title: Improved Parameters for the Martini Coarse-Grained Protein Force Field.
abstract: The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Djurre H
authors.initials: DH
authors.lastname: de Jong
authors.affiliation: Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4.
authors.forename: Gurpreet
authors.initials: G
authors.lastname: Singh
authors.affiliation: Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4.
authors.forename: W F Drew
authors.initials: WF
authors.lastname: Bennett
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Clement
authors.initials: C
authors.lastname: Arnarez
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Tsjerk A
authors.initials: TA
authors.lastname: Wassenaar
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Lars V
authors.initials: LV
authors.lastname: Schäfer
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Xavier
authors.initials: X
authors.lastname: Periole
authors.affiliation: Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4.
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink