Molecular dynamics of water and monovalent‐ions transportation mechanisms of pentameric sarcolipin

The Sarcolipin (SLN) is a transmembrane protein that can form a self‐assembled pentamer. In this work, the homology modeling and all‐atom molecular dynamic (MD) simulation was performed to study the model of SLN pentamer in POPC (1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine) membrane. The potential of mean force (PMF) was calculated for transmembrane transportation of Na + , Cl − and water molecule along the pore channel of penta‐SLN complex. The root mean square deviation (RMSD) of the SLN pentamer in POPC membrane showed that the stabilized SLN protein complex could exist in the membrane and that the Na + and Cl − could not permeate through the channel when the pore was under the vacuum state, but the water could permeate through from cytoplasm to lumen. Under the aqueous state, our simulation demonstrated that hydrated state of Na + and Cl − could pass through the channel. The PMF and radii of the pore showed that the channel had a gate at Leu 21 that is a key hydrophobicity residue in the channel. Our simulations help to clarify and to understand better the SLN pentamer channel that had a hydrophobic gate and could switch Na + and Cl − ion permeability by hydrated and vacuum states. Proteins 2016; 84:73–81. © 2015 Wiley Periodicals, Inc.