QM/MM Investigation for Protonation States in a Bilin Reductase PcyA‐Biliverdin IXɑ Complex

Abstract

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 IXα (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 O ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.

CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum

“…The elucidation of the molecular origin of such small λ max shifts is not always easy from the experimental point of view and can take benefit from multiscale atomistic models rooted in theoretical chemistry: quantum mechanical (QM), molecular mechanical (MM), or hybrid QM/MM). − Most of the time, the pH effect is introduced thanks to a very specific change of individual protonation states, without considering the relevance (probability) of such a chemical process at a given pH. In the present work, we will demonstrate that, indeed, the number of populated protonation states combinations ( microstates ) is always large.…”

Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states

“…In the WT–BV complex, H 3 O + was considered to be present between His88 and His74. However, a later computational study suggested that this interpretation may be incorrect ( 31 , 32 ).…”

“…However, modeling it as H 3 O + and neutral His88 poses no problem for structural analysis. In the present study, the two N atoms of His88 were interpreted as protonated in I86D–BV, based on computational analysis ( 31 , 32 ).

Figure 6 A key water molecule between His74 and His88.

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