phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids,Journal of Chemical Theory and Computation

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phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2024-08-16 , DOI: 10.1021/acs.jctc.4c00732
Lauren E Raguette _{1,

2} , Abbigayle E Cuomo ₁ , Kellon A A Belfon _{1,

2} , Chuan Tian _{1,

2} , Victoria Hazoglou ₁ , Gabriela Witek ₃ , Stephen M Telehany ₁ , Qin Wu ₄ , Carlos Simmerling _{1,

2}

Affiliation

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

中文翻译：

phosaa14SB 和 phosaa19SB：更新了磷酸化氨基酸的琥珀力场参数

磷酸化氨基酸参与许多细胞调节网络；含有这些翻译后修饰的蛋白质在实验和计算上得到了广泛的研究。模拟用于研究生物分子的各种结构和动态特性，例如配体结合、酶反应机制和蛋白质折叠。然而，使用 Amber 程序模拟含有磷酸化氨基酸的蛋白质的力场参数的开发并没有跟上标准氨基酸参数的开发，并且以与蛋白质相当的精度对这些修饰的氨基酸进行建模具有挑战性仅含有标准氨基酸。特别是，流行的 ff14SB 和 ff19SB 模型不包含磷酸化氨基酸的参数。在这里，最常见磷酸化氨基酸侧链的二面体参数根据采用 ff14SB 方法的 QM 计算的参考数据进行训练，然后根据实验数据进行验证。提供库文件和相应的参数文件，版本兼容ff14SB和ff19SB。

更新日期：2024-08-16

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