Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII.
Structural data of the oxygen-evolving complex (OEC) in photosystem II (PSII) determined by X-ray crystallography, quantum chemistry (QC), and extended X-ray absorption fine structure (EXAFS) analyses are presently inconsistent. Therefore, a detailed study of what information can be gained about the OEC through a comparison of QC and crystallographic structure information combined with the information from range-extended EXAFS spectra was undertaken. An analysis for determining the precision of the atomic coordinates of the OEC by QC is carried out. OEC model structures based on crystallographic data that are obtained by QC from different research groups are compared with one another and with structures obtained by high-resolution crystallography. The theory of EXAFS spectra is summarized, and the application of EXAFS spectra to the experimental determination of the structure of the OEC is detailed. We discriminate three types of parameters entering the formula for the EXAFS spectrum: (1) model-independent, predefined, and fixed; (2) model-dependent that can be computed or adjusted; and (3) model-dependent that must be adjusted. The information content of EXAFS spectra is estimated and is related to the precision of atomic coordinates and resolution power to discriminate different atom-pair distances of the OEC. It is demonstrated how a precise adjustment of atomic coordinates can yield a nearly perfect representation of the experimental OEC EXAFS spectrum, but at the expense of overfitting and losing the knowledge of the initial OEC model structure. Introducing a novel type of penalty function, it is shown that moderate adjustment of atomic coordinates to the EXAFS spectrum limited by constraints avoids overfitting and can be used to validate different OEC model structures. This technique is used to identify the OEC model structures whose computed OEC EXAFS spectra agree best with the measured spectrum. In this way, the most likely S-state and protonation pattern of the OEC for the most recent high-resolution crystal structure of PSII are determined. We find that the X-ray free-electron laser (XFEL) structure is indeed not significantly affected by exposure to XFEL pulses and thus results in a radiation-damage-free model of the OEC.
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Petko
P
Chernev
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Ivelina
I
Zaharieva
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Emanuele
E
Rossini
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Artur
A
Galstyan
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Holger
H
Dau
Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin , D-14195 Berlin, Germany.
Ernst-Walter
EW
Knapp