title: Using the Wimley-White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model.
abstract: The partitioning of proteins and peptides at the membrane/water interface is a key step in many processes, including the action of antimicrobial peptides, cell-penetrating peptides, and toxins, as well as signaling. To develop a computational model that can be used to accurately represent such systems, the underlying model must be able to quantitatively represent the partitioning preferences of amino acids in the lipid membrane. The MARTINI model provides a consistent set of parameters for building coarse-grained models of systems involving lipids and proteins. Even though MARTINI is parametrized to reproduce the partitioning behavior of small molecules, its ability to reproduce partitioning preferences of amino acids at lipid/water interfaces has never been tested. In this study, we measured the partitioning free energies of side chains of amino acids using alchemical simulations and umbrella sampling. The pentapeptides of sequence Ac-WLXLL were simulated at the POPC/water and cyclohexane/water interfaces using MARTINI, and the computed free energies were compared with the Wimley-White hydrophobicity scale. The free energy values obtained using the free energy perturbation, thermodynamic integration, and umbrella sampling methods were compared to gain insight into the most efficient method and the degree of sampling required to obtain statistically accurate free energies for use with atomistic force fields in future work. With the standard MARTINI water model, the amino acids D, E, K, and R were found to be significantly too favorable in hydrophobic environments, whereas with the polarizable water model, the amino acids D, E, K, and R were found to give correct free energies of partitioning. The amino acids P and F showed significant deviations from the experimental values. This model system will be used in future improvements to the MARTINI model.
authors.affiliation: Department of Biological Sciences, and ‡Institute for Biocomplexity and Informatics, 2500 University Drive N.W., University of Calgary , Calgary, Alberta, Canada T2N 1N4.
authors.forename: Gurpreet
authors.initials: G
authors.lastname: Singh
authors.affiliation: Department of Biological Sciences, and ‡Institute for Biocomplexity and Informatics, 2500 University Drive N.W., University of Calgary , Calgary, Alberta, Canada T2N 1N4.
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman