Improved Parameters for the Martini Coarse-Grained Protein Force Field
Improved Parameters for the Martini Coarse-Grained Protein Force Field
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DOI：
10.1021/ct300646g
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发表时间：
2013-01-01
影响因子：
5.5
通讯作者：
Marrink, Siewert J.
中科院分区：
文献类型：
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作者：
de Jong, Djurre H.;Singh, Gurpreet;Marrink, Siewert J.
Martini粗粒力场已被成功地用于模拟广泛的（生物）分子系统。然而，最近我们在测试完全原子力场模型的能力方面取得了进展，发现了一些缺点。最值得注意的是，苯丙氨酸和脯氨酸的疏水性太强，在非极性溶剂中的极性残基形成的二聚体没有足够强的结合力。在这里，我们重新参数化这些残留物通过重新分配的粒子类型或通过引入嵌入的电荷。新的参数进行测试相对于跨脂质双层，膜结合的Wimley白色肽，和二聚自由能在不同极性的溶剂中的分区。此外，我们改进了一些在马提尼蛋白力场，导致更现实的长度的a-螺旋和提高聚丙氨酸和甘氨酸重复的数值稳定性的键合条款。新的参数集表示为Martini版本2.2。
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 a-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.