XVIth International Workshop on
Quantum Systems in
Chemistry and Physics
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Free energy of cell-penetrating peptide in lipid bilayer membrane: coarse-grained simulation
Shuhei Kawamoto1, Takeshi Miyakawa2, Masako Takasu2, Ryota Morikawa2, Tatsuki Oda1, Hiroaki Saito1, Shiroh Futaki3 and Hidemi Nagao1
1Graduate School of Natural Science and Technology, Kanazawa University
2School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
3Institute for Chemical Research, Kyoto University
Cell-penetrating peptides (CPPs) can permeate plasma membrane [1], and are useful for delivery of drugs and transfection of DNA. Free energy ΔG to insert a molecule into lipid bilayer membrane is important to investigate the permeability of the molecule through the membrane. ΔG of small molecules, such as water and oxygen, are obtained by all-atom simulations [2] with cavity insertion method. However, large molecules, such as CPP, are difficult to insert into the cavity in lipid bilayer membrane.
We estimate ΔG of CPP by steered MD method with our coarse-grained model [3]. When there is large attractive potential between CPP and lipid heads, the CPP makes inverted micelle in the lipid bilayer membrane, and the difference of ΔG between water region and lipid bilayer region is more than 66 kBT. It suggests that the spontaneous permeation of CPPs needs large driving force to overcome the barrier.

[1] I. Nakase, T. Takeuchi, G. Tanaka, S. Futaki, Adv. Drug Deliv., 60, 598 (2008)
[2] K. Shinoda, W. Shinoda, T. Baba, M. Mikami, J. Chem. Phys., 121, 9648 (2004)
[3] S. Kawamoto, et al., J. Chem. Phys., 134 095103 (2011)


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