Stote R H, Karplus M
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA.
Proteins. 1995 Sep;23(1):12-31. doi: 10.1002/prot.340230104.
Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.
针对二价锌开发了结合伦纳德 - 琼斯和静电相互作用的力场参数，并在溶液和蛋白质模拟中进行了测试。结果表明，该参数集给出的溶液自由能与实验结果吻合良好。使用这些锌参数和CHARMM 22β全原子参数集对羧肽酶A和碳酸酐酶进行了分子动力学模拟。结构结果与已发表的使用锌离子特定键合模型和AMBER力场的模拟结果一样准确。发现通过使用扩展静电模型包含长程静电相互作用可改善活性位点的平衡构象。得出的结论是，本参数集允许锌离子具有不同的配位几何结构和配体交换，可有效地用于含锌体系的溶液和蛋白质模拟。
