Summarizing recent chemical literature
Authors: *Yasufumi Umena, +Keisuke Kawakami, +Jian-Ren Shen, and *Nobou Kamiya
Affiliation: *Department of Chemistry, Graduate School of Science, Osaka City University. + Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University
Above: The structure of Photosystem II.
It seems like there has been a bunch of nanotech posts lately, so I thought I would switch it up with some biochemistry. Recently, a high resolution solid state molecular structure of Photosystem II was published in the journal Nature. Photosystem II is a massive (350 kDa) membrane protein that is the first in a series of membrane proteins that play a part in utilizing photons for chemical energy. Photosystem II contains 70 chlorophyll a‘s and 24 beta-carotenes which are specifically situated so that they can absorb photons and transfer electrons along a pathway, eventually storing them by reducing NAD or NADP, which can be used by the organism later. The chlorophylls, now lacking an electron, takes one from one of two “oxygen evolving centers” in the protein. After the absorption of four photons and the transfer of four electrons, two molecules of H2O are oxidized to one molecule of O2, and the cycle begins again.
Although this protein has been crystallized before, x-ray diffraction studies to determine it’s structure have been at fairly low resolution (which is to be expected for such a large and difficult-to-crystallize molecule). X-ray crystallography relies on the fact that electrons scatter x-rays, and the result of this is a 3D map of electron density, if the crystal being studied is of poor quality, electron density map is not detailed enough to correctly identify certain atoms and connectivities. Before the publication of this article, the structure of the oxygen evolving complex was only speculated based on spectroscopic evidence, but no one could be sure of its actual structure because of the low resolution crystallographic studies. This article is significant because it identifies the nature of the oxygen evolving complex.
We now know that the oxygen evolving complex is a cube containing three manganese (Mn) atoms one calcium (Ca) ion, and four oxygen (O) atoms. One additional Mn is attached to the cluster through two O’s and has two water molecules coordinated to it. As opposed to the cube Mn’s, which are bound to the protein though various histidines, aspartates and glutamates, this Mn is the only one containing any water molecules attached to it, making it likely that they are involved in O2 formation either directly (by forming an O-O bond with the other water or an O in the cube) or indirectly (by replacing cube O’s which may for an O-O bond with each other), but it is important to remember that crystal structures of proteins cannot prove catalytic mechanisms.
Above: The structure of the oxygen evolving complex
Most of the rest of the paper is confirming structural features observed in earlier structures, and the oxygen evolving complex determination is the most impressive part of the paper. Also notable is their method of crystallization. Protein crystallography seems a little like voodoo to me, I have seen strange experimental procedures including manipulating protein crystals using cat eyelashes and crystallizations which could not be reproduced because the initial crystallization only took place a certain distance from an old freezer which vibrated at a certain frequency. This experimental section seems full of really tedious practices including collection of microcrystals for multiple recrystallizations and gradual introduction of polyethylene glycol in order to remove unwanted water molecules.
It’s great to see an article that answers a long-held question in science, and there was quite a bit of buzz surrounding this paper. Future research in numerous groups will works towards determining the actual mechanism of O-O bond formation.