), each of the residues in PLN are alchemically transformed to alanine to determine the change in Gibbs free energy (Δ;Δ;G) relative to the wild-type SERCA-PLN complex. Together, the complementary in vitro and in silico mutational studies provide novel insights into a membrane protein-peptide complex. The PLN variants are quantified in terms of their physiological significance – gain-of-function, loss-of-function, or neutral – and the molecular determinants that control binding specificity.