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Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II
Author(s) -
Adam Suliman,
KnappMohammady Michaela,
Yi Jun,
Bondar AnaNicoleta
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24918
Subject(s) - photosystem ii , chemistry , force field (fiction) , molecular dynamics , cofactor , moiety , molecule , heme , chemical physics , photosystem i , computational chemistry , histidine , stereochemistry , photosynthesis , physics , biochemistry , organic chemistry , enzyme , quantum mechanics
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.