Calcium Pump And Phospholamban By Molecular Dynamics Simulations

Ca2+ plays an important role in cell physiology of biology as a second messenger. Large concentration difference of Ca2+ between cytosol and extracellular matrix as well as lumen of some organelles, separated by membrane, is a prerequisite for its function. The flow of Ca2+ through membrane is achieved by specific integral proteins, an example of which is Ca2+ pumps. Ca2+ pumps transport Ca2+ against its concentration gradient using the energy given by ATP hydrolysis. Mechanisms of Ca2+ transportation and energy transformation in Ca2+ pumps are still unclear. The activity of sarcoplasmic reticulum Ca2+ is regulated by a protein called phospholamban. But its regulation mechanism is unclear. Phospholamban pentamer can function as an ion channel and the mechanism is also unclear. Dysfunction of these proteins will lead to some diseases. The structure–function correlation of these proteins is hot research area now. Quickly growing in the number of high resolution protein structures plus the increase in computing power make molecular modeling more and more important in the understanding of the connection between three–dimension structure and dynamics of proteins. Molecular dynamics simulation is especially important for it can give dynamic information of molecules at atomic levels.Based on some crystal structures of Ca2+ pump published recently, we have constructed all–atomic models of Ca2+ pump on four different states and every model includes about 1.7 million atoms. 7.5 ns simulations were performed on each model. Statistical analysis on the simulation results showed that the concentration of Ca2+ around the protein near the membrane was one fold higher than that in other area. To find the reason, Poisson–Boltzmann electrostatic potential calculations were performed on the system including the protein and membrane then. It is shown that it is mainly negative electrostatic potential distribution around the protein near the membrane. We conclude that Ca2+ is to bind to Ca2+ pump by electrostatic attraction rather than a stochastic process.Phospholamban, the main inhibitor of Ca2+ pump, was also studied by molecular dynamics simulations based on a atomic level NMR structure to find the mechanism of ion permeability through its pentamer transmembrane pore. Potential of mean force was also calculated to obtain the free energy profiles when an ion moved though its pore. It is found that the free energy barrier for a Ca2+ permeation is more than 90 kcal/mol, which indicates that the conformation of NMR experiment is close for Ca2+ permeation. However, when there exists a stream of water in the pore, Cl- can always move through the pore spontaneously, which indicates that phospholamban pentamer can function as a Cl- channel as suggested before.