Exploring the Effects of 2.Deoxy-Atp on SERCA 2A Using Multiscale Modeling

This study seeks to determine the effect of potential therapeutic 2-deoxy-ATP (dATP) on the SR-ATPase (SERCA), an ATP- driven pump which expels Ca2+ from the cytosol during cardiac relaxation, at the molecular and cellular level. We are the first to perform Gaussian accelerated Molecular Dynamics (GaMD) simulations on a new crystal structure of cardiac SERCA 2A (PDB: 5MPM). Three 160 ns simulation cases were investigated - apo, ATP-bound, and dATP-bound (2 replicates). dATP was found to cause slight separation of cytosolic domains, which could indicate increased pump speed during dATP treatment. This behavior is consistent with faster calcium transient decay seen in isolated cardiomyocytes. Transmembrane domains surrounding calcium binding Sites I and II were found to stabilize when either nucleotide was added to the system. Simulations were performed on representative structures from each simulation to determine nucleotide and calcium association rates. dATP was found to have an 80% higher association rate to apo SERCA than ATP. For dATP-bound SERCA, simulations showed a higher Ca2+ association rate for Site II than Site I, which is the opposite effect seen in simulations with ATP-bound SERCA. This “site swap” phenomenon is likely an effect of altered electrostatic surfaces in the critical Ca2+ pathway into the transmembrane region as well as altered position of Ca2+ gating residue E309. Rate changes for nucleotide and Ca2+ binding were able to partially explain the effects of dATP treatment observed experimentally when integrated into a cell-scale ODE model of calcium handling. This study represents the first biophysical evidence of mechanistic differences in SERCA pump function caused by interactions with dATP.