UCIBIO-REQUIMTE, Departamento de Química e Bioquímica , Faculdade de Ciências, Universidade do Porto , s/n, 4169-007 Porto , Portugal.
J Chem Theory Comput. 2018 May 8;14(5):2538-2548. doi: 10.1021/acs.jctc.8b00137. Epub 2018 Apr 16.
Molybdenum-containing enzymes have been receiving significant attention from the scientific community since they participate in important biological processes and in the global biogeochemical cycles of carbon, nitrogen, and sulfur. Molecular modeling studies of these metalloproteins with classical force fields are, however, often hampered by the "missing parameter" problem. In this article, a set of parameters have been determined for the AMBER force field from nine different molybdenum cofactors. All of these cofactors were optimized and parametrized using a bonded model approach. All of the bonds and angles involving the Mo ion were parametrized. The Restrained Electrostatic Potential charges of the coordination sphere of each cofactor were also determined. Finally, we demonstrated the stability of our parameters in a showcase of nine enzymes. The parameters presented in this work provide a valuable resource for the molecular simulation community as they extend the range of metal ions that can be studied using classical approaches while also providing a starting point for subsequent parametrization of similar metal centers. All of the developed parameters can be found in the Supporting Information .
含钼酶自被科学界关注以来，一直是研究热点，因为它们参与了许多重要的生物过程，以及碳、氮和硫的全球生物地球化学循环。然而，使用经典力场对这些金属蛋白酶进行分子建模研究常常受到“缺失参数”问题的困扰。在本文中，我们从 9 种不同的钼辅因子中确定了一套适用于 AMBER 力场的参数。所有这些辅因子都采用键合模型方法进行了优化和参数化。所有涉及 Mo 离子的键和角都进行了参数化。每个辅因子配位球的静电势受限电荷也被确定。最后，我们通过展示 9 种酶来证明我们参数的稳定性。本文工作中提出的参数为分子模拟界提供了有价值的资源，因为它们扩展了可以使用经典方法研究的金属离子范围，同时也为后续类似金属中心的参数化提供了起点。所有开发的参数都可以在支持信息中找到。
