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

Tom Vlaar; An Ghysels

doi:10.5281/zenodo.17435360

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

Tom Vlaar; An Ghysels

Publisher: Zenodo
DOI: 10.5281/zenodo.17435360
Repository: zenodo.org
Language: en

Abstract

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.

Full text

(2) ∞RETIS L-proline total permeability probability of 1.8 x 10-12 Exact kinetics of amino acids through chiral phospholipid membranes via path sampling Tom Vlaar and An Ghysels IbiTech – BioMMedA, Ghent University, Belgium [email protected] Introduction Methodology Results Conclusions L-proline D-proline System (CHARMM-GUI): 110 DOPC + 22 POPC lipids 32 water molecules per lipid, 0.15 M NaCl 310 K (body temperature) CHARMM36 all-atom force field TIP3P water model Proline with and without -yne group (2) ∞RETIS simulations: create trajectories Infinite swapping moves of trajectories between ensembles Wirefencing Monte Carlo moves  15000 iterations (1) US Lower entry and internal but higher escape barriers may contribute to faster permeation of L-proline than D-proline Entry Internal Escape Biological L-proline observed to have lower entry and internal barrier but higher escape barrier than D-proline ∞RETIS total permeability probability for L-proline is 1.8 x 10-12 ∞RETIS and WE simulations show similar free energy trends as US ∞RETIS and WE simulations of the Dand -yne systems Comparing proline with polar amino acids Identifying the energetic and steric considerations defining the permeation process. 0 -10 -20 -30 (Å) Future work (3) Weighted Ensemble (WE) simulations: create trajectories Configuration space divided into bins Statistical weights of all bins sum to 1 Trajectories pruned or merged in bins to 5 500 iterations of 100 ps MD trajectories (3) WE As an alternative method for ∞RETIS Same trend in barrier heights observed as US, values differ. Entry (kJ/mol) Internal (kJ/mol) Escape (kJ/mol) L-PRO 1.4 17.6 8.8 D-PRO 1.7 18.4 6.7 L-PRO-yne 0.7 11.8 11.8 D-PRO-yne 1.3 12.8 10.3 Entry (kJ/mol) Internal (kJ/mol) Escape (kJ/mol) L-PRO (US) 1.4 17.6 8.8 L-PRO (WE) 1.8 19.5 5.2 D-PRO (US) 1.7 18.4 6.7 D-PRO (WE) 2.4 23.4 4.9 In all domains of life, biological functions are organized by homochiral bilayers. An essential property of the membrane is the permeability, which correlates with a molecule’s lipophilicity. Similar molecules can exhibit different passive permeability rates. The role of the membrane’s stereochemistry is largely ignored in experiments and simulations. The structure of membranes suggests an ancient role for bilayers in the emergence of life. The biological L-amino acids permeate up to 6 times faster in experiments than D-amino acids.[1] Understanding how membranes biophysical properties influence cellular function may guide drug design. 1 Hu, J., Cochrane, W.G., Jones, A.X. et al. Nat. Chem. 2021, 13, 786–791. Mirror plane Water Water Membrane Proline [2] [3] 2. van Erp, T. S., Phys. Rev. Lett. 2007, 98, 268301. 3. Zhang, D. T., Baldauf, L. Roet, S. Lervik, A. van Erp, T. S., Proc. Natl. Acad. Sci. 2024, 121, (7), e2318731121 4. Zuckerman, D. M., Chong, L. T. Annu. Rev. Biophys. 2017, 46, 43-57. 5. Zhang, S., et al. J. Chem. Inf. Model. 2022, 62, 8, 1891–1904 [4] [5] Water WaterMembrane Entry Internal Escape Will be combined to the total permeation rate Entry Internal Escape Proline (1) Umbrella Sampling (US) simulations: sample free energy Pull molecule at 0.05 nm · ns-1 with 1000 kJ · mol-1 · nm-2 harmonic potential 55 ns umbrella simulations 3000 kJ · mol-1 · nm-2 restraint z 10-3 10-4 10-6