Publication: Simulation studies of the trace amine, 2PE diffusing through a neuronal membrane

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Title Simulation studies of the trace amine, 2PE diffusing through a neuronal membrane
Authors/Editors* Nickel, J., Berry, M. D. and Tomberli B
Where published* Biophysical Journal
How published* Proceedings
Year* 2009
Volume 94
Number 2
Pages 799
The trace amine phenylethylamine (2PE) has been the focus of a number of recent studies attempting to ascertain its physiological role (M.D. Berry, J. Neurochem, 90, 257-271, (2004)). An important unknown is the role of passive diffusion in allowing 2PE to cross the synaptic cleft. Although molecular dynamics (MD) can be be used to determine the diffusion rate, a key difficulty is evaluating the penetration energy or Potential of Mean Force (PMF) inside the membrane. Penetration energies have been determined by other workers for small anesthetic molecules like NO and butanol (A. Pohorille, M.A. Wilson, M.H. New and C. Chipot, Toxicology Letters, 100-101, 421-430,(1998)) but little work has been done on penetration energies for larger molecules. Using specially developed free energy simulation techniques, approximately twenty several nanosecond MD trajectories have been generated and analyzed to determine the mean force exerted on the trace amine at distances ranging from 20 angstrom right to the middle of a symmetric sphingomyelin membrane. From this data, the PMF and diffusion rate for 2PE through the membrane will be calculated. The techniques developed may be extended to study the binding of antimicrobial peptides to phospholipid membranes.
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