Paper Citing NAMD - Abstract
Peters, Gunther H.; Werge, Mikkel; Elf-Lind, Maria Northved; Madsen, Jesper J.; Velardez, Gustavo F.; Westh, Peter
Interaction of neurotransmitters with a phospholipid bilayer: A molecular dynamics study
CHEMISTRY AND PHYSICS OF LIPIDS, 184:7-17, DEC 2014
We have performed a series of molecular dynamics simulations to study the interactions between the neurotransmitters (NTs) gamma-aminobutyrate (GABA), glycine (GLY), acetylcholine (ACH) and glutamate (GLU) as well as the amidated/acetylated gamma-aminobutyrate (GABA(neu)) and the osmolyte molecule glycerol (GOL) with a dipalmitoylphosphatidylcholine (DPPC) bilayer. In agreement with previously published experimental data, we found the lowest membrane affinity for the charged molecules and a moderate affinity for zwitterionic and polar molecules. The affinity can be ranked as follows: ACH-GLU << GABA < GLY << GABA(neu) << GOL. The latter three penetrated the bilayer at most with the deepest location being close to the glycerol backbone of the phospholipids. Even at that position, these solutes were noticeably hydrated and carried similar to 30-80% of the bulk water along. The mobility of hydration water at the solute is also affected by the penetration into the bilayer. Two time scales of exchanging water molecules could be determined. In the bulk phase, the hydration layer contains similar to 20% slow exchanging water molecules which increases 2-3 times as the solutes entered the bilayer. Our results indicate that there is no intermediate exchange of slow moving water molecules from the solutes to the lipid atoms and vice versa. Instead, the exchange relies on the reservoir of unbounded ("free") water molecules in the interfacial bilayer region. Results from the equilibrium simulations are in good agreement with the results from umbrella sampling simulations, which were conducted for the four naturally occurring NTs. Free energy profiles for ACH and GLU show a minimum of 2-3 kJ/mol close to the bilayer interface, while for GABA and GLY, a minimum of respectively 2 kJ/mol and 5 kJ/mol is observed when these NTs are located in the vicinity of the lipid glycerol backbone. The most important interaction of NTs with the bilayer is the charged amino group of NTs with the lipid phosphate group. (C) 2014 Elsevier Ireland Ltd. All rights reserved.
