Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
J Biomol Struct Dyn. 2022 May;40(8):3481-3491. doi: 10.1080/07391102.2020.1847687. Epub 2020 Nov 13.
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [FeS] that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [FeS] through the CHARMM36 force field.
使用密度泛函理论（DFT）计算获得了与 dissimilatory adenosine-5'-phosphosulfate reductase（APSrAB）配位的 [FeS] 型铁硫簇（Fe-S）相容的 CHARMM36 力场参数。对两个 APSrAB 系统进行了经典分子动力学（MD）模拟，以验证参数并验证研究系统的稳定性。插入力场中的参数的时间分析与实验 X 射线衍射数据吻合良好。对研究系统的时间演化分析表明，这些系统，特别是它们各自腔中的簇，具有良好的稳定性，与以前的工作观察到的结果一致。所获得的参数为通过 CHARMM36 力场研究 APSrAB 以及其他包含 [FeS] 的系统提供了基础。
