(742g) Characterizing the Translocation of Charged Peptide Loops across Lipid Bilayers with Molecular Dynamics Simulations

Authors: 
Patel, S. J., University of Wisconsin-Madison
Van Lehn, R. C., University of Wisconsin-Madison
The hydrophobic core of the cell membrane is considered largely impermeable to charged molecules because of the large free energy barrier and corresponding long timescale (~hours) for charge translocation. Contradicting this view, a variety of water-soluble peptides are known to translocate charged groups across the cell membrane on a surprisingly rapid ~seconds timescale, for at least some peptides. In this work, we study the interconversion of single α-helix peptides with charged flanking loops between a surface-adsorbed and membrane-embedded state, which requires the translocation (or “flipping”) of charged loops across the bilayer. We utilize all-atom Temperature Accelerated Molecular Dynamics (TAMD) simulations to predict the likelihood of loop flipping without predefining a specific translocation pathway. We further use the string method with swarms of trajectories to determine minimum free energy paths and compare corresponding free energy barriers associated with various translocation pathways identified by TAMD simulations. We show that membrane-exposed charged residues accelerate the flipping of charged peptide loops by stabilizing intramembrane water defects. The position of charged residues in the transmembrane helix also affects the flipping pathway and the flipping free energy barrier. These detailed molecular-level insights of peptide translocation pathways may be valuable for designing small cationic peptides for applications in gene and drug delivery. Moreover, the methodology and findings discussed here can generalize to more complex behaviors, such as the large-scale conformational rearrangements of integral membrane proteins.