Koca Fındık Basak, Jafari Majid, Song Lin Frank, Li Zhen, Aviyente Viktorya, Merz Kenneth M
Department of Chemistry, Bogazici University, Bebek, Istanbul 34342, Turkey.
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.
J Chem Theory Comput. 2024 May 28;20(10):4298-4307. doi: 10.1021/acs.jctc.4c00218. Epub 2024 May 8.
Phosphate derivatives and their interaction with metal cations are involved in many important biological phenomena, so an accurate characterization of the phosphate-metal interaction is necessary to properly understand the role of phosphate-metal contacts in mediating biological function. Herein, we improved the standard 12-6 Lennard-Jones (LJ) potential via the usage of the 12-6-4 LJ model, which incorporates ion-induced dipole interactions. Via parameter scanning, we fine-tuned the 12-6-4 LJ polarizability values to obtain accurate absolute binding free energies for the phosphate anions HPO, HPO, PO coordinating with Ca and Mg. First, we modified the phosphate 12-6-4 LJ parameters to reproduce the solvation free energies of the series of phosphate anions using the thermodynamic integration (TI) method. Then, using the potential mean force (PMF) method, the polarizability of the metal-phosphate interaction was obtained. We show that the free energy profiles of phosphate ions coordinated to Ca and Mg generally show similar trends at longer metal-phosphate distances, while the absolute binding energy values increased with deprotonation. The resulting parameters demonstrate the flexibility of the 12-6-4 LJ-type nonbonded model and its usefulness in accurately describing cation-anion interactions.
磷酸盐衍生物及其与金属阳离子的相互作用涉及许多重要的生物学现象,因此准确表征磷酸盐 - 金属相互作用对于正确理解磷酸盐 - 金属接触在介导生物学功能中的作用是必要的。在此,我们通过使用包含离子诱导偶极相互作用的12 - 6 - 4 Lennard - Jones(LJ)模型改进了标准的12 - 6 LJ势。通过参数扫描,我们微调了12 - 6 - 4 LJ极化率值,以获得与Ca和Mg配位的磷酸根阴离子HPO、HPO、PO的准确绝对结合自由能。首先,我们修改了磷酸盐12 - 6 - 4 LJ参数,使用热力学积分(TI)方法重现了一系列磷酸根阴离子的溶剂化自由能。然后,使用势平均力(PMF)方法,获得了金属 - 磷酸盐相互作用的极化率。我们表明,在较长的金属 - 磷酸盐距离下,与Ca和Mg配位的磷酸根离子的自由能分布通常显示出相似的趋势,而绝对结合能值随着去质子化而增加。所得参数证明了12 - 6 - 4 LJ型非键合模型的灵活性及其在准确描述阳离子 - 阴离子相互作用方面的有用性。