Partitioning free energies and induced dipole response of small molecules across a POPC membrane using polarizable molecular dynamics.

Abstract

The cell membrane is the semi-permeable barrier that regulates flux of materials in and out of the cell. The membrane has a characteristic dielectric gradient due to the amphiphilic nature of its constituent lipids, which have polar head groups and hydrophobic tails. This gradient plays governs many aspects of small-molecule partitioning and membrane protein folding and function. Atomistic details of small-molecule partitioning related to hydration and electronic polarization are still largely unknown. Here, we used polarizable molecular dynamics simulations to understand how the electronic environment influences the process of partitioning. We performed a series of unbiased and umbrella sampling (US) simulations using the Drude polarizable force field (FF) for six different amino-acid sidechain analogs in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. Using a polarizable FF such as Drude allows for the investigation of explicit dipole responses as a function of local electric fields along the membrane normal. We assessed molecular dipole moments, which vary as a function of localization within the membrane, and compared outcomes of the Drude FF simulations to those of the nonpolarizable CHARMM36 FF to investigate the differences in the free energy surfaces of partitioning for our different amino-acid analogs. In doing so, we sought to quantify the effects of using the fixed-charge convention of nonpolarizable FFs, which may average out the influence of the membrane dielectric gradient. We show how polarity of small molecules influences their partitioning and describe key differences in the free energy surfaces between polarizable and nonpolarizable systems in these contexts. This work serves as a foundation for future investigations into polarizable simulations of drug partitioning, as well as simulations of membrane proteins.