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Full Paper
Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients
Article first published online: 28 FEB 2013
DOI: 10.1002/jcc.23262
Copyright © 2013 Wiley Periodicals, Inc.
Additional Information
How to Cite
Jakobtorweihen, S., Ingram, T. and Smirnova, I. (2013), Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients. J. Comput. Chem., 34: 1332–1340. doi: 10.1002/jcc.23262
Publication History
- Issue published online: 25 APR 2013
- Article first published online: 28 FEB 2013
- Manuscript Accepted: 3 FEB 2013
- Manuscript Revised: 1 FEB 2013
- Manuscript Received: 29 NOV 2012
Keywords:
- molecular dynamics simulations;
- COSMO-RS;
- lipid bilayer;
- partition coefficient;
- screening
Abstract
The importance of membrane-water partition coefficients led to the recent extension of the conductor-like screening model for realistic solvation (COSMO-RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO-RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.