Large scale molecular dynamics simulation of Cytochrome C on synthetic bilayer membrane

We herein report a large scale molecular dynamics (MD) simulation of heme proteins on lipid surface in water. For this purpose, we employed a molecular dynamics machine (MDM) which is specially designed for MD calculation in RIKEN. As a first simulation, a phosphate compound was employed as a simplified alternative of phosphate-bearing synthetic membrane. In this calculation, the conformation change of cytochrome c was observed when His18 is located between heme and membrane surface. This result shows good agreement with the experimental result. As more precise modeling, a bilayer membrane which is composed of 512 molecules of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) was used to mimick dipalmitoylphosphatidylcholine. The latter large scale MD simulations was successfully performed, and the result was consistent with the experimental data. MD simulations of various lipid membrane and cytochrome c will be discussed.