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Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H 2 Binding Site in Open and Closed Protein Conformations
Author(s) -
Hedegård Erik Donovan,
Kongsted Jacob,
Ryde Ulf
Publication year - 2015
Publication title -
angewandte chemie
Language(s) - English
Resource type - Journals
eISSN - 1521-3757
pISSN - 0044-8249
DOI - 10.1002/ange.201501737
Subject(s) - hydride , hydrogenase , active site , chemistry , cofactor , ligand (biochemistry) , crystallography , binding site , hydrogen , stereochemistry , computational chemistry , catalysis , enzyme , biochemistry , organic chemistry , receptor
A series of QM/MM optimizations of the full protein of [Fe] hydrogenase were performed. The FeGP cofactor has been optimized in the water‐bound resting state ( 1 ), with a side‐on bound dihydrogen ( 2 ), or as a hydride intermediate ( 3 ). For inclusion of H 4 MPT in the closed structure, advanced multiscale modeling appears to be necessary, especially to obtain reliable distances between CH‐H 4 MPT + and the dihydrogen (H 2 ) or hydride (H − ) ligand in the FeGP cofactor. Inclusion of the full protein is further important for the relative energies of the two intermediates 2 and 3 . We finally find that hydride transfer from 3 has a significantly higher barrier than found in previous studies neglecting the full protein environment.