3 research outputs found
Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure
Extensive quantum chemical DFT calculations were performed
on the
high-resolution (1.9 Ã…) crystal structure of photosystem II in
order to determine the protonation pattern and the oxidation states
of the oxygen-evolving Mn cluster. First, our data suggest that the
experimental structure is not in the S<sub>1</sub>-state. Second,
a rather complete set of possible protonation patterns is studied,
resulting in very few alternative protonation patterns whose relevance
is discussed. Finally, we show that the experimental structure is
a mixture of states containing highly reduced forms, with the largest
contribution (almost 60%) from the S<sub>–3</sub>-state, MnÂ(II,II,III,III)
Exploring the Possible Role of Glu286 in C<i>c</i>O by Electrostatic Energy Computations Combined with Molecular Dynamics
Cytochrome <i>c</i> oxidase (C<i>c</i>O) is
a central enzyme in aerobic life catalyzing the conversion of molecular
oxygen to water and utilizing the chemical energy to pump protons
and establish an electrochemical gradient. Despite intense research,
it is not understood how C<i>c</i>O achieves unidirectional
proton transport and avoids short circuiting the proton pump. Within
this work, we analyzed the potential role of Glu286 as a proton valve.
We performed unconstrained MD simulations of C<i>c</i>O
with an explicit membrane for up to 80 ns. Those MD simulations revealed
that deprotonated Glu286 (Glu286-) is repelled by the negatively charged
propionic acid PRD of heme a<sub>3</sub>. Thus, it destabilizes a
potential linear chain of waters in the hydrophobic cavity connecting
Glu286 with PRD and the binuclear center (BNC). Conversely, protonated
Glu286 (Glu286H) may remain in an upward position (oriented toward
PRD) and can stabilize the connecting linear water chain in the hydrophobic
cavity. We calculated the p<i>K</i><sub>a</sub> of Glu286
under physiological conditions to be above 12, but this value decreases
to about 9 under increased water accessibility of Glu286. The latter
value is in accordance with experimental measurements. In the time
course of MD simulation, we also observed conformations where Glu286
bridges between water molecules located on both sides (the D channel
being connected to the N side and the hydrophobic cavity), which might
lead to proton backflow
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