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Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model

This paper illustrates the use of computer simulation in understanding the interaction of nano-scale synthetic molecules with cellular membranes, which are themselves a few nanometres thick. Specifically, the interaction of a membrane-bound synthetic molecule with a model membrane has been studied using so-called coarse-grain (CG) molecular dynamics (MD). The reported CG-MD simulations have been carried out for a pore-promoting hydraphile molecule in a dimyristoylphosphatidylcholine (DMPC) lipid bilayer. Analysis of the CG-MD simulation provides insights into the nature of the interaction of the hydraphile with the lipid molecules and how an initially fully extended trans-membrane hydraphile adjusts its end-to-end distance to match the bilayer thickness. The equilibrium membrane-bound hydraphile conformation observed in the CG-MD simulation agrees well with deductions based on experimental observations. The success of the CG-MD approach in the present example suggests that the methodology could be used as a design tool in related nano-science and engineering applications.