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bioRxiv · 10.1101/373183

A new lipid force field (FUJI)

Kamiya, N.·Shinoda, K.·Fujitani, H.
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Abstract

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method was applied without a traditional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrank when using LJ-PME method. A new lipid force field (FUJI) was developed on the basis of the AMBER force field scheme including the Lipid14 van der Waals parameters. Point charges were calculated by the restrained electrostatic potentials of many lipid conformers. The torsion energy profiles were calculated by high level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ); then, the molecular mechanical dihedral parameters were derived by means of a fast Fourier transform. Incorporating these parameters into a new lipid force field without any fittings to experimental data, desirable lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained by GROMACS molecular dynamics simulations using the LJ-PME method and hydrogen virtual sites. The stability and structures of large membranes with undulatory fluctuations were studied by a multidrug efflux transporter (AcrABZ-TolC) with inner and outer membranes.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/373183_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (92K):\norg.highwire.dtl.DTLVardef@12cf574org.highwire.dtl.DTLVardef@a6cdbforg.highwire.dtl.DTLVardef@10dbd16org.highwire.dtl.DTLVardef@f8fd3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kamiya, N., Shinoda, K., Fujitani, H.. 2018-07-20. A new lipid force field (FUJI). https://doi.org/10.1101/373183

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