Exact kinetics of amino acids through chiral phospholipid membranes via path sampling

Cell membranes, composed of phospholipid bilayers, act as barriers that enable the localization and compartmentalization essential to life. Understanding the permeation of small molecules through membranes is crucial for various biological and pharmacological applications. In molecular dynamics (MD) simulations, the permeation event is considered a rare event due to the infrequent occurrence. Capturing such a rare event and determining the kinetics requires immense computational resources. Substantial reduction of simulation time and exact assessment of the rate kinetics can be accomplished with replica exchange transition interface path sampling (RETIS) method. RETIS works by randomly generating new trajectories from an initial trajectory by shooting moves which are next accepted or rejected according to the Metropolis-Hastings algorithm. Enabling paths to be exchanged between different ensembles, enhances the sampling efficiency greatly. While no external bias potentials are used, the reactive paths with true dynamics resulting from this method allow for the qualitative information about rare events to be obtained. To further increase the exchange rate of RETIS, a parallelizable version called infinity-RETIS was developed. This advanced approach increases the exchange rate without steep factorial scaling and thus significantly increases computational efficiency while still maintaining accuracy. In this study, the permeation rate of different amino acids enantiomers is investigated, i.e. of proline. Enantiomers consist of the same atoms but the structures are each other's mirror image. The permeation through a 5 : 1 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) is investigated. Experimentally, the biological L- amino acids have been found to passively permeate up to 6 times faster through a membrane. The role of chiral membranes in the selective permeation of small molecules still remains partially elusive. Understanding the determinants of membrane permeation, can aid in pharmacokinetic property tuning as well as shed light on the fundamental studies of symmetry in the origins of life.