Identifying carboxylate ligand vibrational modes in photosystem II with QM/MM methods

Abstract

The light-driven oxidation of water in photosystem II (PSII) produces nearly all of the molecular oxygen on Earth and drives the production of nearly all of Earth’s biomass. Determining the mechanism of O2 formation in PSII is one of the hottest topics in photosynthesis and has stimulated much interest in the development of artificial photosynthesis. The catalytic water-oxidizing center (WOC) consists of a Mn4CaO5 cluster, nearby amino acid residues, and numerous surrounding water molecules (Fig. 1). Rapid progress in understanding the mechanism of O2 formation has been made in the last 5 years because of developments in crystallography (e.g., the development of free electron laser sources) and the interplay between new structural information, computational studies, and advanced biophysical methods such as pulsed EPR spectroscopy, X-ray absorbance spectroscopy, and membrane inlet mass spectrometry (1⇓⇓–4). FTIR spectroscopy is an additional biophysical method that has the advantage of being sensitive to the amino acid residues and water molecules that surround the Mn4CaO5 cluster. However, the interpretation of much of the FTIR literature on PSII has been hampered by an inability to assign spectral features to specific residues or functional groups. In PNAS, Nakamura and Noguchi (5) address this problem by simulating FTIR difference spectra of the WOC in the symmetric carboxylate stretching region on the basis of quantum mechanics/molecular mechanics (QM/MM) methods. Fig. 1. The Mn4CaO5 cluster and its ligation environment from the 1.95-A X-ray crystallographic structure (7) (Protein Data Bank ID code 4UB6). For clarity, only selected residues are shown. Except as noted otherwise, all residues are from the D1 polypeptide. Purple spheres, manganese ions; yellow sphere, calcium; large red spheres, μ-oxo bridges; blue sphere, chloride; small red spheres, water molecules including the four water molecules bound to Mn4 … [↵][1]1Email: richard.debus{at}ucr.edu. [1]: #xref-corresp-1-1