Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany.
Division of Functional Genome Analysis, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, Heidelberg D-69120, Germany.
J Comput Chem. 2018 Jan 5;39(1):7-20. doi: 10.1002/jcc.24918. Epub 2017 Aug 28.
Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines. The force field parameters presented here give water interaction energies and geometries in good agreement with the quantum mechanical target data. © 2017 Wiley Periodicals, Inc.
光系统 II 是一种复杂的蛋白质辅因子机器，它将水分子分解为分子氧、质子和电子。全原子分子动力学模拟有可能有助于我们全面了解光系统 II 的工作原理。为了进行可靠的全原子模拟，我们需要对辅因子分子有准确的力场参数。我们在此介绍了光系统 II 中含铁辅因子的 CHARMM 键合和非键合参数，其中包括由两个组氨酸基团配位的六配位血红素部分，以及由碳酸氢盐和四个组氨酸配位的非血红素铁配合物。这里提出的力场参数给出了与量子力学目标数据吻合良好的水相互作用能和几何形状。© 2017 威利父子公司
