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QM/MM Investigation for Protonation States in a Bilin Reductase PcyA‐Biliverdin IXɑ Complex
Author(s) -
Iijima Eri,
Gleeson M. Paul,
Unno Masaki,
Mori Seiji
Publication year - 2018
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.201800031
Subject(s) - protonation , chemistry , phycocyanobilin , deprotonation , hydronium , crystallography , biliverdin , biliverdin reductase , ring (chemistry) , stereochemistry , molecule , ion , heme , organic chemistry , cyanobacteria , heme oxygenase , phycocyanin , biology , bacteria , genetics , enzyme
Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXɑ (BV), which has the C‐pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two‐electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H 3 O + ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C‐ring of BV is not protonated.