期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 39, 期 1, 页码 7-20出版社
WILEY
DOI: 10.1002/jcc.24918
关键词
CHARMM force field; heme; non-heme iron; parametrization; photosystem II
资金
- German Research Foundation (DFG) Collaborative Research Center [SFB 1078]
- North-German Supercomputing Alliance, HLRN [bec00063]
- National Natural Science Foundation of China [21271104, 21671103]
- Excellence Initiative of the German Federal Government via the Freie Universitat Berlin
- Excellence Initiative of the German State Government via the Freie Universitat Berlin
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. (c) 2017 Wiley Periodicals, Inc.
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