Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation
Creators: name: Lee, Brent L.
name: Kuczera, Krzysztof
name: Lee, Kyung-Hoon
name: Childs, Ed W.
name: Jas, Gouri S.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: Biological membranes are essential to preserve structural integrity and regulate functional properties through the permeability of nutrients, pharmaceutical drugs, and neurotransmitters of a living cell. The movement of acetylated and amidated phenylalanine (NAFA) across 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine (POPC) membrane bilayers is investigated to probe physical transport. The rate of transport is measured experimentally applying parallel artificial membrane permeation assay (PAMPA). At the physiological temperature, 310 K, the measured time constants in the neutral pH were ∼6 h in DOPC and ∼3 h in POPC, while in a more acidic condition, at a pH 4.8, the time constants were ∼8 h in both lipids. Computationally, we have expanded our transport study of three aromatic dipeptides across a bilayer composed of DOPC<sup>18</sup>. In this study, we have examined the effects of lipid composition and bilayer size on the passive transport of NAFA by simulating the dipeptide in three different bilayers, with 50 DOPC lipids, 50 POPC lipids, and 40 POPC molecules. Specifically, atomistic molecular dynamics simulations with umbrella sampling were used to calculate the potential of mean force for the passive permeation of NAFA across the bilayers. Diffusion constants were then calculated by numerically solving the Smoluchowski equation. Permeability coefficients and mean first passage times were then calculated. Structural properties – Ramachandran plots, sidechain torsions, peptide insertion angles, radial distribution functions, and proximal peptide water molecules – were also examined to determine the effect of system size and lipid type. In terms of systems size, we observed a small decrease in the highest barrier of the potential of mean force and fewer sampled sidechain dihedral angle conformations with 40 versus 50 POPC lipids due to weaker membrane deformations within a smaller lipid bilayer. In terms of lipid type, DOPC contains two monounsaturated acyl chains compared to only one such acyl chain in POPC; therefore, DOPC bilayers are less ordered and more easily deformed, as seen by a much broader potential of mean force profile. The NAFA in DOPC lipid also transitioned to an internally hydrogen-bonded backbone conformation at lower membrane depths than in POPC. Similarly, as for other aromatic dipeptides, NAFA tends to insert into the membrane sidechain-first, remains mostly desolvated in the membrane center, and exhibits slow reorientations within the bilayer in both DOPC and POPC. With a joint experimental and computational study we have gained a new insight into the rate of transport and the underlying microscopic mechanism in different lipid bilayer conditions of the simplest hydrophobic aromatic dipeptide. Communicated by Ramaswamy H. Sarma